From 97bfc35ca22e1bf6109ee088b91885c37d494152 Mon Sep 17 00:00:00 2001
From:  <>
Date: Thu, 18 Jan 2024 14:46:08 +0000
Subject: [PATCH] Deployed 84f794d3 with MkDocs version: 1.5.3

---
 404.html                                      |  646 ++-
 assets/_mkdocstrings.css                      |   91 +-
 assets/imgs/gentropy.svg                      |  292 +
 development/_development/index.html           |  648 ++-
 development/airflow/index.html                |  656 ++-
 development/contributing/index.html           |  654 ++-
 development/troubleshooting/index.html        |  646 ++-
 development/workflows/index.html              |  646 ++-
 {usage => howto/_howto}/index.html            |  711 ++-
 howto/run_step_in_cli/index.html              | 2716 +++++++++
 howto/run_step_using_config/index.html        | 2722 +++++++++
 index.html                                    |  748 ++-
 installation/index.html                       |  767 ++-
 objects.inv                                   |  Bin 2336 -> 2658 bytes
 python_api/_python_api/index.html             |  667 ++-
 .../_datasets}/index.html                     |  760 ++-
 .../colocalisation/index.html                 |  653 ++-
 .../gene_index/index.html                     |  706 ++-
 .../intervals/index.html                      |  707 ++-
 .../l2g_feature/index.html                    |  651 ++-
 .../l2g_feature_matrix/index.html             |  922 +--
 .../l2g_gold_standard/index.html              |  733 ++-
 .../l2g_prediction/index.html                 |  774 ++-
 .../{dataset => datasets}/ld_index/index.html |  651 ++-
 .../study_index/index.html                    | 1221 +++-
 .../study_locus/index.html                    | 1571 ++++--
 .../study_locus_overlap/index.html            |  692 ++-
 .../summary_statistics/index.html             |  702 ++-
 .../variant_annotation/index.html             |  837 +--
 .../variant_index/index.html                  |  672 ++-
 .../variant_to_gene/index.html                |  687 ++-
 .../ukbiobank/study_index/index.html          | 3075 ----------
 .../_datasources}/index.html                  |  723 ++-
 .../_eqtl_catalogue}/index.html               |  668 ++-
 .../eqtl_catalogue/study_index/index.html     | 1275 +++--
 .../eqtl_catalogue/summary_stats/index.html   |  651 ++-
 .../finngen/_finngen/index.html               |  621 ++-
 .../finngen/study_index/index.html            |  683 ++-
 .../finngen/summary_stats/index.html          | 3178 +++++++++++
 .../gnomad/_gnomad/index.html                 |  616 +-
 .../gnomad/gnomad_ld/index.html               |  681 ++-
 .../gnomad/gnomad_variants/index.html         |  649 ++-
 .../gwas_catalog/_gwas_catalog/index.html     |  624 ++-
 .../gwas_catalog/associations/index.html      |  851 ++-
 .../gwas_catalog/study_index/index.html       | 2636 ++++++---
 .../gwas_catalog/study_splitter/index.html    |  647 ++-
 .../summary_statistics/index.html             |  645 ++-
 .../intervals/_intervals/index.html           |  641 ++-
 .../intervals/andersson/index.html            |  662 ++-
 .../intervals/javierre/index.html             |  662 ++-
 .../intervals/jung/index.html                 |  662 ++-
 .../intervals/thurman/index.html              |  662 ++-
 .../open_targets/_open_targets/index.html     |  640 ++-
 .../open_targets/l2g_gold_standard/index.html |  683 ++-
 .../open_targets/target/index.html            |  645 ++-
 python_api/method/clumping/index.html         | 2858 ----------
 .../_method => methods/_methods}/index.html   |  654 ++-
 python_api/methods/carma/index.html           | 4950 +++++++++++++++++
 .../clumping}/index.html                      | 1077 ++--
 .../{method => methods}/coloc/index.html      |  847 +--
 .../{method => methods}/ecaviar/index.html    |  675 ++-
 .../{method => methods}/l2g/_l2g/index.html   |  669 ++-
 .../l2g/evaluator/index.html                  |  970 ++--
 .../l2g/feature_factory/index.html            | 1162 ++--
 .../{method => methods}/l2g/model/index.html  |  920 +--
 .../l2g/trainer/index.html                    |  698 ++-
 .../ld_annotator/index.html                   |  691 ++-
 .../{method => methods}/pics/index.html       |  757 ++-
 python_api/step/ukbiobank/index.html          | 2698 ---------
 .../{step/_step => steps/_steps}/index.html   |  640 ++-
 .../{step => steps}/colocalisation/index.html |  977 ++--
 .../{step => steps}/eqtl_catalogue/index.html | 1031 ++--
 .../finngen_studies}/index.html               |  902 +--
 .../finngen_sumstat_preprocess/index.html     | 2952 ++++++++++
 .../{step => steps}/gene_index/index.html     |  854 ++-
 .../gwas_catalog_curation}/index.html         | 1011 ++--
 .../steps/gwas_catalog_inclusion/index.html   | 4054 ++++++++++++++
 .../steps/gwas_catalog_ingestion/index.html   | 3253 +++++++++++
 .../index.html                                |  840 ++-
 python_api/{step => steps}/l2g/index.html     | 1711 ++++--
 .../{step/clump => steps/ld_clump}/index.html | 1075 ++--
 .../{step => steps}/ld_index/index.html       |  856 ++-
 python_api/{step => steps}/pics/index.html    |  862 ++-
 .../variant_annotation_step/index.html        |  845 ++-
 .../variant_index_step/index.html             |  899 ++-
 .../variant_to_gene_step/index.html           | 1208 ++--
 .../steps/window_based_clumping/index.html    | 3074 ++++++++++
 roadmap/index.html                            |  662 ++-
 search/search_index.json                      |    2 +-
 sitemap.xml.gz                                |  Bin 127 -> 127 bytes
 90 files changed, 66649 insertions(+), 29714 deletions(-)
 create mode 100644 assets/imgs/gentropy.svg
 rename {usage => howto/_howto}/index.html (73%)
 create mode 100644 howto/run_step_in_cli/index.html
 create mode 100644 howto/run_step_using_config/index.html
 rename python_api/{dataset/_dataset => datasets/_datasets}/index.html (87%)
 rename python_api/{dataset => datasets}/colocalisation/index.html (81%)
 rename python_api/{dataset => datasets}/gene_index/index.html (84%)
 rename python_api/{dataset => datasets}/intervals/index.html (84%)
 rename python_api/{dataset => datasets}/l2g_feature/index.html (81%)
 rename python_api/{dataset => datasets}/l2g_feature_matrix/index.html (80%)
 rename python_api/{dataset => datasets}/l2g_gold_standard/index.html (88%)
 rename python_api/{dataset => datasets}/l2g_prediction/index.html (79%)
 rename python_api/{dataset => datasets}/ld_index/index.html (81%)
 rename python_api/{dataset => datasets}/study_index/index.html (69%)
 rename python_api/{dataset => datasets}/study_locus/index.html (83%)
 rename python_api/{dataset => datasets}/study_locus_overlap/index.html (82%)
 rename python_api/{dataset => datasets}/summary_statistics/index.html (85%)
 rename python_api/{dataset => datasets}/variant_annotation/index.html (87%)
 rename python_api/{dataset => datasets}/variant_index/index.html (84%)
 rename python_api/{dataset => datasets}/variant_to_gene/index.html (83%)
 delete mode 100644 python_api/datasource/ukbiobank/study_index/index.html
 rename python_api/{datasource/_datasource => datasources/_datasources}/index.html (76%)
 rename python_api/{datasource/ukbiobank/_ukbiobank => datasources/eqtl_catalogue/_eqtl_catalogue}/index.html (81%)
 rename python_api/{datasource => datasources}/eqtl_catalogue/study_index/index.html (61%)
 rename python_api/{datasource => datasources}/eqtl_catalogue/summary_stats/index.html (85%)
 rename python_api/{datasource => datasources}/finngen/_finngen/index.html (80%)
 rename python_api/{datasource => datasources}/finngen/study_index/index.html (83%)
 create mode 100644 python_api/datasources/finngen/summary_stats/index.html
 rename python_api/{datasource => datasources}/gnomad/_gnomad/index.html (80%)
 rename python_api/{datasource => datasources}/gnomad/gnomad_ld/index.html (91%)
 rename python_api/{datasource => datasources}/gnomad/gnomad_variants/index.html (89%)
 rename python_api/{datasource => datasources}/gwas_catalog/_gwas_catalog/index.html (80%)
 rename python_api/{datasource => datasources}/gwas_catalog/associations/index.html (91%)
 rename python_api/{datasource => datasources}/gwas_catalog/study_index/index.html (67%)
 rename python_api/{datasource => datasources}/gwas_catalog/study_splitter/index.html (86%)
 rename python_api/{datasource => datasources}/gwas_catalog/summary_statistics/index.html (88%)
 rename python_api/{datasource => datasources}/intervals/_intervals/index.html (77%)
 rename python_api/{datasource => datasources}/intervals/andersson/index.html (89%)
 rename python_api/{datasource => datasources}/intervals/javierre/index.html (90%)
 rename python_api/{datasource => datasources}/intervals/jung/index.html (87%)
 rename python_api/{datasource => datasources}/intervals/thurman/index.html (87%)
 rename python_api/{datasource => datasources}/open_targets/_open_targets/index.html (80%)
 rename python_api/{datasource => datasources}/open_targets/l2g_gold_standard/index.html (86%)
 rename python_api/{datasource => datasources}/open_targets/target/index.html (85%)
 delete mode 100644 python_api/method/clumping/index.html
 rename python_api/{method/_method => methods/_methods}/index.html (80%)
 create mode 100644 python_api/methods/carma/index.html
 rename python_api/{method/window_based_clumping => methods/clumping}/index.html (82%)
 rename python_api/{method => methods}/coloc/index.html (81%)
 rename python_api/{method => methods}/ecaviar/index.html (83%)
 rename python_api/{method => methods}/l2g/_l2g/index.html (77%)
 rename python_api/{method => methods}/l2g/evaluator/index.html (78%)
 rename python_api/{method => methods}/l2g/feature_factory/index.html (63%)
 rename python_api/{method => methods}/l2g/model/index.html (87%)
 rename python_api/{method => methods}/l2g/trainer/index.html (86%)
 rename python_api/{method => methods}/ld_annotator/index.html (86%)
 rename python_api/{method => methods}/pics/index.html (83%)
 delete mode 100644 python_api/step/ukbiobank/index.html
 rename python_api/{step/_step => steps/_steps}/index.html (79%)
 rename python_api/{step => steps}/colocalisation/index.html (69%)
 rename python_api/{step => steps}/eqtl_catalogue/index.html (67%)
 rename python_api/{step/finngen => steps/finngen_studies}/index.html (73%)
 create mode 100644 python_api/steps/finngen_sumstat_preprocess/index.html
 rename python_api/{step => steps}/gene_index/index.html (72%)
 rename python_api/{step/gwas_catalog_ingestion => steps/gwas_catalog_curation}/index.html (65%)
 create mode 100644 python_api/steps/gwas_catalog_inclusion/index.html
 create mode 100644 python_api/steps/gwas_catalog_ingestion/index.html
 rename python_api/{step => steps}/gwas_catalog_sumstat_preprocess/index.html (71%)
 rename python_api/{step => steps}/l2g/index.html (56%)
 rename python_api/{step/clump => steps/ld_clump}/index.html (67%)
 rename python_api/{step => steps}/ld_index/index.html (72%)
 rename python_api/{step => steps}/pics/index.html (72%)
 rename python_api/{step => steps}/variant_annotation_step/index.html (73%)
 rename python_api/{step => steps}/variant_index_step/index.html (71%)
 rename python_api/{step => steps}/variant_to_gene_step/index.html (61%)
 create mode 100644 python_api/steps/window_based_clumping/index.html

diff --git a/404.html b/404.html
index 82f9664b6..82063ca78 100644
--- a/404.html
+++ b/404.html
@@ -12,11 +12,11 @@
       
       
       <link rel="icon" href="/assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Open Targets Genetics</title>
+        <title>Open Targets Gentropy</title>
       
     
     
@@ -85,7 +85,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="/." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="/." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="/assets/imgs/otlogo.png" alt="logo">
 
@@ -98,7 +98,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -183,13 +183,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -206,6 +206,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="/." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="/installation/" class="md-tabs__link">
         
@@ -224,7 +241,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="/usage/" class="md-tabs__link">
+      <a href="/howto/_howto/" class="md-tabs__link">
         
   
     
@@ -240,6 +257,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="/roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="/development/_development/" class="md-tabs__link">
         
@@ -298,22 +332,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="/." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="/." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="/assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -327,11 +361,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/installation/" class="md-nav__link">
+      <a href="/." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -347,11 +381,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/usage/" class="md-nav__link">
+      <a href="/installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -384,11 +418,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/development/_development/" class="md-nav__link ">
+            <a href="/howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -403,6 +437,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="/development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -518,7 +669,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
         
           
           
@@ -534,14 +685,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -563,32 +714,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/dataset/_dataset/" class="md-nav__link ">
+            <a href="/python_api/datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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               </label>
             
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-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -599,7 +750,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/colocalisation/" class="md-nav__link">
+      <a href="/python_api/datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -620,7 +771,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/gene_index/" class="md-nav__link">
+      <a href="/python_api/datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -641,7 +792,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/intervals/" class="md-nav__link">
+      <a href="/python_api/datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -662,7 +813,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/l2g_feature/" class="md-nav__link">
+      <a href="/python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -683,7 +834,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="/python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -704,7 +855,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="/python_api/datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -725,7 +876,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/l2g_prediction/" class="md-nav__link">
+      <a href="/python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -746,7 +897,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/ld_index/" class="md-nav__link">
+      <a href="/python_api/datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -767,7 +918,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/study_index/" class="md-nav__link">
+      <a href="/python_api/datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -788,7 +939,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/study_locus/" class="md-nav__link">
+      <a href="/python_api/datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -809,7 +960,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="/python_api/datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -830,7 +981,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/summary_statistics/" class="md-nav__link">
+      <a href="/python_api/datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -851,7 +1002,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/variant_annotation/" class="md-nav__link">
+      <a href="/python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -872,7 +1023,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/variant_index/" class="md-nav__link">
+      <a href="/python_api/datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -893,7 +1044,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="/python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -931,32 +1082,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="/python_api/datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -976,12 +1127,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="/python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -992,14 +1143,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1012,7 +1163,28 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="/python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1050,12 +1222,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="/python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1066,14 +1238,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1086,7 +1258,28 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/finngen/study_index/" class="md-nav__link">
+      <a href="/python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1124,12 +1317,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="/python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1140,14 +1333,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1160,7 +1353,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="/python_api/datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1181,7 +1374,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="/python_api/datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1219,12 +1412,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="/python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1235,14 +1428,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1255,7 +1448,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="/python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1276,7 +1469,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="/python_api/datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1297,7 +1490,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="/python_api/datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1318,7 +1511,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="/python_api/datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1356,12 +1549,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="/python_api/datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1372,14 +1565,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1392,7 +1585,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/intervals/andersson/" class="md-nav__link">
+      <a href="/python_api/datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1413,7 +1606,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/intervals/javierre/" class="md-nav__link">
+      <a href="/python_api/datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1434,7 +1627,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/intervals/jung/" class="md-nav__link">
+      <a href="/python_api/datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1455,7 +1648,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/intervals/thurman/" class="md-nav__link">
+      <a href="/python_api/datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1493,12 +1686,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="/python_api/datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1509,14 +1702,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1529,7 +1722,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="/python_api/datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1550,7 +1743,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/datasource/open_targets/target/" class="md-nav__link">
+      <a href="/python_api/datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1572,80 +1765,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
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-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="/python_api/datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="/python_api/datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
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         </nav>
       
@@ -1670,32 +1789,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/method/_method/" class="md-nav__link ">
+            <a href="/python_api/methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1706,11 +1825,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/clumping/" class="md-nav__link">
+      <a href="/python_api/methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1727,11 +1846,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/coloc/" class="md-nav__link">
+      <a href="/python_api/methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1748,11 +1867,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/ecaviar/" class="md-nav__link">
+      <a href="/python_api/methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1769,11 +1888,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/ld_annotator/" class="md-nav__link">
+      <a href="/python_api/methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1790,11 +1909,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/pics/" class="md-nav__link">
+      <a href="/python_api/methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1811,11 +1930,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/window_based_clumping/" class="md-nav__link">
+      <a href="/python_api/methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1841,12 +1960,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/method/l2g/_l2g/" class="md-nav__link ">
+            <a href="/python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1857,14 +1976,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1877,7 +1996,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/l2g/evaluator/" class="md-nav__link">
+      <a href="/python_api/methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1898,7 +2017,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/l2g/feature_factory/" class="md-nav__link">
+      <a href="/python_api/methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1919,7 +2038,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/l2g/model/" class="md-nav__link">
+      <a href="/python_api/methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1940,7 +2059,7 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/method/l2g/trainer/" class="md-nav__link">
+      <a href="/python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1986,32 +2105,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="/python_api/step/_step/" class="md-nav__link ">
+            <a href="/python_api/steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2022,11 +2141,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/clump/" class="md-nav__link">
+      <a href="/python_api/steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2043,11 +2162,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/colocalisation/" class="md-nav__link">
+      <a href="/python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2064,11 +2183,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/eqtl_catalogue/" class="md-nav__link">
+      <a href="/python_api/steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2085,11 +2204,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/finngen/" class="md-nav__link">
+      <a href="/python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2106,11 +2225,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/gene_index/" class="md-nav__link">
+      <a href="/python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2127,11 +2246,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="/python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2148,11 +2267,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="/python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2169,11 +2288,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/l2g/" class="md-nav__link">
+      <a href="/python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2190,11 +2309,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/ld_index/" class="md-nav__link">
+      <a href="/python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2211,11 +2330,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/pics/" class="md-nav__link">
+      <a href="/python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2232,11 +2351,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="/python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2253,11 +2372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="/python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2274,11 +2393,11 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="/python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2295,11 +2414,74 @@
   
   
     <li class="md-nav__item">
-      <a href="/python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="/python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="/python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2392,7 +2574,7 @@ <h1>404 - Not found</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/assets/_mkdocstrings.css b/assets/_mkdocstrings.css
index 049a254b9..4b7d98b83 100644
--- a/assets/_mkdocstrings.css
+++ b/assets/_mkdocstrings.css
@@ -26,39 +26,84 @@
   float: right;
 }
 
-/* Keep headings consistent. */
-h1.doc-heading,
-h2.doc-heading,
-h3.doc-heading,
-h4.doc-heading,
-h5.doc-heading,
-h6.doc-heading {
-  font-weight: 400;
-  line-height: 1.5;
-  color: inherit;
-  text-transform: none;
+/* Symbols in Navigation and ToC. */
+:root,
+[data-md-color-scheme="default"] {
+  --doc-symbol-attribute-fg-color: #953800;
+  --doc-symbol-function-fg-color: #8250df;
+  --doc-symbol-method-fg-color: #8250df;
+  --doc-symbol-class-fg-color: #0550ae;
+  --doc-symbol-module-fg-color: #5cad0f;
+
+  --doc-symbol-attribute-bg-color: #9538001a;
+  --doc-symbol-function-bg-color: #8250df1a;
+  --doc-symbol-method-bg-color: #8250df1a;
+  --doc-symbol-class-bg-color: #0550ae1a;
+  --doc-symbol-module-bg-color: #5cad0f1a;
+}
+
+[data-md-color-scheme="slate"] {
+  --doc-symbol-attribute-fg-color: #ffa657;
+  --doc-symbol-function-fg-color: #d2a8ff;
+  --doc-symbol-method-fg-color: #d2a8ff;
+  --doc-symbol-class-fg-color: #79c0ff;
+  --doc-symbol-module-fg-color: #baff79;
+
+  --doc-symbol-attribute-bg-color: #ffa6571a;
+  --doc-symbol-function-bg-color: #d2a8ff1a;
+  --doc-symbol-method-bg-color: #d2a8ff1a;
+  --doc-symbol-class-bg-color: #79c0ff1a;
+  --doc-symbol-module-bg-color: #baff791a;
+}
+
+code.doc-symbol {
+  border-radius: .1rem;
+  font-size: .85em;
+  padding: 0 .3em;
+  font-weight: bold;
+}
+
+code.doc-symbol-attribute {
+  color: var(--doc-symbol-attribute-fg-color);
+  background-color: var(--doc-symbol-attribute-bg-color);
+}
+
+code.doc-symbol-attribute::after {
+  content: "attr";
+}
+
+code.doc-symbol-function {
+  color: var(--doc-symbol-function-fg-color);
+  background-color: var(--doc-symbol-function-bg-color);
+}
+
+code.doc-symbol-function::after {
+  content: "func";
 }
 
-h1.doc-heading {
-  font-size: 1.6rem;
+code.doc-symbol-method {
+  color: var(--doc-symbol-method-fg-color);
+  background-color: var(--doc-symbol-method-bg-color);
 }
 
-h2.doc-heading {
-  font-size: 1.2rem;
+code.doc-symbol-method::after {
+  content: "meth";
 }
 
-h3.doc-heading {
-  font-size: 1.15rem;
+code.doc-symbol-class {
+  color: var(--doc-symbol-class-fg-color);
+  background-color: var(--doc-symbol-class-bg-color);
 }
 
-h4.doc-heading {
-  font-size: 1.10rem;
+code.doc-symbol-class::after {
+  content: "class";
 }
 
-h5.doc-heading {
-  font-size: 1.05rem;
+code.doc-symbol-module {
+  color: var(--doc-symbol-module-fg-color);
+  background-color: var(--doc-symbol-module-bg-color);
 }
 
-h6.doc-heading {
-  font-size: 1rem;
+code.doc-symbol-module::after {
+  content: "mod";
 }
\ No newline at end of file
diff --git a/assets/imgs/gentropy.svg b/assets/imgs/gentropy.svg
new file mode 100644
index 000000000..9a0186638
--- /dev/null
+++ b/assets/imgs/gentropy.svg
@@ -0,0 +1,292 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<svg width="100%" height="100%" viewBox="0 0 1170 159" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" xmlns:serif="http://www.serif.com/" style="fill-rule:evenodd;clip-rule:evenodd;stroke-linejoin:round;stroke-miterlimit:2;">
+    <g transform="matrix(1,0,0,1,-224.53,-127.05)">
+        <path d="M480.06,198.44L480.06,198.28C480.06,182.71 492.08,169.66 509.07,169.66C526.06,169.66 537.93,182.55 537.93,198.12L537.93,198.28C537.93,213.85 525.91,226.9 508.92,226.9C491.93,226.9 480.06,214.01 480.06,198.44ZM527.73,198.45L527.73,198.28C527.73,187.53 519.9,178.6 508.91,178.6C497.92,178.6 490.25,187.38 490.25,198.13L490.25,198.29C490.25,209.04 498.08,217.9 509.07,217.9C520.06,217.9 527.73,209.2 527.73,198.45Z" style="fill:rgb(90,95,95);fill-rule:nonzero;"/>
+    </g>
+    <g transform="matrix(1,0,0,1,-224.53,-127.05)">
+        <path d="M548.61,188.55C548.61,185.86 550.67,183.73 553.35,183.73C556.03,183.73 558.17,185.86 558.17,188.55L558.17,191.16C561.25,186.81 565.6,183.33 572.4,183.33C582.2,183.33 591.77,191.08 591.77,204.99L591.77,205.15C591.77,218.98 582.28,226.81 572.4,226.81C565.44,226.81 561.1,223.33 558.17,219.46L558.17,234.24C558.17,236.93 556.04,238.98 553.35,238.98C550.66,238.98 548.61,236.92 548.61,234.24L548.61,188.55ZM582.05,205.16L582.05,205C582.05,196.94 576.59,191.64 570.11,191.64C563.63,191.64 557.94,197.02 557.94,205L557.94,205.16C557.94,213.15 563.63,218.52 570.11,218.52C576.59,218.52 582.05,213.38 582.05,205.16Z" style="fill:rgb(90,95,95);fill-rule:nonzero;"/>
+    </g>
+    <g transform="matrix(1,0,0,1,-224.53,-127.05)">
+        <path d="M620.79,226.9C608.69,226.9 599.37,218.13 599.37,205.24L599.37,205.08C599.37,193.14 607.83,183.34 619.77,183.34C633.05,183.34 639.61,194.25 639.61,203.89C639.61,206.58 637.55,208.47 635.1,208.47L608.93,208.47C609.96,215.27 614.78,219.06 620.95,219.06C624.98,219.06 628.14,217.64 630.83,215.42C631.54,214.87 632.17,214.55 633.28,214.55C635.41,214.55 637.07,216.21 637.07,218.42C637.07,219.61 636.52,220.63 635.81,221.35C632.02,224.75 627.27,226.88 620.79,226.88L620.79,226.9ZM630.28,202.15C629.65,195.98 626.01,191.16 619.69,191.16C613.84,191.16 609.73,195.67 608.86,202.15L630.28,202.15Z" style="fill:rgb(90,95,95);fill-rule:nonzero;"/>
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+    </g>
+    <g transform="matrix(1,0,0,1,-224.53,-127.05)">
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diff --git a/development/_development/index.html b/development/_development/index.html
index 445298d7d..3bc43bfd4 100644
--- a/development/_development/index.html
+++ b/development/_development/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../usage/">
+        <link rel="prev" href="../../roadmap/">
       
       
         <link rel="next" href="../airflow/">
       
       
       <link rel="icon" href="../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Development - Open Targets Genetics</title>
+        <title>Development - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,7 +102,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -187,13 +187,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../installation/" class="md-tabs__link">
         
@@ -228,7 +245,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../usage/" class="md-tabs__link">
+      <a href="../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -243,6 +260,23 @@
         
   
   
+  
+    <li class="md-tabs__item">
+      <a href="../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
     
   
   
@@ -304,22 +338,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -332,6 +366,26 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../.." class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Home
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       <a href="../../installation/" class="md-nav__link">
         
@@ -352,15 +406,112 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../usage/" class="md-nav__link">
+    
+    
+    
+    
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
         
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
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+          <div class="md-nav__link md-nav__container">
+            <a href="../../howto/_howto/" class="md-nav__link ">
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   <span class="md-ellipsis">
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+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
+
+    
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+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
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@@ -387,7 +538,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
         
           
           
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+              <label class="md-nav__link md-nav__link--active" for="__nav_5" id="__nav_5_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -526,7 +677,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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@@ -571,32 +722,32 @@
         
         
         
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../python_api/dataset/_dataset/" class="md-nav__link ">
+            <a href="../../python_api/datasets/_datasets/" class="md-nav__link ">
               
   
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-    Dataset
+    Datasets
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+          <label class="md-nav__title" for="__nav_6_1">
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+            Datasets
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     <li class="md-nav__item">
-      <a href="../../python_api/dataset/colocalisation/" class="md-nav__link">
+      <a href="../../python_api/datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -628,7 +779,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/gene_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/gene_index/" class="md-nav__link">
         
   
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@@ -649,7 +800,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/intervals/" class="md-nav__link">
+      <a href="../../python_api/datasets/intervals/" class="md-nav__link">
         
   
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@@ -670,7 +821,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -691,7 +842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../python_api/dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../python_api/dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -754,7 +905,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/ld_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/ld_index/" class="md-nav__link">
         
   
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@@ -775,7 +926,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/study_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/study_index/" class="md-nav__link">
         
   
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@@ -796,7 +947,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/study_locus/" class="md-nav__link">
+      <a href="../../python_api/datasets/study_locus/" class="md-nav__link">
         
   
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@@ -817,7 +968,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../python_api/datasets/study_locus_overlap/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../python_api/dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../python_api/datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -859,7 +1010,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -880,7 +1031,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_index/" class="md-nav__link">
         
   
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@@ -901,7 +1052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -939,32 +1090,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="../../python_api/datasources/_datasources/" class="md-nav__link ">
               
   
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-    Datasource
+    Datasources
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../python_api/datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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@@ -1000,14 +1151,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
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     <li class="md-nav__item">
-      <a href="../../python_api/datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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@@ -1058,12 +1230,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../python_api/datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
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@@ -1074,14 +1246,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
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@@ -1094,7 +1266,28 @@
   
   
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-      <a href="../../python_api/datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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@@ -1132,12 +1325,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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@@ -1148,14 +1341,14 @@
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+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
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             Gnomad
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-      <a href="../../python_api/datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../python_api/datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
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@@ -1189,7 +1382,7 @@
   
   
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-      <a href="../../python_api/datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../python_api/datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
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@@ -1227,12 +1420,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
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-            <a href="../../python_api/datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
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@@ -1243,14 +1436,14 @@
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
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             Gwas catalog
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@@ -1263,7 +1456,7 @@
   
   
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-      <a href="../../python_api/datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
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@@ -1284,7 +1477,7 @@
   
   
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@@ -1558,7 +1751,7 @@
   
   
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+      <a href="../../python_api/datasources/open_targets/target/" class="md-nav__link">
         
   
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-            <a href="../../python_api/method/_method/" class="md-nav__link ">
+            <a href="../../python_api/methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+      <a href="../../python_api/methods/carma/" class="md-nav__link">
         
   
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+    CARMA
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+      <a href="../../python_api/methods/clumping/" class="md-nav__link">
         
   
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+    Clumping
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+      <a href="../../python_api/methods/ecaviar/" class="md-nav__link">
         
   
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+      <a href="../../python_api/methods/ld_annotator/" class="md-nav__link">
         
   
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+      <a href="../../python_api/methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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+            <a href="../../python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/methods/l2g/model/" class="md-nav__link">
         
   
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+      <a href="../../python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
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-            <a href="../../python_api/step/_step/" class="md-nav__link ">
+            <a href="../../python_api/steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+      <a href="../../python_api/steps/colocalisation/" class="md-nav__link">
         
   
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-      <a href="../../python_api/step/colocalisation/" class="md-nav__link">
+      <a href="../../python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
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-      <a href="../../python_api/step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../python_api/steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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-      <a href="../../python_api/step/finngen/" class="md-nav__link">
+      <a href="../../python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
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-      <a href="../../python_api/step/gene_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
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@@ -2135,11 +2254,11 @@
   
   
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-      <a href="../../python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
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@@ -2156,11 +2275,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
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@@ -2177,11 +2296,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/l2g/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
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     <li class="md-nav__item">
-      <a href="../../python_api/step/ld_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
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     <li class="md-nav__item">
-      <a href="../../python_api/step/pics/" class="md-nav__link">
+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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@@ -2240,11 +2359,11 @@
   
   
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-      <a href="../../python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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-      <a href="../../python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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-      <a href="../../python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="../../python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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+    pics
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-      <a href="../../python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
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+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
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@@ -2458,7 +2640,7 @@ <h1>Development</h1>
       
       
     
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+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/development/airflow/index.html b/development/airflow/index.html
index d1f4bd1c2..6cd561602 100644
--- a/development/airflow/index.html
+++ b/development/airflow/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Airflow configuration - Open Targets Genetics</title>
+        <title>Airflow configuration - Open Targets Gentropy</title>
       
     
     
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
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-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../.." class="md-tabs__link">
+        
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+  Home
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@@ -233,7 +250,7 @@
   
   
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-      <a href="../../usage/" class="md-tabs__link">
+      <a href="../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -248,6 +265,23 @@
         
   
   
+  
+    <li class="md-tabs__item">
+      <a href="../../roadmap/" class="md-tabs__link">
+        
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+    
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+  Roadmap
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@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
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+    <a href="../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    Open Targets Genetics
+    Open Targets Gentropy
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -337,6 +371,26 @@
   
   
   
+    <li class="md-nav__item">
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@@ -357,15 +411,112 @@
   
   
   
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+    
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+      <a href="../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
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+  
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+      <a href="../../howto/run_step_using_config/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
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             Python API
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+            <a href="../../python_api/datasets/_datasets/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/datasets/colocalisation/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/gene_index/" class="md-nav__link">
         
   
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@@ -781,7 +932,7 @@
   
   
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-      <a href="../../python_api/dataset/intervals/" class="md-nav__link">
+      <a href="../../python_api/datasets/intervals/" class="md-nav__link">
         
   
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-      <a href="../../python_api/dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -823,7 +974,7 @@
   
   
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+      <a href="../../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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-      <a href="../../python_api/dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -886,7 +1037,7 @@
   
   
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-      <a href="../../python_api/dataset/ld_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/ld_index/" class="md-nav__link">
         
   
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@@ -907,7 +1058,7 @@
   
   
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+      <a href="../../python_api/datasets/study_index/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/study_locus/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/study_locus_overlap/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
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-      <a href="../../python_api/dataset/variant_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_index/" class="md-nav__link">
         
   
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-      <a href="../../python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
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-            <a href="../../python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="../../python_api/datasources/_datasources/" class="md-nav__link ">
               
   
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-            <a href="../../python_api/datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
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+      <a href="../../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+      <a href="../../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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+            <a href="../../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/datasources/finngen/study_index/" class="md-nav__link">
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+      <a href="../../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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-            <a href="../../python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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+            <a href="../../python_api/methods/_methods/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/methods/carma/" class="md-nav__link">
         
   
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+            <a href="../../python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
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-            <a href="../../python_api/step/_step/" class="md-nav__link ">
+            <a href="../../python_api/steps/_steps/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
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+      <a href="../../python_api/steps/finngen_studies/" class="md-nav__link">
         
   
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@@ -2246,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gene_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2267,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2288,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2309,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/l2g/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2330,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/ld_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2351,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/pics/" class="md-nav__link">
+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2372,11 +2491,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2393,11 +2512,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2414,11 +2533,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="../../python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2435,11 +2554,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2604,13 +2786,13 @@ <h2 id="install-pre-requisites">Install pre-requisites<a class="headerlink" href
 </ul>
 <div class="admonition warning macos docker memory allocation">
 <p class="admonition-title">Warning</p>
-</div>
 <p>On macOS, the default amount of memory available for Docker might not be enough to get Airflow up and running. Allocate at least 4GB of memory for the Docker Engine (ideally 8GB). <a href="https://airflow.apache.org/docs/apache-airflow/stable/howto/docker-compose/index.html#">More info</a></p>
+</div>
 <h2 id="configure-airflow-access-to-google-cloud-platform">Configure Airflow access to Google Cloud Platform<a class="headerlink" href="#configure-airflow-access-to-google-cloud-platform" title="Permanent link">&para;</a></h2>
 <div class="admonition warning specifying google cloud parameters">
 <p class="admonition-title">Warning</p>
-</div>
 <p>Run the next two command with the appropriate Google Cloud project ID and service account name to ensure the correct Google default application credentials are set up.</p>
+</div>
 <p>Authenticate to Google Cloud:</p>
 <div class="highlight"><pre><span></span><code>gcloud<span class="w"> </span>auth<span class="w"> </span>application-default<span class="w"> </span>login<span class="w"> </span>--project<span class="o">=</span>&lt;PROJECT&gt;
 </code></pre></div>
@@ -2624,15 +2806,15 @@ <h2 id="set-up-airflow">Set up Airflow<a class="headerlink" href="#set-up-airflo
 <h3 id="build-docker-image">Build Docker image<a class="headerlink" href="#build-docker-image" title="Permanent link">&para;</a></h3>
 <div class="admonition note custom docker image for airflow">
 <p class="admonition-title">Note</p>
-</div>
 <p>The custom Dockerfile built by the command below extends the official <a href="https://airflow.apache.org/docs/apache-airflow/stable/docker-compose.yaml">Airflow Docker Compose YAML</a>. We add support for Google Cloud SDK, Google Dataproc operators, and access to GCP credentials.</p>
+</div>
 <div class="highlight"><pre><span></span><code>docker<span class="w"> </span>build<span class="w"> </span>.<span class="w"> </span>--tag<span class="w"> </span>extending_airflow:latest
 </code></pre></div>
 <h3 id="set-airflow-user-id">Set Airflow user ID<a class="headerlink" href="#set-airflow-user-id" title="Permanent link">&para;</a></h3>
 <div class="admonition note setting airflow user id">
 <p class="admonition-title">Note</p>
-</div>
 <p>These commands allow Airflow running inside Docker to access the credentials file which was generated earlier.</p>
+</div>
 <div class="highlight"><pre><span></span><code><span class="c1"># If any user ID is already specified in .env, remove it.</span>
 grep<span class="w"> </span>-v<span class="w"> </span><span class="s2">&quot;AIRFLOW_UID&quot;</span><span class="w"> </span>.env<span class="w"> </span>&gt;<span class="w"> </span>.env.tmp
 <span class="c1"># Add the correct user ID.</span>
@@ -2699,7 +2881,7 @@ <h2 id="troubleshooting">Troubleshooting<a class="headerlink" href="#troubleshoo
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2774,7 +2956,7 @@ <h2 id="troubleshooting">Troubleshooting<a class="headerlink" href="#troubleshoo
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/development/contributing/index.html b/development/contributing/index.html
index 5328b3fb6..fcaf854b4 100644
--- a/development/contributing/index.html
+++ b/development/contributing/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Contributing guidelines - Open Targets Genetics</title>
+        <title>Contributing guidelines - Open Targets Gentropy</title>
       
     
     
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../usage/" class="md-tabs__link">
+      <a href="../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -248,6 +265,23 @@
         
   
   
+  
+    <li class="md-tabs__item">
+      <a href="../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
     
   
   
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -337,6 +371,26 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../.." class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Home
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../installation/" class="md-nav__link">
         
@@ -357,15 +411,112 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../usage/" class="md-nav__link">
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
         
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../howto/_howto/" class="md-nav__link ">
+              
   
   <span class="md-ellipsis">
     How-to
   </span>
   
 
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_3" id="__nav_3_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
       </a>
     </li>
   
@@ -392,7 +543,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
         
           
           
@@ -408,14 +559,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_3" id="__nav_3_label" tabindex="">
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -649,7 +800,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
         
           
           
@@ -665,14 +816,14 @@
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+      <a href="../../python_api/methods/ld_annotator/" class="md-nav__link">
         
   
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-    GWAS Catalog sumstat preprocess
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+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
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+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
         
   
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-    PICS
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@@ -2363,11 +2482,11 @@
   
   
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+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
         
   
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-    UK Biobank
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-    Variant-to-gene
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+  
+
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+    variant_index
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+  
+
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+              
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+  
+  
+  
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+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
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+    variant_to_gene
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+  
+
+      </a>
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+  
+
+              
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+              
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+  
+  
+  
+  
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+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
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@@ -2580,7 +2762,7 @@
 <h1 id="contributing-guidelines">Contributing guidelines<a class="headerlink" href="#contributing-guidelines" title="Permanent link">&para;</a></h1>
 <h2 id="one-time-configuration">One-time configuration<a class="headerlink" href="#one-time-configuration" title="Permanent link">&para;</a></h2>
 <p>The steps in this section only ever need to be done once on any particular system.</p>
-<p>Google Cloud configuration:</p>
+<p>For Google Cloud configuration:</p>
 <ol>
 <li>
 <p>Install Google Cloud SDK: https://cloud.google.com/sdk/docs/install.</p>
@@ -2655,8 +2837,8 @@ <h3 id="configuration">Configuration<a class="headerlink" href="#configuration"
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 <h3 id="classes">Classes<a class="headerlink" href="#classes" title="Permanent link">&para;</a></h3>
 <ul>
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-<li>Step main running class in <code>src/otg/STEP.py</code> (example: <code>src/otg/finngen.py</code>)</li>
+<li>Dataset class in <code>src/gentropy/datasource/STEP</code> (example: <code>src/gentropy/datasource/finngen/study_index.py</code> → <code>FinnGenStudyIndex</code>)</li>
+<li>Step main running class in <code>src/gentropy/STEP.py</code> (example: <code>src/gentropy/finngen.py</code>)</li>
 </ul>
 <h3 id="tests">Tests<a class="headerlink" href="#tests" title="Permanent link">&para;</a></h3>
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
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@@ -2761,7 +2943,7 @@ <h3 id="tests">Tests<a class="headerlink" href="#tests" title="Permanent link">&
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/development/troubleshooting/index.html b/development/troubleshooting/index.html
index 92c35d4b3..5dda18d0c 100644
--- a/development/troubleshooting/index.html
+++ b/development/troubleshooting/index.html
@@ -16,11 +16,11 @@
       
       
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Troubleshooting - Open Targets Genetics</title>
+        <title>Troubleshooting - Open Targets Gentropy</title>
       
     
     
@@ -94,7 +94,7 @@
 
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   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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@@ -107,7 +107,7 @@
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-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
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-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -215,6 +215,23 @@
   
   
   
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+      <a href="../.." class="md-tabs__link">
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../usage/" class="md-tabs__link">
+      <a href="../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -248,6 +265,23 @@
         
   
   
+  
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+      <a href="../../roadmap/" class="md-tabs__link">
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+    
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+  Roadmap
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@@ -309,22 +343,22 @@
 
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+    <a href="../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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+    Open Targets Gentropy
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -337,6 +371,26 @@
   
   
   
+    <li class="md-nav__item">
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@@ -357,15 +411,112 @@
   
   
   
-    <li class="md-nav__item">
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+    
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+      <a href="../../howto/run_step_in_cli/" class="md-nav__link">
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+  <span class="md-ellipsis">
+    Run step in CLI
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+      <a href="../../howto/run_step_using_config/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step using YAML config
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+    Roadmap
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
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+            <a href="../../python_api/datasets/_datasets/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/datasets/colocalisation/" class="md-nav__link">
         
   
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-      <a href="../../python_api/dataset/gene_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/gene_index/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/intervals/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/ld_index/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/study_index/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/study_locus/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/summary_statistics/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/variant_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -1020,32 +1171,32 @@
         
         
         
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
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-            <a href="../../python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="../../python_api/datasources/_datasources/" class="md-nav__link ">
               
   
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-    Datasource
+    Datasources
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+            Datasources
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-            <a href="../../python_api/datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
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-      <a href="../../python_api/datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
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+    </li>
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+
+              
+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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@@ -1139,12 +1311,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../python_api/datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
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-      <a href="../../python_api/datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Study Index
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+  
+
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+              
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+  
+  
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+      <a href="../../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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-            <a href="../../python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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             Gnomad
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-            <a href="../../python_api/datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
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+            <a href="../../python_api/datasources/intervals/_intervals/" class="md-nav__link ">
               
   
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-            <a href="../../python_api/datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../python_api/datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
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@@ -1639,7 +1832,7 @@
   
   
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+      <a href="../../python_api/datasources/open_targets/target/" class="md-nav__link">
         
   
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-            <a href="../../python_api/method/_method/" class="md-nav__link ">
+            <a href="../../python_api/methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+    Methods
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+            Methods
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     <li class="md-nav__item">
-      <a href="../../python_api/method/clumping/" class="md-nav__link">
+      <a href="../../python_api/methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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+    CARMA
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@@ -1816,11 +1935,11 @@
   
   
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-      <a href="../../python_api/method/coloc/" class="md-nav__link">
+      <a href="../../python_api/methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
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@@ -1837,11 +1956,11 @@
   
   
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-      <a href="../../python_api/method/ecaviar/" class="md-nav__link">
+      <a href="../../python_api/methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
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@@ -1858,11 +1977,11 @@
   
   
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-      <a href="../../python_api/method/ld_annotator/" class="md-nav__link">
+      <a href="../../python_api/methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
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@@ -1879,11 +1998,11 @@
   
   
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-      <a href="../../python_api/method/pics/" class="md-nav__link">
+      <a href="../../python_api/methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
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@@ -1900,11 +2019,11 @@
   
   
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-      <a href="../../python_api/method/window_based_clumping/" class="md-nav__link">
+      <a href="../../python_api/methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
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           <div class="md-nav__link md-nav__container">
-            <a href="../../python_api/method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
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@@ -1946,14 +2065,14 @@
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
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-      <a href="../../python_api/method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/evaluator/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../python_api/method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2008,7 +2127,7 @@
   
   
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-      <a href="../../python_api/method/l2g/model/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2029,7 +2148,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/method/l2g/trainer/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
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@@ -2075,32 +2194,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../python_api/step/_step/" class="md-nav__link ">
+            <a href="../../python_api/steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
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+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
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@@ -2111,11 +2230,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/clump/" class="md-nav__link">
+      <a href="../../python_api/steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
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@@ -2132,11 +2251,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/colocalisation/" class="md-nav__link">
+      <a href="../../python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
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@@ -2153,11 +2272,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../python_api/steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
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@@ -2174,11 +2293,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/finngen/" class="md-nav__link">
+      <a href="../../python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
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@@ -2195,11 +2314,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gene_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2216,11 +2335,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2237,11 +2356,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2258,11 +2377,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/l2g/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
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@@ -2279,11 +2398,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/ld_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2300,11 +2419,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/pics/" class="md-nav__link">
+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2321,11 +2440,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2342,11 +2461,11 @@
   
   
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-      <a href="../../python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
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-      <a href="../../python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="../../python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
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@@ -2384,11 +2503,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
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@@ -2606,7 +2788,7 @@ <h2 id="pre-commit">Pre-commit<a class="headerlink" href="#pre-commit" title="Pe
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/development/workflows/index.html b/development/workflows/index.html
index 675f077fb..04af7fa5a 100644
--- a/development/workflows/index.html
+++ b/development/workflows/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Pipeline workflows - Open Targets Genetics</title>
+        <title>Pipeline workflows - Open Targets Gentropy</title>
       
     
     
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
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+  
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+      
+        
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../usage/" class="md-tabs__link">
+      <a href="../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -248,6 +265,23 @@
         
   
   
+  
+    <li class="md-tabs__item">
+      <a href="../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
     
   
   
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
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@@ -337,6 +371,26 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../.." class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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@@ -357,15 +411,112 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../usage/" class="md-nav__link">
+    
+    
+    
+    
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
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+            <a href="../../howto/_howto/" class="md-nav__link ">
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   <span class="md-ellipsis">
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+            <span class="md-nav__icon md-icon"></span>
+            How-to
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+    <li class="md-nav__item">
+      <a href="../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
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+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
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+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+      <a href="../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
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@@ -392,7 +543,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" checked>
         
           
           
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -598,7 +749,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
         
           
           
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../python_api/dataset/_dataset/" class="md-nav__link ">
+            <a href="../../python_api/datasets/_datasets/" class="md-nav__link ">
               
   
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+    Datasets
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+      <a href="../../python_api/datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -700,7 +851,7 @@
   
   
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-      <a href="../../python_api/dataset/gene_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/gene_index/" class="md-nav__link">
         
   
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@@ -721,7 +872,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/intervals/" class="md-nav__link">
+      <a href="../../python_api/datasets/intervals/" class="md-nav__link">
         
   
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@@ -742,7 +893,7 @@
   
   
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-      <a href="../../python_api/dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -763,7 +914,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -784,7 +935,7 @@
   
   
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-      <a href="../../python_api/dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -805,7 +956,7 @@
   
   
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-      <a href="../../python_api/dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -826,7 +977,7 @@
   
   
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-      <a href="../../python_api/dataset/ld_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/ld_index/" class="md-nav__link">
         
   
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@@ -847,7 +998,7 @@
   
   
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-      <a href="../../python_api/dataset/study_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/study_index/" class="md-nav__link">
         
   
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+      <a href="../../python_api/datasets/study_locus/" class="md-nav__link">
         
   
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-      <a href="../../python_api/dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../python_api/datasets/study_locus_overlap/" class="md-nav__link">
         
   
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-      <a href="../../python_api/dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../python_api/datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -931,7 +1082,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -952,7 +1103,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_index/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_index/" class="md-nav__link">
         
   
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@@ -973,7 +1124,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -1011,32 +1162,32 @@
         
         
         
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
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-            <a href="../../python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="../../python_api/datasources/_datasources/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
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+      <a href="../../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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@@ -1130,12 +1302,12 @@
         
         
         
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+            <a href="../../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
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-      <a href="../../python_api/datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
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+      <a href="../../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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@@ -1204,12 +1397,12 @@
         
         
         
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-            <a href="../../python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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@@ -1299,12 +1492,12 @@
         
         
         
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+            <a href="../../python_api/datasources/intervals/_intervals/" class="md-nav__link ">
               
   
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+            <a href="../../python_api/methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+      <a href="../../python_api/methods/carma/" class="md-nav__link">
         
   
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+      <a href="../../python_api/methods/ld_annotator/" class="md-nav__link">
         
   
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+            <a href="../../python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
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+      <a href="../../python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
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-            <a href="../../python_api/step/_step/" class="md-nav__link ">
+            <a href="../../python_api/steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+      <a href="../../python_api/steps/colocalisation/" class="md-nav__link">
         
   
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-      <a href="../../python_api/step/colocalisation/" class="md-nav__link">
+      <a href="../../python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
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-      <a href="../../python_api/step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../python_api/steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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     <li class="md-nav__item">
-      <a href="../../python_api/step/finngen/" class="md-nav__link">
+      <a href="../../python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2186,11 +2305,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gene_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2207,11 +2326,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2228,11 +2347,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2249,11 +2368,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/l2g/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2270,11 +2389,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/ld_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2291,11 +2410,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/pics/" class="md-nav__link">
+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2312,11 +2431,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2333,11 +2452,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2354,11 +2473,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="../../python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2375,11 +2494,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2596,7 +2778,7 @@ <h2 id="dag-2-etl">DAG 2: ETL<a class="headerlink" href="#dag-2-etl" title="Perm
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/usage/index.html b/howto/_howto/index.html
similarity index 73%
rename from usage/index.html
rename to howto/_howto/index.html
index 4615b85db..527d39f8f 100644
--- a/usage/index.html
+++ b/howto/_howto/index.html
@@ -9,25 +9,25 @@
       
       
       
-        <link rel="prev" href="../installation/">
+        <link rel="prev" href="../../installation/">
       
       
-        <link rel="next" href="../development/_development/">
+        <link rel="next" href="../run_step_in_cli/">
       
       
-      <link rel="icon" href="../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <link rel="icon" href="../../assets/imgs/favicon.png">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>How-to - Open Targets Genetics</title>
+        <title>How-to - Open Targets Gentropy</title>
       
     
     
-      <link rel="stylesheet" href="../assets/stylesheets/main.50c56a3b.min.css">
+      <link rel="stylesheet" href="../../assets/stylesheets/main.50c56a3b.min.css">
       
         
-        <link rel="stylesheet" href="../assets/stylesheets/palette.06af60db.min.css">
+        <link rel="stylesheet" href="../../assets/stylesheets/palette.06af60db.min.css">
       
       
 
@@ -46,13 +46,13 @@
       
     
     
-      <link rel="stylesheet" href="../css/timeago.css">
+      <link rel="stylesheet" href="../../css/timeago.css">
     
-      <link rel="stylesheet" href="../assets/_mkdocstrings.css">
+      <link rel="stylesheet" href="../../assets/_mkdocstrings.css">
     
-      <link rel="stylesheet" href="../assets/stylesheets/extra.css">
+      <link rel="stylesheet" href="../../assets/stylesheets/extra.css">
     
-    <script>__md_scope=new URL("..",location),__md_hash=e=>[...e].reduce((e,_)=>(e<<5)-e+_.charCodeAt(0),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
+    <script>__md_scope=new URL("../..",location),__md_hash=e=>[...e].reduce((e,_)=>(e<<5)-e+_.charCodeAt(0),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
     
       
 
@@ -94,9 +94,9 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href=".." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
-  <img src="../assets/imgs/otlogo.png" alt="logo">
+  <img src="../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
     <label class="md-header__button md-icon" for="__drawer">
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -216,7 +216,24 @@
   
   
     <li class="md-tabs__item">
-      <a href="../installation/" class="md-tabs__link">
+      <a href="../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
+    <li class="md-tabs__item">
+      <a href="../../installation/" class="md-tabs__link">
         
   
     
@@ -252,7 +269,24 @@
   
   
     <li class="md-tabs__item">
-      <a href="../development/_development/" class="md-tabs__link">
+      <a href="../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
+    <li class="md-tabs__item">
+      <a href="../../development/_development/" class="md-tabs__link">
         
   
     
@@ -269,7 +303,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../python_api/_python_api/" class="md-tabs__link">
+      <a href="../../python_api/_python_api/" class="md-tabs__link">
         
   
     
@@ -298,9 +332,7 @@
           
             
               
-                
-              
-              <div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" hidden>
+              <div class="md-sidebar md-sidebar--primary" data-md-component="sidebar" data-md-type="navigation" >
                 <div class="md-sidebar__scrollwrap">
                   <div class="md-sidebar__inner">
                     
@@ -311,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href=".." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
-  <img src="../assets/imgs/otlogo.png" alt="logo">
+  <img src="../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -340,7 +372,27 @@
   
   
     <li class="md-nav__item">
-      <a href="../installation/" class="md-nav__link">
+      <a href="../.." class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Home
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -361,23 +413,92 @@
   
   
   
-    <li class="md-nav__item md-nav__item--active">
+    
+    
+    
+    
+    
       
-      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
       
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
       
         
-      
-      
-      <a href="./" class="md-nav__link md-nav__link--active">
         
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="./" class="md-nav__link md-nav__link--active">
+              
   
   <span class="md-ellipsis">
     How-to
   </span>
   
 
+            </a>
+            
+              
+              <label class="md-nav__link md-nav__link--active" for="__nav_3" id="__nav_3_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
       </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
       
     </li>
   
@@ -389,6 +510,26 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
     
     
     
@@ -402,12 +543,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../development/_development/" class="md-nav__link ">
+            <a href="../../development/_development/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -418,14 +559,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_3" id="__nav_3_label" tabindex="">
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -438,7 +579,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../development/airflow/" class="md-nav__link">
+      <a href="../../development/airflow/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -459,7 +600,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../development/contributing/" class="md-nav__link">
+      <a href="../../development/contributing/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -480,7 +621,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../development/troubleshooting/" class="md-nav__link">
+      <a href="../../development/troubleshooting/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -501,7 +642,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../development/workflows/" class="md-nav__link">
+      <a href="../../development/workflows/" class="md-nav__link">
         
   
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@@ -541,12 +682,12 @@
         
         
         
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-            <a href="../python_api/method/_method/" class="md-nav__link ">
+            <a href="../../python_api/methods/_methods/" class="md-nav__link ">
               
   
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+    Methods
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@@ -1729,11 +1838,11 @@
   
   
     <li class="md-nav__item">
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+      <a href="../../python_api/methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
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@@ -1750,11 +1859,11 @@
   
   
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+      <a href="../../python_api/methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
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@@ -1771,11 +1880,11 @@
   
   
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-      <a href="../python_api/method/ecaviar/" class="md-nav__link">
+      <a href="../../python_api/methods/coloc/" class="md-nav__link">
         
   
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-    eCAVIAR
+    Coloc
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@@ -1792,11 +1901,11 @@
   
   
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-      <a href="../python_api/method/ld_annotator/" class="md-nav__link">
+      <a href="../../python_api/methods/ecaviar/" class="md-nav__link">
         
   
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-    LDAnnotator
+    eCAVIAR
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@@ -1813,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/pics/" class="md-nav__link">
+      <a href="../../python_api/methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
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@@ -1834,11 +1943,11 @@
   
   
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-      <a href="../python_api/method/window_based_clumping/" class="md-nav__link">
+      <a href="../../python_api/methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
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@@ -1864,12 +1973,12 @@
         
         
         
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-            <a href="../python_api/method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
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+          <label class="md-nav__title" for="__nav_6_3_7">
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-      <a href="../python_api/method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1921,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/feature_factory/" class="md-nav__link">
         
   
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@@ -1942,7 +2051,7 @@
   
   
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-      <a href="../python_api/method/l2g/model/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/model/" class="md-nav__link">
         
   
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@@ -1963,7 +2072,7 @@
   
   
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-      <a href="../python_api/method/l2g/trainer/" class="md-nav__link">
+      <a href="../../python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
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@@ -2009,32 +2118,32 @@
         
         
         
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-            <a href="../python_api/step/_step/" class="md-nav__link ">
+            <a href="../../python_api/steps/_steps/" class="md-nav__link ">
               
   
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-    Step
+    Steps
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+          <label class="md-nav__title" for="__nav_6_4">
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-      <a href="../python_api/step/clump/" class="md-nav__link">
+      <a href="../../python_api/steps/colocalisation/" class="md-nav__link">
         
   
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-      <a href="../python_api/step/colocalisation/" class="md-nav__link">
+      <a href="../../python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
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-    Colocalisation
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+      <a href="../../python_api/steps/finngen_studies/" class="md-nav__link">
         
   
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+      <a href="../../python_api/steps/gene_index/" class="md-nav__link">
         
   
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-      <a href="../python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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+      <a href="../../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
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-      <a href="../python_api/step/l2g/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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-      <a href="../python_api/step/ld_index/" class="md-nav__link">
+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
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-      <a href="../python_api/step/pics/" class="md-nav__link">
+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
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-      <a href="../python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
         
   
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-      <a href="../python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../python_api/steps/ld_index/" class="md-nav__link">
         
   
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-      <a href="../python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="../../python_api/steps/pics/" class="md-nav__link">
         
   
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-      <a href="../python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
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+  
+
+              
+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
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+  
+
+      </a>
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+  
+
+              
+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
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+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
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@@ -2355,9 +2527,7 @@
             
             
               
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+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
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@@ -2386,7 +2556,8 @@
 
 
 <h1 id="how-to">How-to<a class="headerlink" href="#how-to" title="Permanent link">&para;</a></h1>
-<p>TBC</p>
+<p>This page contains a collection of how-to guides for the project.</p>
+<p>For additional information please visit <a href="https://community.opentargets.org/">https://community.opentargets.org/</a></p>
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-12T12:08:48+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-12</span> </span>
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-12T12:08:48+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-12</span> </span>
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@@ -0,0 +1,2716 @@
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+      <a href="../run_step_using_config/" class="md-nav__link">
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+  <span class="md-ellipsis">
+    Troubleshooting
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../development/workflows/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Pipeline workflows
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/_python_api/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Python API
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
+            <span class="md-nav__icon md-icon"></span>
+            Python API
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
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+                
+  
+  
+  
+  
+    
+    
+    
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+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasets/_datasets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
+            <span class="md-nav__icon md-icon"></span>
+            Datasets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Gene Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/intervals/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_feature/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_prediction/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Prediction
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/study_locus/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/study_locus_overlap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus Overlap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/variant_annotation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/variant_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/variant_to_gene/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant-to-gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/_datasources/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasources
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
+            <span class="md-nav__icon md-icon"></span>
+            Datasources
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Eqtl catalogue
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
+            <span class="md-nav__icon md-icon"></span>
+            Eqtl catalogue
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Stats
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Finngen
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
+            <span class="md-nav__icon md-icon"></span>
+            Finngen
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gnomad
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/methods/_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/carma/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/coloc/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Coloc
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/ecaviar/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/ld_annotator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LDAnnotator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    PICS
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/methods/l2g/_l2g/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    L2g
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
+            <span class="md-nav__icon md-icon"></span>
+            L2g
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/evaluator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    W&B evaluator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/feature_factory/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Factory
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/model/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Model
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/trainer/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Trainer
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/steps/_steps/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Steps
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
+            <span class="md-nav__icon md-icon"></span>
+            Steps
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/finngen_studies/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+<h1 id="run-step-in-cli">Run step in CLI<a class="headerlink" href="#run-step-in-cli" title="Permanent link">&para;</a></h1>
+<p>To run a step in the command line interface (CLI), you need to know the step's name. To list what steps are avaiable in your current environment, simply run <code>gentropy</code> with no arguments. This will list all the steps:</p>
+<div class="highlight"><pre><span></span><code>You must specify &#39;step&#39;, e.g, step=&lt;OPTION&gt;
+Available options:
+        clump
+        colocalisation
+        eqtl_catalogue
+        finngen_studies
+        finngen_sumstat_preprocess
+        gene_index
+        gwas_catalog_ingestion
+        gwas_catalog_sumstat_preprocess
+        ld_index
+        locus_to_gene
+        overlaps
+        pics
+        ukbiobank
+        variant_annotation
+        variant_index
+        variant_to_gene
+
+Set the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.
+</code></pre></div>
+<p>As indicated, you can run a step by specifying the step's name with the <code>step</code> argument. For example, to run the <code>gene_index</code> step, you can run:</p>
+<div class="highlight"><pre><span></span><code>gentropy<span class="w"> </span><span class="nv">step</span><span class="o">=</span>gene_index
+</code></pre></div>
+<p>In most occassions, some mandatory values will be required to run the step. For example, the <code>gene_index</code> step requires the <code>step.target_path</code> and <code>step.gene_index_path</code> argument to be specified. You can complete the necessary arguments by adding them to the command line:</p>
+<div class="highlight"><pre><span></span><code>gentropy<span class="w"> </span><span class="nv">step</span><span class="o">=</span>gene_index<span class="w"> </span>step.target_path<span class="o">=</span>/path/to/target<span class="w"> </span>step.gene_index_path<span class="o">=</span>/path/to/gene_index
+</code></pre></div>
+<p>You can find more about the available steps in the <a href="../../python_api/steps/_steps/">documentation</a>.</p>
+<hr />
+<div class="md-source-file">
+  <small>
+    <ul
+      class="metadata page-metadata"
+      data-bi-name="page info"
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
+      </li>
+      
+
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+  <ul class="md-nav__list" data-md-scrollfix>
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../.." class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Home
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../installation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Installation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
+      
+        
+        
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../_howto/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    How-to
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_3" id="__nav_3_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+        
+      
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            Development
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../development/airflow/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Airflow configuration
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../development/contributing/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Contributing guidelines
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../development/troubleshooting/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Troubleshooting
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../development/workflows/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Pipeline workflows
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/_python_api/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Python API
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
+            <span class="md-nav__icon md-icon"></span>
+            Python API
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasets/_datasets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
+            <span class="md-nav__icon md-icon"></span>
+            Datasets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Gene Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/intervals/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_feature/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/l2g_prediction/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Prediction
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/study_locus/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/study_locus_overlap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus Overlap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/variant_annotation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/variant_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasets/variant_to_gene/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant-to-gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/_datasources/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasources
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
+            <span class="md-nav__icon md-icon"></span>
+            Datasources
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Eqtl catalogue
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
+            <span class="md-nav__icon md-icon"></span>
+            Eqtl catalogue
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Stats
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Finngen
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
+            <span class="md-nav__icon md-icon"></span>
+            Finngen
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gnomad
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/datasources/open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/datasources/open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/methods/_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/carma/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/coloc/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Coloc
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/ecaviar/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/ld_annotator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LDAnnotator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    PICS
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/methods/l2g/_l2g/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    L2g
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
+            <span class="md-nav__icon md-icon"></span>
+            L2g
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/evaluator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    W&B evaluator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/feature_factory/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Factory
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/model/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Model
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/methods/l2g/trainer/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Trainer
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../python_api/steps/_steps/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Steps
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
+            <span class="md-nav__icon md-icon"></span>
+            Steps
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/finngen_studies/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+<h1 id="run-step-using-yaml-config">Run step using YAML config<a class="headerlink" href="#run-step-using-yaml-config" title="Permanent link">&para;</a></h1>
+<p>It's possible to parametrise the functionality of a step using a YAML configuration file. This is useful when you want to run a step multiple times with different parameters or simply to avoid having to specify the same parameters every time you run a step.</p>
+<div class="admonition info configuration files using hydra">
+<p class="admonition-title">Info</p>
+<p>The package uses <a href="https://hydra.cc">Hydra</a> to handle configuration files. For more information, please visit the <a href="https://hydra.cc/docs/intro/">Hydra documentation</a>.</p>
+</div>
+<p>To run a step using a configuration file, you need to create a configuration file in YAML format.</p>
+<div class="no-copy highlight"><pre><span></span><code>config/
+├─<span class="w"> </span>step/
+│<span class="w">  </span>└─<span class="w"> </span>my_gene_index.md
+└─<span class="w"> </span>my_config.yml
+</code></pre></div>
+<p>The configuration file should contain the parameters you want to use to run the step. For example, to run the <code>gene_index</code> step, you need to specify the <code>step.target_path</code> and <code>step.gene_index_path</code> parameters. The configuration file should look like this:</p>
+<div class="tabbed-set tabbed-alternate" data-tabs="1:2"><input checked="checked" id="__tabbed_1_1" name="__tabbed_1" type="radio" /><input id="__tabbed_1_2" name="__tabbed_1" type="radio" /><div class="tabbed-labels"><label for="__tabbed_1_1">my_config.yaml</label><label for="__tabbed_1_2">step/my_gene_index.md</label></div>
+<div class="tabbed-content">
+<div class="tabbed-block">
+<div class="highlight"><pre><span></span><code><span class="nt">defaults</span><span class="p">:</span>
+<span class="w">    </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">config</span>
+<span class="w">    </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">_self_</span>
+</code></pre></div>
+<p>This config file will specify that your configuration file will inherit the default configuration (<code>config</code>) and everything provided (<code>_self_</code>) will overwrite the default configuration.</p>
+</div>
+<div class="tabbed-block">
+<div class="highlight"><pre><span></span><code><span class="nt">defaults</span><span class="p">:</span>
+<span class="w">    </span><span class="p p-Indicator">-</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">gene_index</span>
+
+<span class="nt">target_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/path/to/target</span>
+<span class="nt">gene_index_path</span><span class="p">:</span><span class="w"> </span><span class="l l-Scalar l-Scalar-Plain">/path/to/gene_index</span>
+</code></pre></div>
+<p>This config file will inherit the default configuration for the <code>gene_index</code> step and overwrite the <code>target_path</code> and <code>gene_index_path</code> parameters.</p>
+</div>
+</div>
+</div>
+<p>Once you have created the configuration file, you can run your own new <code>my_gene_index</code>:</p>
+<div class="highlight"><pre><span></span><code>gentropy<span class="w"> </span><span class="nv">step</span><span class="o">=</span>my_gene_index<span class="w"> </span>--config-dir<span class="o">=</span>config<span class="w"> </span>--config-name<span class="o">=</span>my_config
+</code></pre></div>
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diff --git a/index.html b/index.html
index 78d4362fa..f7fa6f048 100644
--- a/index.html
+++ b/index.html
@@ -14,11 +14,11 @@
       
       
       <link rel="icon" href="assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Open Targets Genetics - Open Targets Genetics</title>
+        <title>Open Targets Gentropy - Open Targets Gentropy</title>
       
     
     
@@ -75,6 +75,11 @@
     <label class="md-overlay" for="__drawer"></label>
     <div data-md-component="skip">
       
+        
+        <a href="#about-open-targets" class="md-skip">
+          Skip to content
+        </a>
+      
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     <div data-md-component="announce">
       
@@ -87,7 +92,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="assets/imgs/otlogo.png" alt="logo">
 
@@ -100,13 +105,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Open Targets Genetics
+              Open Targets Gentropy
             
           </span>
         </div>
@@ -185,13 +190,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -207,6 +212,25 @@
         
   
   
+    
+  
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+      <a href="." class="md-tabs__link">
+        
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+    </li>
+  
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     <li class="md-tabs__item">
       <a href="installation/" class="md-tabs__link">
@@ -226,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="usage/" class="md-tabs__link">
+      <a href="howto/_howto/" class="md-tabs__link">
         
   
     
@@ -242,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="roadmap/" class="md-tabs__link">
+        
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+    
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@@ -302,22 +343,22 @@
 
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-    <a href="." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -328,6 +369,71 @@
       
   
   
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@@ -350,15 +456,112 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="usage/" class="md-nav__link">
+    
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+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
       </a>
     </li>
   
@@ -383,7 +586,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
           
@@ -399,14 +602,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_3" id="__nav_3_label" tabindex="">
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -522,7 +725,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
         
           
           
@@ -538,14 +741,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -567,32 +770,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/dataset/_dataset/" class="md-nav__link ">
+            <a href="python_api/datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -603,7 +806,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/colocalisation/" class="md-nav__link">
+      <a href="python_api/datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -624,7 +827,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/gene_index/" class="md-nav__link">
+      <a href="python_api/datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -645,7 +848,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/intervals/" class="md-nav__link">
+      <a href="python_api/datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -666,7 +869,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/l2g_feature/" class="md-nav__link">
+      <a href="python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -687,7 +890,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -708,7 +911,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="python_api/datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -729,7 +932,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/l2g_prediction/" class="md-nav__link">
+      <a href="python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -750,7 +953,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/ld_index/" class="md-nav__link">
+      <a href="python_api/datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -771,7 +974,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/study_index/" class="md-nav__link">
+      <a href="python_api/datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -792,7 +995,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/study_locus/" class="md-nav__link">
+      <a href="python_api/datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -813,7 +1016,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="python_api/datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -834,7 +1037,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/summary_statistics/" class="md-nav__link">
+      <a href="python_api/datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -855,7 +1058,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/variant_annotation/" class="md-nav__link">
+      <a href="python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -876,7 +1079,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/variant_index/" class="md-nav__link">
+      <a href="python_api/datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -897,7 +1100,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -935,32 +1138,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="python_api/datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -980,12 +1183,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -996,14 +1199,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1016,7 +1219,28 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1054,12 +1278,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1070,14 +1294,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1090,7 +1314,28 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/finngen/study_index/" class="md-nav__link">
+      <a href="python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1128,12 +1373,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1144,14 +1389,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1164,7 +1409,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="python_api/datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1185,7 +1430,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="python_api/datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1223,12 +1468,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1239,14 +1484,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1259,7 +1504,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1280,7 +1525,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="python_api/datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1301,7 +1546,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="python_api/datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1322,7 +1567,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="python_api/datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1360,12 +1605,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="python_api/datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1376,14 +1621,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1396,7 +1641,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/intervals/andersson/" class="md-nav__link">
+      <a href="python_api/datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1417,7 +1662,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/intervals/javierre/" class="md-nav__link">
+      <a href="python_api/datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1438,7 +1683,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/intervals/jung/" class="md-nav__link">
+      <a href="python_api/datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1459,7 +1704,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/intervals/thurman/" class="md-nav__link">
+      <a href="python_api/datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1497,12 +1742,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="python_api/datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1513,14 +1758,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1533,7 +1778,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="python_api/datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1554,7 +1799,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/datasource/open_targets/target/" class="md-nav__link">
+      <a href="python_api/datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1576,80 +1821,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="python_api/datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="python_api/datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1674,32 +1845,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/method/_method/" class="md-nav__link ">
+            <a href="python_api/methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1710,11 +1881,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/clumping/" class="md-nav__link">
+      <a href="python_api/methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1731,11 +1902,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/coloc/" class="md-nav__link">
+      <a href="python_api/methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1752,11 +1923,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/ecaviar/" class="md-nav__link">
+      <a href="python_api/methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1773,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/ld_annotator/" class="md-nav__link">
+      <a href="python_api/methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1794,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/pics/" class="md-nav__link">
+      <a href="python_api/methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1815,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/window_based_clumping/" class="md-nav__link">
+      <a href="python_api/methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1845,12 +2016,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/method/l2g/_l2g/" class="md-nav__link ">
+            <a href="python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1861,14 +2032,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1881,7 +2052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/l2g/evaluator/" class="md-nav__link">
+      <a href="python_api/methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1902,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/l2g/feature_factory/" class="md-nav__link">
+      <a href="python_api/methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1923,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/l2g/model/" class="md-nav__link">
+      <a href="python_api/methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1944,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/method/l2g/trainer/" class="md-nav__link">
+      <a href="python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1990,32 +2161,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="python_api/step/_step/" class="md-nav__link ">
+            <a href="python_api/steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2026,11 +2197,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/clump/" class="md-nav__link">
+      <a href="python_api/steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2047,11 +2218,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/colocalisation/" class="md-nav__link">
+      <a href="python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2068,11 +2239,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/eqtl_catalogue/" class="md-nav__link">
+      <a href="python_api/steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2089,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/finngen/" class="md-nav__link">
+      <a href="python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2110,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/gene_index/" class="md-nav__link">
+      <a href="python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2131,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2152,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2173,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/l2g/" class="md-nav__link">
+      <a href="python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2194,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/ld_index/" class="md-nav__link">
+      <a href="python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2215,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/pics/" class="md-nav__link">
+      <a href="python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2236,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2257,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2278,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2299,11 +2470,74 @@
   
   
     <li class="md-nav__item">
-      <a href="python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2348,6 +2582,23 @@
   
   
   
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#about-open-targets" class="md-nav__link">
+    <span class="md-ellipsis">
+      About Open Targets
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
 </nav>
                   </div>
                 </div>
@@ -2364,11 +2615,10 @@
   
 
 
-  <h1>Open Targets Genetics</h1>
+  <h1>Home</h1>
 
-<p align="center">
-  <img width="460" height="300" src="assets/imgs/Open_Targets_Genetics_Portal_Logo_v2_font.svg">
-</p>
+<p></br></p>
+<p><img width="800" height="300" src="assets/imgs/gentropy.svg"></p>
 <style>
   .md-typeset h1,
   .md-content__button {
@@ -2376,16 +2626,16 @@ <h1>Open Targets Genetics</h1>
   }
 </style>
 
-<hr />
-<p><a href="https://github.com/GIScience/badges#experimental"><img alt="status: experimental" src="https://github.com/GIScience/badges/raw/master/status/experimental.svg" /></a>
-<img alt="docs" src="https://github.com/opentargets/genetics_etl_python/actions/workflows/docs.yaml/badge.svg" />
-<a href="https://codecov.io/gh/opentargets/genetics_etl_python"><img alt="codecov" src="https://codecov.io/gh/opentargets/genetics_etl_python/branch/main/graph/badge.svg?token=5ixzgu8KFP" /></a>
+<p></br></p>
+<p><a href="https://github.com/astral-sh/ruff"><img alt="Ruff" src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" /></a>
+<a href="https://opentargets.github.io/gentropy/"><img alt="image" src="https://github.com/opentargets/gentropy/actions/workflows/release.yaml/badge.svg" /></a>
+<a href="https://codecov.io/gh/opentargets/gentropy"><img alt="codecov" src="https://codecov.io/gh/opentargets/gentropy/branch/main/graph/badge.svg?token=5ixzgu8KFP" /></a>
 <a href="https://opensource.org/licenses/Apache-2.0"><img alt="License" src="https://img.shields.io/badge/License-Apache_2.0-blue.svg" /></a>
-<a href="https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python"><img alt="pre-commit.ci status" src="https://results.pre-commit.ci/badge/github/opentargets/genetics_etl_python/main.svg" /></a></p>
+<a href="https://doi.org/10.5281/zenodo.10527086"><img alt="DOI" src="https://zenodo.org/badge/DOI/10.5281/zenodo.10527086.svg" /></a></p>
 <hr />
-<p>Ingestion and analysis of genetic and functional genomic data for the identification and prioritisation of drug targets.</p>
-<p>This project is still in experimental phase. Please refer to the <a href="roadmap/">roadmap section</a> for more information.</p>
-<p>For all development information, including running the code, troubleshooting, or contributing, see the <a href="./development/">development section</a>.</p>
+<p>Open Targets Gentropy is a Python package to facilitate the interpretation and analysis of GWAS and functional genomic studies for target identification. This package contains a toolkit for the harmonisation, statistical analysis and prioritisation of genetic signals to assist drug discovery.</p>
+<h2 id="about-open-targets">About Open Targets<a class="headerlink" href="#about-open-targets" title="Permanent link">&para;</a></h2>
+<p>Open Targets is a pre-competitive, public-private partnership that uses human genetics and genomics data to systematically identify and prioritise drug targets. Through large-scale genomic experiments and the development of innovative computational techniques, the partnership aims to help researchers select the best targets for the development of new therapies. For more information, visit the Open Targets <a href="https://www.opentargets.org">website</a>.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2413,6 +2663,14 @@ <h1>Open Targets Genetics</h1>
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
+          </li><li>
+            <a
+              href="https://github.com/addramir"
+              title="addramir"
+              data-bi-name="contributorprofile"
+              target="_blank"
+              ><img src="https://avatars.githubusercontent.com/u/22906976?v=4" alt="addramir"
+            /></a>
           </li><li>
             <a
               href="https://github.com/tskir"
@@ -2487,7 +2745,7 @@ <h1>Open Targets Genetics</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/installation/index.html b/installation/index.html
index bf5ddabf6..e6b6ac339 100644
--- a/installation/index.html
+++ b/installation/index.html
@@ -9,16 +9,18 @@
       
       
       
+        <link rel="prev" href="..">
       
-        <link rel="next" href="../usage/">
+      
+        <link rel="next" href="../howto/_howto/">
       
       
       <link rel="icon" href="../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Installation - Open Targets Genetics</title>
+        <title>Installation - Open Targets Gentropy</title>
       
     
     
@@ -92,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href=".." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href=".." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../assets/imgs/otlogo.png" alt="logo">
 
@@ -105,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -190,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -212,6 +214,23 @@
         
   
   
+  
+    <li class="md-tabs__item">
+      <a href=".." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
     
   
   
@@ -233,7 +252,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../usage/" class="md-tabs__link">
+      <a href="../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +268,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../development/_development/" class="md-tabs__link">
         
@@ -309,22 +345,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href=".." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href=".." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -335,6 +371,26 @@
       
   
   
+  
+  
+    <li class="md-nav__item">
+      <a href=".." class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Home
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
     
   
   
@@ -347,6 +403,17 @@
         
       
       
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    Installation
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
       <a href="./" class="md-nav__link md-nav__link--active">
         
   
@@ -357,6 +424,52 @@
 
       </a>
       
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+    
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#pypi" class="md-nav__link">
+    <span class="md-ellipsis">
+      Pypi
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#source" class="md-nav__link">
+    <span class="md-ellipsis">
+      Source
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#uninstall" class="md-nav__link">
+    <span class="md-ellipsis">
+      Uninstall
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
     </li>
   
 
@@ -367,15 +480,112 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../usage/" class="md-nav__link">
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
         
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../howto/_howto/" class="md-nav__link ">
+              
   
   <span class="md-ellipsis">
     How-to
   </span>
   
 
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_3" id="__nav_3_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
       </a>
     </li>
   
@@ -400,7 +610,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
         
           
           
@@ -416,14 +626,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_3" id="__nav_3_label" tabindex="">
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_3">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -539,7 +749,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
         
           
           
@@ -555,14 +765,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -584,32 +794,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/dataset/_dataset/" class="md-nav__link ">
+            <a href="../python_api/datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -620,7 +830,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/colocalisation/" class="md-nav__link">
+      <a href="../python_api/datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -641,7 +851,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/gene_index/" class="md-nav__link">
+      <a href="../python_api/datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -662,7 +872,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/intervals/" class="md-nav__link">
+      <a href="../python_api/datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -683,7 +893,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_feature/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -704,7 +914,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -725,7 +935,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -746,7 +956,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -767,7 +977,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/ld_index/" class="md-nav__link">
+      <a href="../python_api/datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -788,7 +998,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/study_index/" class="md-nav__link">
+      <a href="../python_api/datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -809,7 +1019,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/study_locus/" class="md-nav__link">
+      <a href="../python_api/datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -830,7 +1040,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../python_api/datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -851,7 +1061,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/summary_statistics/" class="md-nav__link">
+      <a href="../python_api/datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -872,7 +1082,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/variant_annotation/" class="md-nav__link">
+      <a href="../python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -893,7 +1103,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/variant_index/" class="md-nav__link">
+      <a href="../python_api/datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -914,7 +1124,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -952,32 +1162,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="../python_api/datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -997,12 +1207,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1013,14 +1223,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1033,7 +1243,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1071,12 +1302,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1087,14 +1318,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1107,7 +1338,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1145,12 +1397,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1161,14 +1413,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1181,7 +1433,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../python_api/datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1202,7 +1454,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../python_api/datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1240,12 +1492,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1256,14 +1508,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1276,7 +1528,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1297,7 +1549,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1318,7 +1570,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1339,7 +1591,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1377,12 +1629,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../python_api/datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1393,14 +1645,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1413,7 +1665,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1434,7 +1686,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1455,7 +1707,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/jung/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1476,7 +1728,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1514,12 +1766,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../python_api/datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1530,14 +1782,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1550,7 +1802,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../python_api/datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1571,7 +1823,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/open_targets/target/" class="md-nav__link">
+      <a href="../python_api/datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1593,80 +1845,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../python_api/datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1691,32 +1869,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/method/_method/" class="md-nav__link ">
+            <a href="../python_api/methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1727,11 +1905,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/clumping/" class="md-nav__link">
+      <a href="../python_api/methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1748,11 +1926,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/coloc/" class="md-nav__link">
+      <a href="../python_api/methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1769,11 +1947,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/ecaviar/" class="md-nav__link">
+      <a href="../python_api/methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1790,11 +1968,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/ld_annotator/" class="md-nav__link">
+      <a href="../python_api/methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1811,11 +1989,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/pics/" class="md-nav__link">
+      <a href="../python_api/methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1832,11 +2010,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/window_based_clumping/" class="md-nav__link">
+      <a href="../python_api/methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1862,12 +2040,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1878,14 +2056,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1898,7 +2076,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/evaluator/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1919,7 +2097,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1940,7 +2118,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/model/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1961,7 +2139,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/trainer/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2007,32 +2185,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/step/_step/" class="md-nav__link ">
+            <a href="../python_api/steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2043,11 +2221,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/clump/" class="md-nav__link">
+      <a href="../python_api/steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2064,11 +2242,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/colocalisation/" class="md-nav__link">
+      <a href="../python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2085,11 +2263,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../python_api/steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2106,11 +2284,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/finngen/" class="md-nav__link">
+      <a href="../python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2127,11 +2305,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/gene_index/" class="md-nav__link">
+      <a href="../python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2148,11 +2326,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2169,11 +2347,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2190,11 +2368,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/l2g/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2211,11 +2389,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/ld_index/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2232,11 +2410,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/pics/" class="md-nav__link">
+      <a href="../python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2253,11 +2431,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="../python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2274,11 +2452,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="../python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2295,11 +2473,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="../python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2316,11 +2494,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2367,6 +2608,41 @@
     
   
   
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#pypi" class="md-nav__link">
+    <span class="md-ellipsis">
+      Pypi
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#source" class="md-nav__link">
+    <span class="md-ellipsis">
+      Source
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#uninstall" class="md-nav__link">
+    <span class="md-ellipsis">
+      Uninstall
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
 </nav>
                   </div>
                 </div>
@@ -2384,7 +2660,20 @@
 
 
 <h1 id="installation">Installation<a class="headerlink" href="#installation" title="Permanent link">&para;</a></h1>
-<p>TBC</p>
+<div class="admonition note python compatibility">
+<p class="admonition-title">Note</p>
+<p>In the early stages of development, we are using Python version 3.10. We recommend using <a href="https://github.com/pyenv/pyenv">pyenv</a> or similar tools to manage your local Python version. We intend to support more Python versions in the future.</p>
+</div>
+<h2 id="pypi">Pypi<a class="headerlink" href="#pypi" title="Permanent link">&para;</a></h2>
+<p>We recommend installing Open Targets Gentropy using Pypi:</p>
+<div class="highlight"><pre><span></span><code>pip<span class="w"> </span>install<span class="w"> </span>gentropy
+</code></pre></div>
+<h2 id="source">Source<a class="headerlink" href="#source" title="Permanent link">&para;</a></h2>
+<p>Alternatively, you can install Open Targets Gentropy from source. Check the <a href="../development/contributing/">contributing</a> section for more information.</p>
+<h2 id="uninstall">Uninstall<a class="headerlink" href="#uninstall" title="Permanent link">&para;</a></h2>
+<div class="highlight"><pre><span></span><code>pip<span class="w"> </span>uninstall<span class="w"> </span>gentropy<span class="w"> </span>-y
+</code></pre></div>
+<p>For any issues with the installation, check the <a href="../development/troubleshooting/">troubleshooting section</a>.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2407,7 +2696,7 @@ <h1 id="installation">Installation<a class="headerlink" href="#installation" tit
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2426,6 +2715,14 @@ <h1 id="installation">Installation<a class="headerlink" href="#installation" tit
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
+          </li><li>
+            <a
+              href="https://github.com/addramir"
+              title="addramir"
+              data-bi-name="contributorprofile"
+              target="_blank"
+              ><img src="https://avatars.githubusercontent.com/u/22906976?v=4" alt="addramir"
+            /></a>
           </li></ul>
       </li>
     </ul>
@@ -2476,7 +2773,7 @@ <h1 id="installation">Installation<a class="headerlink" href="#installation" tit
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/objects.inv b/objects.inv
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diff --git a/python_api/_python_api/index.html b/python_api/_python_api/index.html
index 39b851e17..6716d7e7c 100644
--- a/python_api/_python_api/index.html
+++ b/python_api/_python_api/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../../development/workflows/">
       
       
-        <link rel="next" href="../dataset/_dataset/">
+        <link rel="next" href="../datasets/_datasets/">
       
       
       <link rel="icon" href="../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Python API - Open Targets Genetics</title>
+        <title>Python API - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,7 +102,7 @@
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-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -187,13 +187,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../.." class="md-tabs__link">
+        
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+  Home
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-      <a href="../../usage/" class="md-tabs__link">
+      <a href="../../howto/_howto/" class="md-tabs__link">
         
   
     
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+    <li class="md-tabs__item">
+      <a href="../../roadmap/" class="md-tabs__link">
+        
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-    <a href="../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -333,11 +367,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../installation/" class="md-nav__link">
+      <a href="../.." class="md-nav__link">
         
   
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+    Home
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+      <a href="../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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-            <a href="../../development/_development/" class="md-nav__link ">
+            <a href="../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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+            <span class="md-nav__icon md-icon"></span>
+            How-to
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+          <ul class="md-nav__list" data-md-scrollfix>
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+    <li class="md-nav__item">
+      <a href="../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
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+    </li>
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+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
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+  
+
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+            
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+    <li class="md-nav__item">
+      <a href="../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+  
+
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+      
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+      
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+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
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+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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-              <label class="md-nav__link md-nav__link--active" for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
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             Python API
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../dataset/_dataset/" class="md-nav__link ">
+            <a href="../datasets/_datasets/" class="md-nav__link ">
               
   
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+    Datasets
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+      <a href="../datasets/colocalisation/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../datasets/gene_index/" class="md-nav__link">
         
   
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+      <a href="../datasets/l2g_feature/" class="md-nav__link">
         
   
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-      <a href="../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -901,7 +1052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -939,32 +1090,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../datasource/_datasource/" class="md-nav__link ">
+            <a href="../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -984,12 +1135,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1000,14 +1151,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1020,7 +1171,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1058,12 +1230,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1074,14 +1246,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1094,7 +1266,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1132,12 +1325,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1148,14 +1341,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1168,7 +1361,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1189,7 +1382,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1227,12 +1420,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1243,14 +1436,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1263,7 +1456,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1284,7 +1477,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1305,7 +1498,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1326,7 +1519,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1364,12 +1557,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1380,14 +1573,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1400,7 +1593,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1421,7 +1614,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1442,7 +1635,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1463,7 +1656,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1501,12 +1694,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1517,14 +1710,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1537,7 +1730,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1558,7 +1751,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1580,80 +1773,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1678,32 +1797,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../method/_method/" class="md-nav__link ">
+            <a href="../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1714,11 +1833,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/clumping/" class="md-nav__link">
+      <a href="../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1735,11 +1854,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/coloc/" class="md-nav__link">
+      <a href="../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1756,11 +1875,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/ecaviar/" class="md-nav__link">
+      <a href="../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1777,11 +1896,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/ld_annotator/" class="md-nav__link">
+      <a href="../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1798,11 +1917,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/pics/" class="md-nav__link">
+      <a href="../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1819,11 +1938,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/window_based_clumping/" class="md-nav__link">
+      <a href="../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1849,12 +1968,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1865,14 +1984,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1885,7 +2004,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1906,7 +2025,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1927,7 +2046,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/l2g/model/" class="md-nav__link">
+      <a href="../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1948,7 +2067,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../method/l2g/trainer/" class="md-nav__link">
+      <a href="../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1994,32 +2113,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../step/_step/" class="md-nav__link ">
+            <a href="../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2030,11 +2149,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/clump/" class="md-nav__link">
+      <a href="../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2051,11 +2170,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/colocalisation/" class="md-nav__link">
+      <a href="../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2072,11 +2191,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2093,11 +2212,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/finngen/" class="md-nav__link">
+      <a href="../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2114,11 +2233,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/gene_index/" class="md-nav__link">
+      <a href="../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2135,11 +2254,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2156,11 +2275,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2177,11 +2296,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/l2g/" class="md-nav__link">
+      <a href="../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2198,11 +2317,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/ld_index/" class="md-nav__link">
+      <a href="../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2219,11 +2338,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/pics/" class="md-nav__link">
+      <a href="../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2240,11 +2359,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/ukbiobank/" class="md-nav__link">
+      <a href="../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2261,11 +2380,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2282,11 +2401,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/variant_index_step/" class="md-nav__link">
+      <a href="../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2303,11 +2422,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2368,7 +2550,14 @@
 
   <h1>Python API</h1>
 
-
+<p>Open Targets Gentropy is a Python package to facilitate the interpretation and analysis of GWAS and functional genomic studies for target identification. The package contains a toolkit for the harmonisation, statistical analysis and prioritisation of genetic signals to assist drug discovery.</p>
+<p>The overall architecture of the package distinguishes between:</p>
+<ul>
+<li><a href="../datasources/_datasources/"><strong>Data Sources</strong></a>: data sources harmonisation tools</li>
+<li><a href="../datasets/_datasets/"><strong>Datasets</strong></a>: data model</li>
+<li><a href="../methods/_methods/"><strong>Methods</strong></a>: statistical analysis tools</li>
+<li><a href="../steps/_steps/"><strong>Steps</strong></a>: pipeline steps</li>
+</ul>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2391,7 +2580,7 @@ <h1>Python API</h1>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-16T08:22:37+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-16</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2410,6 +2599,14 @@ <h1>Python API</h1>
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
+          </li><li>
+            <a
+              href="https://github.com/addramir"
+              title="addramir"
+              data-bi-name="contributorprofile"
+              target="_blank"
+              ><img src="https://avatars.githubusercontent.com/u/22906976?v=4" alt="addramir"
+            /></a>
           </li></ul>
       </li>
     </ul>
@@ -2458,7 +2655,7 @@ <h1>Python API</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/_dataset/index.html b/python_api/datasets/_datasets/index.html
similarity index 87%
rename from python_api/dataset/_dataset/index.html
rename to python_api/datasets/_datasets/index.html
index 9e4fdaa92..e2e2f67a9 100644
--- a/python_api/dataset/_dataset/index.html
+++ b/python_api/datasets/_datasets/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Dataset - Open Targets Genetics</title>
+        <title>Datasets - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.dataset.Dataset" class="md-skip">
+        <a href="#gentropy.dataset.dataset.Dataset" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Dataset
+              Datasets
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,7 +729,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
@@ -587,23 +738,23 @@
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1027,7 +1178,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1065,12 +1237,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1101,7 +1273,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1139,12 +1332,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1175,7 +1368,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1196,7 +1389,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1234,12 +1427,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1250,14 +1443,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1270,7 +1463,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1291,7 +1484,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1312,7 +1505,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1333,7 +1526,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1371,12 +1564,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1387,14 +1580,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1407,7 +1600,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1428,7 +1621,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1449,7 +1642,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1470,7 +1663,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1508,12 +1701,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1524,14 +1717,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1544,7 +1737,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1565,7 +1758,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1587,80 +1780,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,32 +1804,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1742,11 +1861,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1763,11 +1882,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1903,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1924,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1826,11 +1945,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1856,12 +1975,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1872,14 +1991,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1892,7 +2011,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1913,7 +2032,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1934,7 +2053,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1955,7 +2074,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2121,11 +2240,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2142,11 +2261,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2163,11 +2282,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2184,11 +2303,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2205,11 +2324,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2226,11 +2345,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2247,11 +2366,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2268,11 +2387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2289,11 +2408,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2310,11 +2429,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2364,7 +2546,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset" class="md-nav__link">
     <span class="md-ellipsis">
       Dataset
     </span>
@@ -2374,7 +2556,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.df" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.df" class="md-nav__link">
     <span class="md-ellipsis">
       df
     </span>
@@ -2383,7 +2565,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.schema" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.schema" class="md-nav__link">
     <span class="md-ellipsis">
       schema
     </span>
@@ -2392,63 +2574,63 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.coalesce" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.coalesce" class="md-nav__link">
     <span class="md-ellipsis">
-      coalesce()
+      coalesce
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.from_parquet" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.from_parquet" class="md-nav__link">
     <span class="md-ellipsis">
-      from_parquet()
+      from_parquet
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.persist" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.persist" class="md-nav__link">
     <span class="md-ellipsis">
-      persist()
+      persist
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.repartition" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.repartition" class="md-nav__link">
     <span class="md-ellipsis">
-      repartition()
+      repartition
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.unpersist" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.unpersist" class="md-nav__link">
     <span class="md-ellipsis">
-      unpersist()
+      unpersist
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.dataset.Dataset.validate_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.dataset.Dataset.validate_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      validate_schema()
+      validate_schema
     </span>
   </a>
   
@@ -2477,22 +2659,24 @@
   
 
 
-  <h1>Dataset</h1>
+  <h1>Datasets</h1>
 
-<div class="doc doc-object doc-class">
+<p>The Dataset classes define the data model behind Open Targets Gentropy. Every class inherits from the <code>Dataset</code> class and contains a dataframe with a predefined schema that can be found in the respective classes.</p>
 
 
+<div class="doc doc-object doc-class">
+
 
 
-<h2 id="otg.dataset.dataset.Dataset" class="doc doc-heading">
-          <code>otg.dataset.dataset.Dataset</code>
+<h2 id="gentropy.dataset.dataset.Dataset" class="doc doc-heading">
+          <code>gentropy.dataset.dataset.Dataset</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.dataset.Dataset" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.dataset.Dataset" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2500,11 +2684,11 @@ <h2 id="otg.dataset.dataset.Dataset" class="doc doc-heading">
             Bases: <code><span title="abc.ABC">ABC</span></code></p>
 
   
-      <p>Open Targets Genetics Dataset.</p>
+      <p>Open Targets Gentropy Dataset.</p>
 <p><code>Dataset</code> is a wrapper around a Spark DataFrame with a predefined schema. Schemas for each child dataset are described in the <code>schemas</code> module.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 19</span>
 <span class="normal"> 20</span>
 <span class="normal"> 21</span>
@@ -2688,7 +2872,7 @@ <h2 id="otg.dataset.dataset.Dataset" class="doc doc-heading">
 <span class="normal">199</span>
 <span class="normal">200</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">Dataset</span><span class="p">(</span><span class="n">ABC</span><span class="p">):</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Open Targets Genetics Dataset.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Open Targets Gentropy Dataset.</span>
 
 <span class="sd">    `Dataset` is a wrapper around a Spark DataFrame with a predefined schema. Schemas for each child dataset are described in the `schemas` module.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
@@ -2742,14 +2926,14 @@ <h2 id="otg.dataset.dataset.Dataset" class="doc doc-heading">
     <span class="k">def</span> <span class="nf">from_parquet</span><span class="p">(</span>
         <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">Self</span><span class="p">],</span>
         <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
-        <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
         <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">float</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Self</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Reads a parquet file into a Dataset with a given schema.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Reads parquet into a Dataset with a given schema.</span>
 
 <span class="sd">        Args:</span>
 <span class="sd">            session (Session): Spark session</span>
-<span class="sd">            path (str): Path to the parquet file</span>
+<span class="sd">            path (str | list[str]): Path to the parquet dataset</span>
 <span class="sd">            **kwargs (bool | float | int | str | None): Additional arguments to pass to spark.read.parquet</span>
 
 <span class="sd">        Returns:</span>
@@ -2759,7 +2943,7 @@ <h2 id="otg.dataset.dataset.Dataset" class="doc doc-heading">
 <span class="sd">            ValueError: Parquet file is empty</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">schema</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">()</span>
-        <span class="n">df</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="n">path</span><span class="o">=</span><span class="n">path</span><span class="p">,</span> <span class="n">schema</span><span class="o">=</span><span class="n">schema</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">schema</span><span class="o">=</span><span class="n">schema</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
         <span class="k">if</span> <span class="n">df</span><span class="o">.</span><span class="n">isEmpty</span><span class="p">():</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Parquet file is empty: </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
         <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">_df</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">_schema</span><span class="o">=</span><span class="n">schema</span><span class="p">)</span>
@@ -2885,8 +3069,7 @@ <h2 id="otg.dataset.dataset.Dataset" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.df" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.df" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">df</span><span class="p">:</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
@@ -2894,7 +3077,7 @@ <h3 id="otg.dataset.dataset.Dataset.df" class="doc doc-heading">
       <small class="doc doc-label doc-label-writable"><code>writable</code></small>
   </span>
 
-<a href="#otg.dataset.dataset.Dataset.df" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.df" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2932,15 +3115,14 @@ <h3 id="otg.dataset.dataset.Dataset.df" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">schema</span><span class="p">:</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-property"><code>property</code></small>
   </span>
 
-<a href="#otg.dataset.dataset.Dataset.schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2981,11 +3163,10 @@ <h3 id="otg.dataset.dataset.Dataset.schema" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.coalesce" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.coalesce" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">coalesce</span><span class="p">(</span><span class="n">num_partitions</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="n">Any</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Self</span></code>
 
-<a href="#otg.dataset.dataset.Dataset.coalesce" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.coalesce" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3062,7 +3243,7 @@ <h3 id="otg.dataset.dataset.Dataset.coalesce" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">172</span>
 <span class="normal">173</span>
 <span class="normal">174</span>
@@ -3101,20 +3282,19 @@ <h3 id="otg.dataset.dataset.Dataset.coalesce" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">float</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Self</span></code>
+<h3 id="gentropy.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">float</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Self</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.dataset.Dataset.from_parquet" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.from_parquet" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
   
-      <p>Reads a parquet file into a Dataset with a given schema.</p>
+      <p>Reads parquet into a Dataset with a given schema.</p>
 
 
 
@@ -3132,7 +3312,7 @@ <h3 id="otg.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3146,11 +3326,11 @@ <h3 id="otg.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
         <tr>
           <td><code>path</code></td>
           <td>
-                <code>str</code>
+                <code>str | list[str]</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Path to the parquet file</p>
+              <p>Path to the parquet dataset</p>
             </div>
           </td>
           <td>
@@ -3223,7 +3403,7 @@ <h3 id="otg.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">71</span>
 <span class="normal">72</span>
 <span class="normal">73</span>
@@ -3252,14 +3432,14 @@ <h3 id="otg.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
 <span class="k">def</span> <span class="nf">from_parquet</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">Self</span><span class="p">],</span>
     <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
-    <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
     <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">|</span> <span class="nb">float</span> <span class="o">|</span> <span class="nb">int</span> <span class="o">|</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Self</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Reads a parquet file into a Dataset with a given schema.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Reads parquet into a Dataset with a given schema.</span>
 
 <span class="sd">    Args:</span>
 <span class="sd">        session (Session): Spark session</span>
-<span class="sd">        path (str): Path to the parquet file</span>
+<span class="sd">        path (str | list[str]): Path to the parquet dataset</span>
 <span class="sd">        **kwargs (bool | float | int | str | None): Additional arguments to pass to spark.read.parquet</span>
 
 <span class="sd">    Returns:</span>
@@ -3269,7 +3449,7 @@ <h3 id="otg.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
 <span class="sd">        ValueError: Parquet file is empty</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="n">schema</span> <span class="o">=</span> <span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">()</span>
-    <span class="n">df</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="n">path</span><span class="o">=</span><span class="n">path</span><span class="p">,</span> <span class="n">schema</span><span class="o">=</span><span class="n">schema</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+    <span class="n">df</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">read_parquet</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">schema</span><span class="o">=</span><span class="n">schema</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
     <span class="k">if</span> <span class="n">df</span><span class="o">.</span><span class="n">isEmpty</span><span class="p">():</span>
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Parquet file is empty: </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
     <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span><span class="n">_df</span><span class="o">=</span><span class="n">df</span><span class="p">,</span> <span class="n">_schema</span><span class="o">=</span><span class="n">schema</span><span class="p">)</span>
@@ -3284,8 +3464,7 @@ <h3 id="otg.dataset.dataset.Dataset.from_parquet" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
@@ -3293,7 +3472,7 @@ <h3 id="otg.dataset.dataset.Dataset.get_schema" class="doc doc-heading">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.dataset.Dataset.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3325,7 +3504,7 @@ <h3 id="otg.dataset.dataset.Dataset.get_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">61</span>
 <span class="normal">62</span>
 <span class="normal">63</span>
@@ -3354,11 +3533,10 @@ <h3 id="otg.dataset.dataset.Dataset.get_schema" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.persist" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.persist" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">persist</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Self</span></code>
 
-<a href="#otg.dataset.dataset.Dataset.persist" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.persist" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3390,7 +3568,7 @@ <h3 id="otg.dataset.dataset.Dataset.persist" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">154</span>
 <span class="normal">155</span>
 <span class="normal">156</span>
@@ -3417,11 +3595,10 @@ <h3 id="otg.dataset.dataset.Dataset.persist" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.repartition" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.repartition" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">repartition</span><span class="p">(</span><span class="n">num_partitions</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="n">Any</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Self</span></code>
 
-<a href="#otg.dataset.dataset.Dataset.repartition" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.repartition" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3498,7 +3675,7 @@ <h3 id="otg.dataset.dataset.Dataset.repartition" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">187</span>
 <span class="normal">188</span>
 <span class="normal">189</span>
@@ -3537,11 +3714,10 @@ <h3 id="otg.dataset.dataset.Dataset.repartition" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.unpersist" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.unpersist" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">unpersist</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Self</span></code>
 
-<a href="#otg.dataset.dataset.Dataset.unpersist" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.unpersist" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3573,7 +3749,7 @@ <h3 id="otg.dataset.dataset.Dataset.unpersist" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">163</span>
 <span class="normal">164</span>
 <span class="normal">165</span>
@@ -3600,11 +3776,10 @@ <h3 id="otg.dataset.dataset.Dataset.unpersist" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.dataset.Dataset.validate_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.dataset.Dataset.validate_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">validate_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
 
-<a href="#otg.dataset.dataset.Dataset.validate_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.dataset.Dataset.validate_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3636,7 +3811,7 @@ <h3 id="otg.dataset.dataset.Dataset.validate_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/dataset.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/dataset.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 97</span>
 <span class="normal"> 98</span>
 <span class="normal"> 99</span>
@@ -3760,6 +3935,7 @@ <h3 id="otg.dataset.dataset.Dataset.validate_schema" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3776,14 +3952,14 @@ <h3 id="otg.dataset.dataset.Dataset.validate_schema" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M14.47 15.08 11 13V7h1.5v5.25l3.08 1.83c-.41.28-.79.62-1.11 1m-1.39 4.84c-.36.05-.71.08-1.08.08-4.42 0-8-3.58-8-8s3.58-8 8-8 8 3.58 8 8c0 .37-.03.72-.08 1.08.69.1 1.33.32 1.92.64.1-.56.16-1.13.16-1.72 0-5.5-4.5-10-10-10S2 6.5 2 12s4.47 10 10 10c.59 0 1.16-.06 1.72-.16-.32-.59-.54-1.23-.64-1.92M18 15v3h-3v2h3v3h2v-3h3v-2h-3v-3h-2Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-01-15T17:06:06+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-01-15</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
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         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3850,7 +4026,7 @@ <h3 id="otg.dataset.dataset.Dataset.validate_schema" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/dataset/colocalisation/index.html b/python_api/datasets/colocalisation/index.html
similarity index 81%
rename from python_api/dataset/colocalisation/index.html
rename to python_api/datasets/colocalisation/index.html
index 956edc116..652773636 100644
--- a/python_api/dataset/colocalisation/index.html
+++ b/python_api/datasets/colocalisation/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../_dataset/">
+        <link rel="prev" href="../_datasets/">
       
       
         <link rel="next" href="../gene_index/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Colocalisation - Open Targets Genetics</title>
+        <title>Colocalisation - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.colocalisation.Colocalisation" class="md-skip">
+        <a href="#gentropy.dataset.colocalisation.Colocalisation" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
+
+    
+      
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
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+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
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+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
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+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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             Development
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+            Datasets
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         <li class="md-nav__item">
-  <a href="#otg.dataset.colocalisation.Colocalisation" class="md-nav__link">
+  <a href="#gentropy.dataset.colocalisation.Colocalisation" class="md-nav__link">
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-  <a href="#otg.dataset.colocalisation.Colocalisation.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.colocalisation.Colocalisation.get_schema" class="md-nav__link">
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-      get_schema()
+      get_schema
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   </a>
   
@@ -1015,32 +1166,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1076,14 +1227,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
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     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1134,12 +1306,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1150,14 +1322,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1170,7 +1342,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1208,12 +1401,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1224,14 +1417,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1244,7 +1437,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1265,7 +1458,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1303,12 +1496,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1319,14 +1512,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1339,7 +1532,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1360,7 +1553,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1381,7 +1574,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1402,7 +1595,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1440,12 +1633,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1456,14 +1649,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1476,7 +1669,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1497,7 +1690,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
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@@ -1518,7 +1711,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
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@@ -1539,7 +1732,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
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@@ -1577,12 +1770,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
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@@ -1593,14 +1786,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1613,7 +1806,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1634,7 +1827,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
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@@ -1656,80 +1849,6 @@
 
               
             
-              
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-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
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-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
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-            
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-                
-  
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-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
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-  <span class="md-ellipsis">
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-              
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         </nav>
       
@@ -1754,32 +1873,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1790,11 +1909,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1811,11 +1930,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1832,11 +1951,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1853,11 +1972,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1874,11 +1993,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1895,11 +2014,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1925,12 +2044,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1941,14 +2060,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1961,7 +2080,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1982,7 +2101,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2003,7 +2122,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2024,7 +2143,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2070,32 +2189,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2106,11 +2225,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2127,11 +2246,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2148,11 +2267,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2169,11 +2288,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2190,11 +2309,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2211,11 +2330,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2232,11 +2351,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2253,11 +2372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2274,11 +2393,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2295,11 +2414,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2316,11 +2435,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2337,11 +2456,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2358,11 +2477,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2379,11 +2498,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2433,7 +2615,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.colocalisation.Colocalisation" class="md-nav__link">
+  <a href="#gentropy.dataset.colocalisation.Colocalisation" class="md-nav__link">
     <span class="md-ellipsis">
       Colocalisation
     </span>
@@ -2443,9 +2625,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.colocalisation.Colocalisation.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.colocalisation.Colocalisation.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -2489,27 +2671,26 @@ <h1>Colocalisation</h1>
 
 
 
-
-<h2 id="otg.dataset.colocalisation.Colocalisation" class="doc doc-heading">
-          <code>otg.dataset.colocalisation.Colocalisation</code>
+<h2 id="gentropy.dataset.colocalisation.Colocalisation" class="doc doc-heading">
+          <code>gentropy.dataset.colocalisation.Colocalisation</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.colocalisation.Colocalisation" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.colocalisation.Colocalisation" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Colocalisation results for pairs of overlapping study-locus.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/colocalisation.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/colocalisation.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
@@ -2553,15 +2734,14 @@ <h2 id="otg.dataset.colocalisation.Colocalisation" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.colocalisation.Colocalisation.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.colocalisation.Colocalisation.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.colocalisation.Colocalisation.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.colocalisation.Colocalisation.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2593,7 +2773,7 @@ <h3 id="otg.dataset.colocalisation.Colocalisation.get_schema" class="doc doc-hea
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/colocalisation.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/colocalisation.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">18</span>
 <span class="normal">19</span>
 <span class="normal">20</span>
@@ -2621,6 +2801,7 @@ <h3 id="otg.dataset.colocalisation.Colocalisation.get_schema" class="doc doc-hea
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- leftStudyLocusId: long (nullable = false)
@@ -2658,7 +2839,7 @@ <h3 id="otg.dataset.colocalisation.Colocalisation.get_schema" class="doc doc-hea
         <span class="icon twemoji">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
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+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/gene_index/index.html b/python_api/datasets/gene_index/index.html
similarity index 84%
rename from python_api/dataset/gene_index/index.html
rename to python_api/datasets/gene_index/index.html
index b9d50c843..b6c4832f0 100644
--- a/python_api/dataset/gene_index/index.html
+++ b/python_api/datasets/gene_index/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Gene Index - Open Targets Genetics</title>
+        <title>Gene Index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.gene_index.GeneIndex" class="md-skip">
+        <a href="#gentropy.dataset.gene_index.GeneIndex" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
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-            Open Targets Genetics
+            Open Targets Gentropy
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       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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 </a>
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@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
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     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
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+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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-    Development
+    How-to
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           <label class="md-nav__title" for="__nav_3">
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+            How-to
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
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+  
+
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+    </li>
+  
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+              
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+  
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+  
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+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+              
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+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
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+    </li>
+  
+
+    
+      
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+  
+  
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+            <a href="../../../development/_development/" class="md-nav__link ">
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+    Development
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
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+            Datasets
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           <ul class="md-nav__list" data-md-scrollfix>
             
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         <li class="md-nav__item">
-  <a href="#otg.dataset.gene_index.GeneIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex" class="md-nav__link">
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       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.gene_index.GeneIndex.filter_by_biotypes" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.filter_by_biotypes" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_by_biotypes()
+      filter_by_biotypes
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   </a>
   
 </li>
         
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-  <a href="#otg.dataset.gene_index.GeneIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.get_schema" class="md-nav__link">
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   </a>
   
 </li>
         
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-  <a href="#otg.dataset.gene_index.GeneIndex.locations_lut" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.locations_lut" class="md-nav__link">
     <span class="md-ellipsis">
-      locations_lut()
+      locations_lut
     </span>
   </a>
   
 </li>
         
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-  <a href="#otg.dataset.gene_index.GeneIndex.symbols_lut" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.symbols_lut" class="md-nav__link">
     <span class="md-ellipsis">
-      symbols_lut()
+      symbols_lut
     </span>
   </a>
   
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-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+    Datasources
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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             Eqtl catalogue
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-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
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+
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+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1161,12 +1333,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1177,14 +1349,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1197,7 +1369,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1235,12 +1428,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1251,14 +1444,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1271,7 +1464,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1292,7 +1485,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1330,12 +1523,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1346,14 +1539,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1366,7 +1559,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1387,7 +1580,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1408,7 +1601,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1429,7 +1622,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1467,12 +1660,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1483,14 +1676,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1503,7 +1696,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1524,7 +1717,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1545,7 +1738,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1566,7 +1759,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1604,12 +1797,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1620,14 +1813,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1640,7 +1833,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1661,7 +1854,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1683,80 +1876,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1781,32 +1900,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1817,11 +1936,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1838,11 +1957,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1859,11 +1978,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1880,11 +1999,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1901,11 +2020,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1922,11 +2041,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1952,12 +2071,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1968,14 +2087,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1988,7 +2107,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2009,7 +2128,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2030,7 +2149,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2051,7 +2170,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2097,32 +2216,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2133,11 +2252,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2154,11 +2273,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2175,11 +2294,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2196,11 +2315,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2217,11 +2336,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2238,11 +2357,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2259,11 +2378,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2280,11 +2399,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2301,11 +2420,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2322,11 +2441,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2343,11 +2462,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2364,11 +2483,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2385,11 +2504,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2406,11 +2525,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2460,7 +2642,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.gene_index.GeneIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex" class="md-nav__link">
     <span class="md-ellipsis">
       GeneIndex
     </span>
@@ -2470,36 +2652,36 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.gene_index.GeneIndex.filter_by_biotypes" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.filter_by_biotypes" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_by_biotypes()
+      filter_by_biotypes
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.gene_index.GeneIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.gene_index.GeneIndex.locations_lut" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.locations_lut" class="md-nav__link">
     <span class="md-ellipsis">
-      locations_lut()
+      locations_lut
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.gene_index.GeneIndex.symbols_lut" class="md-nav__link">
+  <a href="#gentropy.dataset.gene_index.GeneIndex.symbols_lut" class="md-nav__link">
     <span class="md-ellipsis">
-      symbols_lut()
+      symbols_lut
     </span>
   </a>
   
@@ -2543,28 +2725,27 @@ <h1>Gene Index</h1>
 
 
 
-
-<h2 id="otg.dataset.gene_index.GeneIndex" class="doc doc-heading">
-          <code>otg.dataset.gene_index.GeneIndex</code>
+<h2 id="gentropy.dataset.gene_index.GeneIndex" class="doc doc-heading">
+          <code>gentropy.dataset.gene_index.GeneIndex</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.gene_index.GeneIndex" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.gene_index.GeneIndex" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Gene index dataset.</p>
 <p>Gene-based annotation.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/gene_index.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/gene_index.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">17</span>
 <span class="normal">18</span>
 <span class="normal">19</span>
@@ -2700,11 +2881,10 @@ <h2 id="otg.dataset.gene_index.GeneIndex" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.gene_index.GeneIndex.filter_by_biotypes" class="doc doc-heading">
+<h3 id="gentropy.dataset.gene_index.GeneIndex.filter_by_biotypes" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">filter_by_biotypes</span><span class="p">(</span><span class="n">biotypes</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">GeneIndex</span></code>
 
-<a href="#otg.dataset.gene_index.GeneIndex.filter_by_biotypes" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.gene_index.GeneIndex.filter_by_biotypes" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2754,7 +2934,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.filter_by_biotypes" class="doc doc-head
     <tbody>
         <tr>
 <td><code>GeneIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2766,7 +2946,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.filter_by_biotypes" class="doc doc-head
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/gene_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/gene_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">33</span>
 <span class="normal">34</span>
 <span class="normal">35</span>
@@ -2799,15 +2979,14 @@ <h3 id="otg.dataset.gene_index.GeneIndex.filter_by_biotypes" class="doc doc-head
 
 
 
-
-<h3 id="otg.dataset.gene_index.GeneIndex.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.gene_index.GeneIndex.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.gene_index.GeneIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.gene_index.GeneIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2839,7 +3018,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.get_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/gene_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/gene_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">24</span>
 <span class="normal">25</span>
 <span class="normal">26</span>
@@ -2866,11 +3045,10 @@ <h3 id="otg.dataset.gene_index.GeneIndex.get_schema" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.gene_index.GeneIndex.locations_lut" class="doc doc-heading">
+<h3 id="gentropy.dataset.gene_index.GeneIndex.locations_lut" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">locations_lut</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
 
-<a href="#otg.dataset.gene_index.GeneIndex.locations_lut" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.gene_index.GeneIndex.locations_lut" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2902,7 +3080,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.locations_lut" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/gene_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/gene_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">45</span>
 <span class="normal">46</span>
 <span class="normal">47</span>
@@ -2941,11 +3119,10 @@ <h3 id="otg.dataset.gene_index.GeneIndex.locations_lut" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.gene_index.GeneIndex.symbols_lut" class="doc doc-heading">
+<h3 id="gentropy.dataset.gene_index.GeneIndex.symbols_lut" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">symbols_lut</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
 
-<a href="#otg.dataset.gene_index.GeneIndex.symbols_lut" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.gene_index.GeneIndex.symbols_lut" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2979,7 +3156,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.symbols_lut" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/gene_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/gene_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">60</span>
 <span class="normal">61</span>
 <span class="normal">62</span>
@@ -3021,6 +3198,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.symbols_lut" class="doc doc-heading">
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- geneId: string (nullable = false)
@@ -3057,7 +3235,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.symbols_lut" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3076,14 +3254,6 @@ <h3 id="otg.dataset.gene_index.GeneIndex.symbols_lut" class="doc doc-heading">
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
           </li></ul>
       </li>
     </ul>
@@ -3132,7 +3302,7 @@ <h3 id="otg.dataset.gene_index.GeneIndex.symbols_lut" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/intervals/index.html b/python_api/datasets/intervals/index.html
similarity index 84%
rename from python_api/dataset/intervals/index.html
rename to python_api/datasets/intervals/index.html
index c06d8ab54..47ddd1d5a 100644
--- a/python_api/dataset/intervals/index.html
+++ b/python_api/datasets/intervals/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Intervals - Open Targets Genetics</title>
+        <title>Intervals - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.intervals.Intervals" class="md-skip">
+        <a href="#gentropy.dataset.intervals.Intervals" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
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+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
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-            Dataset
+            Datasets
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         <li class="md-nav__item">
-  <a href="#otg.dataset.intervals.Intervals" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals" class="md-nav__link">
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       Intervals
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@@ -708,27 +859,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.intervals.Intervals.from_source" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
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   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.intervals.Intervals.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
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-  <a href="#otg.dataset.intervals.Intervals.v2g" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals.v2g" class="md-nav__link">
     <span class="md-ellipsis">
-      v2g()
+      v2g
     </span>
   </a>
   
@@ -1033,32 +1184,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1078,12 +1229,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1094,14 +1245,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1114,7 +1265,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1152,12 +1324,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1168,14 +1340,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1188,7 +1360,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1226,12 +1419,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1242,14 +1435,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1262,7 +1455,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1283,7 +1476,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1321,12 +1514,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1337,14 +1530,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1357,7 +1550,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1378,7 +1571,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1399,7 +1592,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1420,7 +1613,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1458,12 +1651,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1474,14 +1667,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1494,7 +1687,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1515,7 +1708,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1536,7 +1729,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1557,7 +1750,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1595,12 +1788,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1611,14 +1804,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1631,7 +1824,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1652,7 +1845,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
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@@ -1674,80 +1867,6 @@
 
               
             
-              
-                
-  
-  
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-      
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-        
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-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
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-            
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1772,32 +1891,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1808,11 +1927,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1829,11 +1948,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1850,11 +1969,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1871,11 +1990,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1892,11 +2011,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1913,11 +2032,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1943,12 +2062,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1959,14 +2078,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1979,7 +2098,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2000,7 +2119,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2021,7 +2140,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2042,7 +2161,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2088,32 +2207,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2124,11 +2243,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2145,11 +2264,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2166,11 +2285,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2187,11 +2306,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2208,11 +2327,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2229,11 +2348,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2250,11 +2369,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2271,11 +2390,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2292,11 +2411,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2313,11 +2432,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2334,11 +2453,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2355,11 +2474,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2376,11 +2495,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2397,11 +2516,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2451,7 +2633,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.intervals.Intervals" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals" class="md-nav__link">
     <span class="md-ellipsis">
       Intervals
     </span>
@@ -2461,27 +2643,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.intervals.Intervals.from_source" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.intervals.Intervals.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.intervals.Intervals.v2g" class="md-nav__link">
+  <a href="#gentropy.dataset.intervals.Intervals.v2g" class="md-nav__link">
     <span class="md-ellipsis">
-      v2g()
+      v2g
     </span>
   </a>
   
@@ -2525,27 +2707,26 @@ <h1>Intervals</h1>
 
 
 
-
-<h2 id="otg.dataset.intervals.Intervals" class="doc doc-heading">
-          <code>otg.dataset.intervals.Intervals</code>
+<h2 id="gentropy.dataset.intervals.Intervals" class="doc doc-heading">
+          <code>gentropy.dataset.intervals.Intervals</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.intervals.Intervals" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.intervals.Intervals" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Intervals dataset links genes to genomic regions based on genome interaction studies.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/intervals.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/intervals.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 22</span>
 <span class="normal"> 23</span>
 <span class="normal"> 24</span>
@@ -2666,10 +2847,10 @@ <h2 id="otg.dataset.intervals.Intervals" class="doc doc-heading">
 <span class="sd">        Raises:</span>
 <span class="sd">            ValueError: If the source name is not recognised</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">otg.datasource.intervals.andersson</span> <span class="kn">import</span> <span class="n">IntervalsAndersson</span>
-        <span class="kn">from</span> <span class="nn">otg.datasource.intervals.javierre</span> <span class="kn">import</span> <span class="n">IntervalsJavierre</span>
-        <span class="kn">from</span> <span class="nn">otg.datasource.intervals.jung</span> <span class="kn">import</span> <span class="n">IntervalsJung</span>
-        <span class="kn">from</span> <span class="nn">otg.datasource.intervals.thurman</span> <span class="kn">import</span> <span class="n">IntervalsThurman</span>
+        <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.andersson</span> <span class="kn">import</span> <span class="n">IntervalsAndersson</span>
+        <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.javierre</span> <span class="kn">import</span> <span class="n">IntervalsJavierre</span>
+        <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.jung</span> <span class="kn">import</span> <span class="n">IntervalsJung</span>
+        <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.thurman</span> <span class="kn">import</span> <span class="n">IntervalsThurman</span>
 
         <span class="n">source_to_class</span> <span class="o">=</span> <span class="p">{</span>
             <span class="s2">&quot;andersson&quot;</span><span class="p">:</span> <span class="n">IntervalsAndersson</span><span class="p">,</span>
@@ -2733,15 +2914,14 @@ <h2 id="otg.dataset.intervals.Intervals" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.intervals.Intervals.from_source" class="doc doc-heading">
+<h3 id="gentropy.dataset.intervals.Intervals.from_source" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span> <span class="n">source_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">source_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span> <span class="n">lift</span><span class="p">:</span> <span class="n">LiftOverSpark</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Intervals</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.intervals.Intervals.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.intervals.Intervals.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2806,7 +2986,7 @@ <h3 id="otg.dataset.intervals.Intervals.from_source" class="doc doc-heading">
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2820,7 +3000,7 @@ <h3 id="otg.dataset.intervals.Intervals.from_source" class="doc doc-heading">
         <tr>
           <td><code>lift</code></td>
           <td>
-                <code><span title="otg.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
+                <code><span title="gentropy.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2847,7 +3027,7 @@ <h3 id="otg.dataset.intervals.Intervals.from_source" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>Intervals</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.intervals.Intervals" href="#otg.dataset.intervals.Intervals">Intervals</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.intervals.Intervals" href="#gentropy.dataset.intervals.Intervals">Intervals</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2883,7 +3063,7 @@ <h3 id="otg.dataset.intervals.Intervals.from_source" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/intervals.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/intervals.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">35</span>
 <span class="normal">36</span>
 <span class="normal">37</span>
@@ -2949,10 +3129,10 @@ <h3 id="otg.dataset.intervals.Intervals.from_source" class="doc doc-heading">
 <span class="sd">    Raises:</span>
 <span class="sd">        ValueError: If the source name is not recognised</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">otg.datasource.intervals.andersson</span> <span class="kn">import</span> <span class="n">IntervalsAndersson</span>
-    <span class="kn">from</span> <span class="nn">otg.datasource.intervals.javierre</span> <span class="kn">import</span> <span class="n">IntervalsJavierre</span>
-    <span class="kn">from</span> <span class="nn">otg.datasource.intervals.jung</span> <span class="kn">import</span> <span class="n">IntervalsJung</span>
-    <span class="kn">from</span> <span class="nn">otg.datasource.intervals.thurman</span> <span class="kn">import</span> <span class="n">IntervalsThurman</span>
+    <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.andersson</span> <span class="kn">import</span> <span class="n">IntervalsAndersson</span>
+    <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.javierre</span> <span class="kn">import</span> <span class="n">IntervalsJavierre</span>
+    <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.jung</span> <span class="kn">import</span> <span class="n">IntervalsJung</span>
+    <span class="kn">from</span> <span class="nn">gentropy.datasource.intervals.thurman</span> <span class="kn">import</span> <span class="n">IntervalsThurman</span>
 
     <span class="n">source_to_class</span> <span class="o">=</span> <span class="p">{</span>
         <span class="s2">&quot;andersson&quot;</span><span class="p">:</span> <span class="n">IntervalsAndersson</span><span class="p">,</span>
@@ -2978,15 +3158,14 @@ <h3 id="otg.dataset.intervals.Intervals.from_source" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.intervals.Intervals.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.intervals.Intervals.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.intervals.Intervals.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.intervals.Intervals.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3018,7 +3197,7 @@ <h3 id="otg.dataset.intervals.Intervals.get_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/intervals.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/intervals.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">26</span>
 <span class="normal">27</span>
 <span class="normal">28</span>
@@ -3045,11 +3224,10 @@ <h3 id="otg.dataset.intervals.Intervals.get_schema" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.intervals.Intervals.v2g" class="doc doc-heading">
+<h3 id="gentropy.dataset.intervals.Intervals.v2g" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">v2g</span><span class="p">(</span><span class="n">variant_index</span><span class="p">:</span> <span class="n">VariantIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">V2G</span></code>
 
-<a href="#otg.dataset.intervals.Intervals.v2g" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.intervals.Intervals.v2g" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3072,7 +3250,7 @@ <h3 id="otg.dataset.intervals.Intervals.v2g" class="doc doc-heading">
         <tr>
           <td><code>variant_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.variant_index.VariantIndex" href="../variant_index/#otg.dataset.variant_index.VariantIndex">VariantIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.variant_index.VariantIndex" href="../variant_index/#gentropy.dataset.variant_index.VariantIndex">VariantIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3099,7 +3277,7 @@ <h3 id="otg.dataset.intervals.Intervals.v2g" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>V2G</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3111,7 +3289,7 @@ <h3 id="otg.dataset.intervals.Intervals.v2g" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/intervals.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/intervals.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 78</span>
 <span class="normal"> 79</span>
 <span class="normal"> 80</span>
@@ -3179,6 +3357,7 @@ <h3 id="otg.dataset.intervals.Intervals.v2g" class="doc doc-heading">
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- chromosome: string (nullable = false)
@@ -3214,7 +3393,7 @@ <h3 id="otg.dataset.intervals.Intervals.v2g" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3281,7 +3460,7 @@ <h3 id="otg.dataset.intervals.Intervals.v2g" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/dataset/l2g_feature/index.html b/python_api/datasets/l2g_feature/index.html
similarity index 81%
rename from python_api/dataset/l2g_feature/index.html
rename to python_api/datasets/l2g_feature/index.html
index 4c4045f46..ee5d6d0a2 100644
--- a/python_api/dataset/l2g_feature/index.html
+++ b/python_api/datasets/l2g_feature/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Feature - Open Targets Genetics</title>
+        <title>L2G Feature - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.l2g.feature_factory.L2GFeature" class="md-skip">
+        <a href="#gentropy.method.l2g.feature_factory.L2GFeature" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
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+    </li>
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+            
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+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step using YAML config
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+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -719,7 +870,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.L2GFeature" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.L2GFeature" class="md-nav__link">
     <span class="md-ellipsis">
       L2GFeature
     </span>
@@ -729,9 +880,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.L2GFeature.get_schema" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.L2GFeature.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -1015,32 +1166,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1060,12 +1211,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1076,14 +1227,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1096,7 +1247,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1134,12 +1306,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1150,14 +1322,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1170,7 +1342,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1208,12 +1401,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1224,14 +1417,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1244,7 +1437,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1265,7 +1458,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1303,12 +1496,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1319,14 +1512,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1339,7 +1532,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1360,7 +1553,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1381,7 +1574,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1402,7 +1595,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1440,12 +1633,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1456,14 +1649,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1476,7 +1669,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1497,7 +1690,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1518,7 +1711,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1539,7 +1732,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1577,12 +1770,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1593,14 +1786,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1613,7 +1806,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1634,7 +1827,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1656,80 +1849,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1754,32 +1873,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1790,11 +1909,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1811,11 +1930,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1832,11 +1951,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1853,11 +1972,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1874,11 +1993,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1895,11 +2014,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1925,12 +2044,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1941,14 +2060,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1961,7 +2080,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1982,7 +2101,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2003,7 +2122,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2024,7 +2143,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2070,32 +2189,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
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               </label>
             
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-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2106,11 +2225,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2127,11 +2246,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2148,11 +2267,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2169,11 +2288,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2190,11 +2309,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2211,11 +2330,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2232,11 +2351,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2253,11 +2372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2274,11 +2393,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2295,11 +2414,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2316,11 +2435,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2337,11 +2456,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2358,11 +2477,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2379,11 +2498,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2433,7 +2615,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.L2GFeature" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.L2GFeature" class="md-nav__link">
     <span class="md-ellipsis">
       L2GFeature
     </span>
@@ -2443,9 +2625,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.L2GFeature.get_schema" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.L2GFeature.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -2489,27 +2671,26 @@ <h1>L2G Feature</h1>
 
 
 
-
-<h2 id="otg.method.l2g.feature_factory.L2GFeature" class="doc doc-heading">
-          <code>otg.method.l2g.feature_factory.L2GFeature</code>
+<h2 id="gentropy.method.l2g.feature_factory.L2GFeature" class="doc doc-heading">
+          <code>gentropy.method.l2g.feature_factory.L2GFeature</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.method.l2g.feature_factory.L2GFeature" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.l2g.feature_factory.L2GFeature" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Locus-to-gene feature dataset.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/l2g_feature.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/l2g_feature.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
@@ -2553,15 +2734,14 @@ <h2 id="otg.method.l2g.feature_factory.L2GFeature" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.l2g.feature_factory.L2GFeature.get_schema" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.feature_factory.L2GFeature.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.l2g.feature_factory.L2GFeature.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.feature_factory.L2GFeature.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2593,7 +2773,7 @@ <h3 id="otg.method.l2g.feature_factory.L2GFeature.get_schema" class="doc doc-hea
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_feature.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_feature.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">18</span>
 <span class="normal">19</span>
 <span class="normal">20</span>
@@ -2621,6 +2801,7 @@ <h3 id="otg.method.l2g.feature_factory.L2GFeature.get_schema" class="doc doc-hea
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- studyLocusId: long (nullable = false)
@@ -2650,7 +2831,7 @@ <h3 id="otg.method.l2g.feature_factory.L2GFeature.get_schema" class="doc doc-hea
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2717,7 +2898,7 @@ <h3 id="otg.method.l2g.feature_factory.L2GFeature.get_schema" class="doc doc-hea
       
       
     
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+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/l2g_feature_matrix/index.html b/python_api/datasets/l2g_feature_matrix/index.html
similarity index 80%
rename from python_api/dataset/l2g_feature_matrix/index.html
rename to python_api/datasets/l2g_feature_matrix/index.html
index 95db24d14..3872f2b1d 100644
--- a/python_api/dataset/l2g_feature_matrix/index.html
+++ b/python_api/datasets/l2g_feature_matrix/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Feature Matrix - Open Targets Genetics</title>
+        <title>L2G Feature Matrix - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="md-skip">
+        <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
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     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="md-nav__link">
     <span class="md-ellipsis">
       L2GFeatureMatrix
     </span>
@@ -750,54 +901,54 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="md-nav__link">
     <span class="md-ellipsis">
-      calculate_feature_missingness_rate()
+      calculate_feature_missingness_rate
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="md-nav__link">
     <span class="md-ellipsis">
-      fill_na()
+      fill_na
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="md-nav__link">
     <span class="md-ellipsis">
-      generate_features()
+      generate_features
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="md-nav__link">
     <span class="md-ellipsis">
-      select_features()
+      select_features
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="md-nav__link">
     <span class="md-ellipsis">
-      train_test_split()
+      train_test_split
     </span>
   </a>
   
@@ -1060,32 +1211,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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           </div>
         
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1105,12 +1256,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1121,14 +1272,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1141,7 +1292,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1179,12 +1351,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1195,14 +1367,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1215,7 +1387,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1253,12 +1446,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1269,14 +1462,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1348,12 +1541,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1364,14 +1557,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1384,7 +1577,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1485,12 +1678,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1501,14 +1694,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1521,7 +1714,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1584,7 +1777,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1622,12 +1815,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1638,14 +1831,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1658,7 +1851,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1679,7 +1872,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1701,80 +1894,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1799,32 +1918,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1835,11 +1954,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1856,11 +1975,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1877,11 +1996,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1898,11 +2017,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1919,11 +2038,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1940,11 +2059,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1970,12 +2089,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1986,14 +2105,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2006,7 +2125,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2027,7 +2146,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2048,7 +2167,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2069,7 +2188,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2115,32 +2234,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2151,11 +2270,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2172,11 +2291,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2193,11 +2312,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2214,11 +2333,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2235,11 +2354,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2256,11 +2375,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2277,11 +2396,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2298,11 +2417,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2319,11 +2438,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2340,11 +2459,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2361,11 +2480,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2382,11 +2501,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2403,11 +2522,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2424,11 +2543,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2478,7 +2660,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="md-nav__link">
     <span class="md-ellipsis">
       L2GFeatureMatrix
     </span>
@@ -2488,54 +2670,54 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="md-nav__link">
     <span class="md-ellipsis">
-      calculate_feature_missingness_rate()
+      calculate_feature_missingness_rate
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="md-nav__link">
     <span class="md-ellipsis">
-      fill_na()
+      fill_na
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="md-nav__link">
     <span class="md-ellipsis">
-      generate_features()
+      generate_features
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="md-nav__link">
     <span class="md-ellipsis">
-      select_features()
+      select_features
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="md-nav__link">
     <span class="md-ellipsis">
-      train_test_split()
+      train_test_split
     </span>
   </a>
   
@@ -2579,21 +2761,20 @@ <h1>L2G Feature Matrix</h1>
 
 
 
-
-<h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading">
-          <code>otg.dataset.l2g_feature_matrix.L2GFeatureMatrix</code>
+<h2 id="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading">
+          <code>gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Dataset with features for Locus to Gene prediction.</p>
@@ -2611,7 +2792,7 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
     </thead>
     <tbody>
         <tr>
-          <td><code>features_list</code></td>
+          <td><code><span title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.features_list">features_list</span></code></td>
           <td>
                 <code>list[str] | None</code>
           </td>
@@ -2625,7 +2806,7 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
   </table>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 22</span>
 <span class="normal"> 23</span>
 <span class="normal"> 24</span>
@@ -2768,7 +2949,12 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
 <span class="normal">161</span>
 <span class="normal">162</span>
 <span class="normal">163</span>
-<span class="normal">164</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">164</span>
+<span class="normal">165</span>
+<span class="normal">166</span>
+<span class="normal">167</span>
+<span class="normal">168</span>
+<span class="normal">169</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">L2GFeatureMatrix</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Dataset with features for Locus to Gene prediction.</span>
 
@@ -2792,15 +2978,16 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
         <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
         <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span>
         <span class="n">variant_gene</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span>
-        <span class="c1"># colocalisation: Colocalisation,</span>
+        <span class="n">colocalisation</span><span class="p">:</span> <span class="n">Colocalisation</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Generate features from the OTG datasets.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Generate features from the gentropy datasets.</span>
 
 <span class="sd">        Args:</span>
 <span class="sd">            features_list (list[str]): List of features to generate</span>
 <span class="sd">            study_locus (StudyLocus): Study locus dataset</span>
 <span class="sd">            study_index (StudyIndex): Study index dataset</span>
 <span class="sd">            variant_gene (V2G): Variant to gene dataset</span>
+<span class="sd">            colocalisation (Colocalisation): Colocalisation dataset</span>
 
 <span class="sd">        Returns:</span>
 <span class="sd">            L2GFeatureMatrix: L2G feature matrix dataset</span>
@@ -2810,10 +2997,11 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">features_dfs</span> <span class="o">:=</span> <span class="p">[</span>
             <span class="c1"># Extract features</span>
-            <span class="c1"># ColocalisationFactory._get_coloc_features(</span>
-            <span class="c1">#     study_locus, study_index, colocalisation</span>
-            <span class="c1"># ).df,</span>
+            <span class="n">ColocalisationFactory</span><span class="o">.</span><span class="n">_get_coloc_features</span><span class="p">(</span>
+                <span class="n">study_locus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">,</span> <span class="n">colocalisation</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
             <span class="n">StudyLocusFactory</span><span class="o">.</span><span class="n">_get_tss_distance_features</span><span class="p">(</span><span class="n">study_locus</span><span class="p">,</span> <span class="n">variant_gene</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
+            <span class="n">StudyLocusFactory</span><span class="o">.</span><span class="n">_get_vep_features</span><span class="p">(</span><span class="n">study_locus</span><span class="p">,</span> <span class="n">variant_gene</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
         <span class="p">]:</span>
             <span class="n">fm</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span>
                 <span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">y</span><span class="p">),</span>
@@ -2823,15 +3011,13 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No features found&quot;</span><span class="p">)</span>
 
         <span class="c1"># raise error if the feature matrix is empty</span>
-        <span class="k">if</span> <span class="n">fm</span><span class="o">.</span><span class="n">limit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
-            <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span>
-                <span class="n">_df</span><span class="o">=</span><span class="n">convert_from_long_to_wide</span><span class="p">(</span>
-                    <span class="n">fm</span><span class="p">,</span> <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span> <span class="s2">&quot;featureName&quot;</span><span class="p">,</span> <span class="s2">&quot;featureValue&quot;</span>
-                <span class="p">),</span>
-                <span class="n">_schema</span><span class="o">=</span><span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
-                <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
-            <span class="p">)</span>
-        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;L2G Feature matrix is empty&quot;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">convert_from_long_to_wide</span><span class="p">(</span>
+                <span class="n">fm</span><span class="p">,</span> <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span> <span class="s2">&quot;featureName&quot;</span><span class="p">,</span> <span class="s2">&quot;featureValue&quot;</span>
+            <span class="p">),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+            <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
+        <span class="p">)</span>
 
     <span class="nd">@classmethod</span>
     <span class="k">def</span> <span class="nf">get_schema</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">L2GFeatureMatrix</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">StructType</span><span class="p">:</span>
@@ -2858,7 +3044,12 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No features found&quot;</span><span class="p">)</span>
 
         <span class="k">return</span> <span class="p">{</span>
-            <span class="n">feature</span><span class="p">:</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="p">[</span><span class="n">feature</span><span class="p">]</span><span class="o">.</span><span class="n">isNull</span><span class="p">())</span><span class="o">.</span><span class="n">count</span><span class="p">()</span> <span class="o">/</span> <span class="n">total_count</span><span class="p">)</span>
+            <span class="n">feature</span><span class="p">:</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+                    <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="p">[</span><span class="n">feature</span><span class="p">]</span><span class="o">.</span><span class="n">isNull</span><span class="p">())</span> <span class="o">|</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="p">[</span><span class="n">feature</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">)</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span>
+                <span class="o">/</span> <span class="n">total_count</span>
+            <span class="p">)</span>
             <span class="k">for</span> <span class="n">feature</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">features_list</span>
         <span class="p">}</span>
 
@@ -2931,11 +3122,10 @@ <h2 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" class="doc doc-heading"
 
 
 
-
-<h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">calculate_feature_missingness_rate</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">float</span><span class="p">]</span></code>
 
-<a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2991,7 +3181,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missin
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 96</span>
 <span class="normal"> 97</span>
 <span class="normal"> 98</span>
@@ -3010,7 +3200,12 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missin
 <span class="normal">111</span>
 <span class="normal">112</span>
 <span class="normal">113</span>
-<span class="normal">114</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">calculate_feature_missingness_rate</span><span class="p">(</span>
+<span class="normal">114</span>
+<span class="normal">115</span>
+<span class="normal">116</span>
+<span class="normal">117</span>
+<span class="normal">118</span>
+<span class="normal">119</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">calculate_feature_missingness_rate</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">float</span><span class="p">]:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Calculate the proportion of missing values in each feature.</span>
@@ -3026,7 +3221,12 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missin
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No features found&quot;</span><span class="p">)</span>
 
     <span class="k">return</span> <span class="p">{</span>
-        <span class="n">feature</span><span class="p">:</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="p">[</span><span class="n">feature</span><span class="p">]</span><span class="o">.</span><span class="n">isNull</span><span class="p">())</span><span class="o">.</span><span class="n">count</span><span class="p">()</span> <span class="o">/</span> <span class="n">total_count</span><span class="p">)</span>
+        <span class="n">feature</span><span class="p">:</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+                <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="p">[</span><span class="n">feature</span><span class="p">]</span><span class="o">.</span><span class="n">isNull</span><span class="p">())</span> <span class="o">|</span> <span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">_df</span><span class="p">[</span><span class="n">feature</span><span class="p">]</span> <span class="o">==</span> <span class="mi">0</span><span class="p">)</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span>
+            <span class="o">/</span> <span class="n">total_count</span>
+        <span class="p">)</span>
         <span class="k">for</span> <span class="n">feature</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">features_list</span>
     <span class="p">}</span>
 </code></pre></div></td></tr></table></div>
@@ -3040,11 +3240,10 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missin
 
 
 
-
-<h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">fill_na</span><span class="p">(</span><span class="n">value</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">,</span> <span class="n">subset</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span></code>
 
-<a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3108,7 +3307,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="doc doc-
     <tbody>
         <tr>
 <td><code>L2GFeatureMatrix</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3120,13 +3319,8 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="doc doc-
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">116</span>
-<span class="normal">117</span>
-<span class="normal">118</span>
-<span class="normal">119</span>
-<span class="normal">120</span>
-<span class="normal">121</span>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">121</span>
 <span class="normal">122</span>
 <span class="normal">123</span>
 <span class="normal">124</span>
@@ -3134,7 +3328,12 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="doc doc-
 <span class="normal">126</span>
 <span class="normal">127</span>
 <span class="normal">128</span>
-<span class="normal">129</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">fill_na</span><span class="p">(</span>
+<span class="normal">129</span>
+<span class="normal">130</span>
+<span class="normal">131</span>
+<span class="normal">132</span>
+<span class="normal">133</span>
+<span class="normal">134</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">fill_na</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.0</span><span class="p">,</span> <span class="n">subset</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Fill missing values in a column with a given value.</span>
@@ -3159,20 +3358,19 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na" class="doc doc-
 
 
 
-
-<h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">generate_features</span><span class="p">(</span><span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">variant_gene</span><span class="p">:</span> <span class="n">V2G</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span></code>
+<h3 id="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">generate_features</span><span class="p">(</span><span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">variant_gene</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span> <span class="n">colocalisation</span><span class="p">:</span> <span class="n">Colocalisation</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
   
-      <p>Generate features from the OTG datasets.</p>
+      <p>Generate features from the gentropy datasets.</p>
 
 
 
@@ -3204,7 +3402,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
         <tr>
           <td><code>study_locus</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3218,7 +3416,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
         <tr>
           <td><code>study_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3232,7 +3430,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
         <tr>
           <td><code>variant_gene</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3243,6 +3441,20 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
               <em>required</em>
           </td>
         </tr>
+        <tr>
+          <td><code>colocalisation</code></td>
+          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.colocalisation.Colocalisation" href="../colocalisation/#gentropy.dataset.colocalisation.Colocalisation">Colocalisation</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Colocalisation dataset</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
     </tbody>
   </table>
 
@@ -3259,7 +3471,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
     <tbody>
         <tr>
 <td><code>L2GFeatureMatrix</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3295,7 +3507,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">39</span>
 <span class="normal">40</span>
 <span class="normal">41</span>
@@ -3349,15 +3561,16 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
     <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
     <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span>
     <span class="n">variant_gene</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span>
-    <span class="c1"># colocalisation: Colocalisation,</span>
+    <span class="n">colocalisation</span><span class="p">:</span> <span class="n">Colocalisation</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Generate features from the OTG datasets.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Generate features from the gentropy datasets.</span>
 
 <span class="sd">    Args:</span>
 <span class="sd">        features_list (list[str]): List of features to generate</span>
 <span class="sd">        study_locus (StudyLocus): Study locus dataset</span>
 <span class="sd">        study_index (StudyIndex): Study index dataset</span>
 <span class="sd">        variant_gene (V2G): Variant to gene dataset</span>
+<span class="sd">        colocalisation (Colocalisation): Colocalisation dataset</span>
 
 <span class="sd">    Returns:</span>
 <span class="sd">        L2GFeatureMatrix: L2G feature matrix dataset</span>
@@ -3367,10 +3580,11 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">if</span> <span class="n">features_dfs</span> <span class="o">:=</span> <span class="p">[</span>
         <span class="c1"># Extract features</span>
-        <span class="c1"># ColocalisationFactory._get_coloc_features(</span>
-        <span class="c1">#     study_locus, study_index, colocalisation</span>
-        <span class="c1"># ).df,</span>
+        <span class="n">ColocalisationFactory</span><span class="o">.</span><span class="n">_get_coloc_features</span><span class="p">(</span>
+            <span class="n">study_locus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">,</span> <span class="n">colocalisation</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
         <span class="n">StudyLocusFactory</span><span class="o">.</span><span class="n">_get_tss_distance_features</span><span class="p">(</span><span class="n">study_locus</span><span class="p">,</span> <span class="n">variant_gene</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
+        <span class="n">StudyLocusFactory</span><span class="o">.</span><span class="n">_get_vep_features</span><span class="p">(</span><span class="n">study_locus</span><span class="p">,</span> <span class="n">variant_gene</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
     <span class="p">]:</span>
         <span class="n">fm</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span>
             <span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">y</span><span class="p">),</span>
@@ -3380,15 +3594,13 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
         <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;No features found&quot;</span><span class="p">)</span>
 
     <span class="c1"># raise error if the feature matrix is empty</span>
-    <span class="k">if</span> <span class="n">fm</span><span class="o">.</span><span class="n">limit</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">count</span><span class="p">()</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
-        <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span>
-            <span class="n">_df</span><span class="o">=</span><span class="n">convert_from_long_to_wide</span><span class="p">(</span>
-                <span class="n">fm</span><span class="p">,</span> <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span> <span class="s2">&quot;featureName&quot;</span><span class="p">,</span> <span class="s2">&quot;featureValue&quot;</span>
-            <span class="p">),</span>
-            <span class="n">_schema</span><span class="o">=</span><span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
-            <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
-        <span class="p">)</span>
-    <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;L2G Feature matrix is empty&quot;</span><span class="p">)</span>
+    <span class="k">return</span> <span class="bp">cls</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="n">convert_from_long_to_wide</span><span class="p">(</span>
+            <span class="n">fm</span><span class="p">,</span> <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span> <span class="s2">&quot;featureName&quot;</span><span class="p">,</span> <span class="s2">&quot;featureValue&quot;</span>
+        <span class="p">),</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
+    <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
           </details>
   </div>
@@ -3400,15 +3612,14 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features" class
 
 
 
-
-<h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3440,7 +3651,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="doc d
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">87</span>
 <span class="normal">88</span>
 <span class="normal">89</span>
@@ -3467,11 +3678,10 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema" class="doc d
 
 
 
-
-<h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">select_features</span><span class="p">(</span><span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span></code>
 
-<a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3521,7 +3731,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="
     <tbody>
         <tr>
 <td><code>L2GFeatureMatrix</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3533,13 +3743,8 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">131</span>
-<span class="normal">132</span>
-<span class="normal">133</span>
-<span class="normal">134</span>
-<span class="normal">135</span>
-<span class="normal">136</span>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">136</span>
 <span class="normal">137</span>
 <span class="normal">138</span>
 <span class="normal">139</span>
@@ -3548,7 +3753,12 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="
 <span class="normal">142</span>
 <span class="normal">143</span>
 <span class="normal">144</span>
-<span class="normal">145</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">select_features</span><span class="p">(</span>
+<span class="normal">145</span>
+<span class="normal">146</span>
+<span class="normal">147</span>
+<span class="normal">148</span>
+<span class="normal">149</span>
+<span class="normal">150</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">select_features</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeatureMatrix</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Select a subset of features from the feature matrix.</span>
@@ -3574,11 +3784,10 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features" class="
 
 
 
-
-<h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">train_test_split</span><span class="p">(</span><span class="n">fraction</span><span class="p">:</span> <span class="nb">float</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">tuple</span><span class="p">[</span><span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">L2GFeatureMatrix</span><span class="p">]</span></code>
 
-<a href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3628,7 +3837,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class=
     <tbody>
         <tr>
           <td>
-                <code>tuple[<a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a>, <a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a>]</code>
+                <code>tuple[<a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a>, <a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a>]</code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3640,13 +3849,8 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class=
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">147</span>
-<span class="normal">148</span>
-<span class="normal">149</span>
-<span class="normal">150</span>
-<span class="normal">151</span>
-<span class="normal">152</span>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">152</span>
 <span class="normal">153</span>
 <span class="normal">154</span>
 <span class="normal">155</span>
@@ -3658,7 +3862,12 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class=
 <span class="normal">161</span>
 <span class="normal">162</span>
 <span class="normal">163</span>
-<span class="normal">164</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">train_test_split</span><span class="p">(</span>
+<span class="normal">164</span>
+<span class="normal">165</span>
+<span class="normal">166</span>
+<span class="normal">167</span>
+<span class="normal">168</span>
+<span class="normal">169</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">train_test_split</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">fraction</span><span class="p">:</span> <span class="nb">float</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">tuple</span><span class="p">[</span><span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">L2GFeatureMatrix</span><span class="p">]:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Split the dataset into training and test sets.</span>
@@ -3688,6 +3897,7 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class=
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- studyLocusId: long (nullable = false)
@@ -3695,18 +3905,22 @@ <h3 id="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split" class=
  |-- goldStandardSet: string (nullable = true)
  |-- distanceTssMean: float (nullable = true)
  |-- distanceTssMinimum: float (nullable = true)
- |-- eqtlColocClppLocalMaximum: double (nullable = true)
- |-- eqtlColocClppNeighborhoodMaximum: double (nullable = true)
- |-- eqtlColocLlrLocalMaximum: double (nullable = true)
- |-- eqtlColocLlrNeighborhoodMaximum: double (nullable = true)
- |-- pqtlColocClppLocalMaximum: double (nullable = true)
- |-- pqtlColocClppNeighborhoodMaximum: double (nullable = true)
- |-- pqtlColocLlrLocalMaximum: double (nullable = true)
- |-- pqtlColocLlrNeighborhoodMaximum: double (nullable = true)
- |-- sqtlColocClppLocalMaximum: double (nullable = true)
- |-- sqtlColocClppNeighborhoodMaximum: double (nullable = true)
- |-- sqtlColocLlrLocalMaximum: double (nullable = true)
- |-- sqtlColocLlrNeighborhoodMaximum: double (nullable = true)
+ |-- vepMaximumNeighborhood: float (nullable = true)
+ |-- vepMaximum: float (nullable = true)
+ |-- vepMeanNeighborhood: float (nullable = true)
+ |-- vepMean: float (nullable = true)
+ |-- eqtlColocClppMaximum: float (nullable = true)
+ |-- eqtlColocClppMaximumNeighborhood: float (nullable = true)
+ |-- eqtlColocLlrMaximum: float (nullable = true)
+ |-- eqtlColocLlrMaximumNeighborhood: float (nullable = true)
+ |-- pqtlColocClppMaximum: float (nullable = true)
+ |-- pqtlColocClppMaximumNeighborhood: float (nullable = true)
+ |-- pqtlColocLlrMaximum: float (nullable = true)
+ |-- pqtlColocLlrMaximumNeighborhood: float (nullable = true)
+ |-- sqtlColocClppMaximum: float (nullable = true)
+ |-- sqtlColocClppMaximumNeighborhood: float (nullable = true)
+ |-- sqtlColocLlrMaximum: float (nullable = true)
+ |-- sqtlColocLlrMaximumNeighborhood: float (nullable = true)
 </code></pre></div>
 <hr />
 <div class="md-source-file">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
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-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
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-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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similarity index 88%
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rename to python_api/datasets/l2g_gold_standard/index.html
index 5aed95112..1edca4158 100644
--- a/python_api/dataset/l2g_gold_standard/index.html
+++ b/python_api/datasets/l2g_gold_standard/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Gold Standard - Open Targets Genetics</title>
+        <title>L2G Gold Standard - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard" class="md-skip">
+        <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
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+  Home
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
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+      
+        
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+  
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       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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 </a>
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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+    Home
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step using YAML config
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+            <a href="../../../development/_development/" class="md-nav__link ">
+              
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+  <span class="md-ellipsis">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
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-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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               </label>
             
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard" class="md-nav__link">
     <span class="md-ellipsis">
       L2GGoldStandard
     </span>
@@ -771,45 +922,45 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_unique_associations()
+      filter_unique_associations
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="md-nav__link">
     <span class="md-ellipsis">
-      from_otg_curation()
+      from_otg_curation
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="md-nav__link">
     <span class="md-ellipsis">
-      process_gene_interactions()
+      process_gene_interactions
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="md-nav__link">
     <span class="md-ellipsis">
-      remove_false_negatives()
+      remove_false_negatives
     </span>
   </a>
   
@@ -1051,32 +1202,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1096,12 +1247,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1112,14 +1263,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1132,7 +1283,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1170,12 +1342,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1186,14 +1358,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1206,7 +1378,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1244,12 +1437,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1260,14 +1453,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1280,7 +1473,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1301,7 +1494,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1339,12 +1532,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1355,14 +1548,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1375,7 +1568,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1396,7 +1589,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1417,7 +1610,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1438,7 +1631,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1476,12 +1669,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1492,14 +1685,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1512,7 +1705,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1533,7 +1726,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1554,7 +1747,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1575,7 +1768,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1613,12 +1806,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1629,14 +1822,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1649,7 +1842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1670,7 +1863,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1692,80 +1885,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1790,32 +1909,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1826,11 +1945,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1847,11 +1966,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1868,11 +1987,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1889,11 +2008,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1910,11 +2029,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1931,11 +2050,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1961,12 +2080,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1977,14 +2096,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1997,7 +2116,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2018,7 +2137,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2039,7 +2158,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2060,7 +2179,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2106,32 +2225,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2142,11 +2261,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2163,11 +2282,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2184,11 +2303,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2205,11 +2324,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2226,11 +2345,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2247,11 +2366,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2268,11 +2387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2289,11 +2408,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2310,11 +2429,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2331,11 +2450,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2352,11 +2471,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2373,11 +2492,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2394,11 +2513,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2415,11 +2534,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2469,7 +2651,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard" class="md-nav__link">
     <span class="md-ellipsis">
       L2GGoldStandard
     </span>
@@ -2479,45 +2661,45 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_unique_associations()
+      filter_unique_associations
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="md-nav__link">
     <span class="md-ellipsis">
-      from_otg_curation()
+      from_otg_curation
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="md-nav__link">
     <span class="md-ellipsis">
-      process_gene_interactions()
+      process_gene_interactions
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="md-nav__link">
     <span class="md-ellipsis">
-      remove_false_negatives()
+      remove_false_negatives
     </span>
   </a>
   
@@ -2561,27 +2743,26 @@ <h1>L2G Gold Standard</h1>
 
 
 
-
-<h2 id="otg.dataset.l2g_gold_standard.L2GGoldStandard" class="doc doc-heading">
-          <code>otg.dataset.l2g_gold_standard.L2GGoldStandard</code>
+<h2 id="gentropy.dataset.l2g_gold_standard.L2GGoldStandard" class="doc doc-heading">
+          <code>gentropy.dataset.l2g_gold_standard.L2GGoldStandard</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>L2G gold standard dataset.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/l2g_gold_standard.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 22</span>
 <span class="normal"> 23</span>
 <span class="normal"> 24</span>
@@ -2786,7 +2967,7 @@ <h2 id="otg.dataset.l2g_gold_standard.L2GGoldStandard" class="doc doc-heading">
 <span class="sd">        Returns:</span>
 <span class="sd">            L2GGoldStandard: L2G Gold Standard dataset</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">otg.datasource.open_targets.l2g_gold_standard</span> <span class="kn">import</span> <span class="p">(</span>
+        <span class="kn">from</span> <span class="nn">gentropy.datasource.open_targets.l2g_gold_standard</span> <span class="kn">import</span> <span class="p">(</span>
             <span class="n">OpenTargetsL2GGoldStandard</span><span class="p">,</span>
         <span class="p">)</span>
 
@@ -2957,11 +3138,10 @@ <h2 id="otg.dataset.l2g_gold_standard.L2GGoldStandard" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">filter_unique_associations</span><span class="p">(</span><span class="n">study_locus_overlap</span><span class="p">:</span> <span class="n">StudyLocusOverlap</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GGoldStandard</span></code>
 
-<a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2988,7 +3168,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations
         <tr>
           <td><code>study_locus_overlap</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus_overlap.StudyLocusOverlap" href="../study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus_overlap.StudyLocusOverlap" href="../study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3015,7 +3195,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations
     <tbody>
         <tr>
 <td><code>L2GGoldStandard</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_gold_standard.L2GGoldStandard" href="#otg.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_gold_standard.L2GGoldStandard" href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3027,7 +3207,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">103</span>
 <span class="normal">104</span>
 <span class="normal">105</span>
@@ -3124,15 +3304,14 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations
 
 
 
-
-<h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_otg_curation</span><span class="p">(</span><span class="n">gold_standard_curation</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span> <span class="n">study_locus_overlap</span><span class="p">:</span> <span class="n">StudyLocusOverlap</span><span class="p">,</span> <span class="n">interactions</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GGoldStandard</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3169,7 +3348,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="
         <tr>
           <td><code>v2g</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3183,7 +3362,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="
         <tr>
           <td><code>study_locus_overlap</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus_overlap.StudyLocusOverlap" href="../study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus_overlap.StudyLocusOverlap" href="../study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3224,7 +3403,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="
     <tbody>
         <tr>
 <td><code>L2GGoldStandard</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_gold_standard.L2GGoldStandard" href="#otg.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_gold_standard.L2GGoldStandard" href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3236,7 +3415,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">30</span>
 <span class="normal">31</span>
 <span class="normal">32</span>
@@ -3285,7 +3464,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="
 <span class="sd">    Returns:</span>
 <span class="sd">        L2GGoldStandard: L2G Gold Standard dataset</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">otg.datasource.open_targets.l2g_gold_standard</span> <span class="kn">import</span> <span class="p">(</span>
+    <span class="kn">from</span> <span class="nn">gentropy.datasource.open_targets.l2g_gold_standard</span> <span class="kn">import</span> <span class="p">(</span>
         <span class="n">OpenTargetsL2GGoldStandard</span><span class="p">,</span>
     <span class="p">)</span>
 
@@ -3307,15 +3486,14 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation" class="
 
 
 
-
-<h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3347,7 +3525,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="doc doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">61</span>
 <span class="normal">62</span>
 <span class="normal">63</span>
@@ -3374,15 +3552,14 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.get_schema" class="doc doc
 
 
 
-
-<h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">process_gene_interactions</span><span class="p">(</span><span class="n">interactions</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3457,7 +3634,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions"
 </code></pre></div>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 70</span>
 <span class="normal"> 71</span>
 <span class="normal"> 72</span>
@@ -3532,11 +3709,10 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions"
 
 
 
-
-<h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">remove_false_negatives</span><span class="p">(</span><span class="n">interactions_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GGoldStandard</span></code>
 
-<a href="#otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3586,7 +3762,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" cl
     <tbody>
         <tr>
 <td><code>L2GGoldStandard</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_gold_standard.L2GGoldStandard" href="#otg.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_gold_standard.L2GGoldStandard" href="#gentropy.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3598,7 +3774,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" cl
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">147</span>
 <span class="normal">148</span>
 <span class="normal">149</span>
@@ -3716,6 +3892,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" cl
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- studyLocusId: long (nullable = false)
@@ -3748,7 +3925,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" cl
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3761,11 +3938,11 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" cl
       <li class="contributors-holder">
         <ul class="contributors" data-bi-name="contributors"><li>
             <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
+              href="https://github.com/d0choa"
+              title="d0choa"
               data-bi-name="contributorprofile"
               target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
+              ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
           </li></ul>
       </li>
@@ -3815,7 +3992,7 @@ <h3 id="otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives" cl
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/l2g_prediction/index.html b/python_api/datasets/l2g_prediction/index.html
similarity index 79%
rename from python_api/dataset/l2g_prediction/index.html
rename to python_api/datasets/l2g_prediction/index.html
index 6d2821136..f52de831c 100644
--- a/python_api/dataset/l2g_prediction/index.html
+++ b/python_api/datasets/l2g_prediction/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Prediction - Open Targets Genetics</title>
+        <title>L2G Prediction - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.l2g_prediction.L2GPrediction" class="md-skip">
+        <a href="#gentropy.dataset.l2g_prediction.L2GPrediction" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
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+  
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       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
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+  
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+      
+        
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@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
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+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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@@ -414,6 +448,123 @@
         
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+            How-to
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step using YAML config
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+        
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+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
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+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
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+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
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-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
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-    Dataset
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-            Dataset
+            Datasets
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     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_prediction.L2GPrediction" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_prediction.L2GPrediction" class="md-nav__link">
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       L2GPrediction
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@@ -792,18 +943,18 @@
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           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="md-nav__link">
     <span class="md-ellipsis">
-      from_credible_set()
+      from_credible_set
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-  <a href="#otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_prediction.L2GPrediction.get_schema" class="md-nav__link">
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+      get_schema
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
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+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1069,12 +1220,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1085,14 +1236,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1105,7 +1256,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1143,12 +1315,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1159,14 +1331,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1179,7 +1351,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1217,12 +1410,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1233,14 +1426,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1253,7 +1446,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1274,7 +1467,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1312,12 +1505,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1328,14 +1521,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1348,7 +1541,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,7 +1562,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1390,7 +1583,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1411,7 +1604,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1449,12 +1642,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1465,14 +1658,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1485,7 +1678,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,7 +1699,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1527,7 +1720,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1548,7 +1741,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1586,12 +1779,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1602,14 +1795,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1622,7 +1815,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1643,7 +1836,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1665,80 +1858,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1763,32 +1882,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1799,11 +1918,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1820,11 +1939,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1841,11 +1960,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1862,11 +1981,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1883,11 +2002,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1904,11 +2023,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1934,12 +2053,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1950,14 +2069,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1970,7 +2089,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1991,7 +2110,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2012,7 +2131,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2033,7 +2152,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2079,32 +2198,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2115,11 +2234,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2136,11 +2255,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2157,11 +2276,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2178,11 +2297,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2199,11 +2318,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2220,11 +2339,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2241,11 +2360,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2262,11 +2381,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2283,11 +2402,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2304,11 +2423,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2325,11 +2444,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2346,11 +2465,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2367,11 +2486,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2388,11 +2507,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2442,7 +2624,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_prediction.L2GPrediction" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_prediction.L2GPrediction" class="md-nav__link">
     <span class="md-ellipsis">
       L2GPrediction
     </span>
@@ -2452,18 +2634,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="md-nav__link">
     <span class="md-ellipsis">
-      from_credible_set()
+      from_credible_set
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.l2g_prediction.L2GPrediction.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -2507,21 +2689,20 @@ <h1>L2G Prediction</h1>
 
 
 
-
-<h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
-          <code>otg.dataset.l2g_prediction.L2GPrediction</code>
+<h2 id="gentropy.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
+          <code>gentropy.dataset.l2g_prediction.L2GPrediction</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_prediction.L2GPrediction" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.l2g_prediction.L2GPrediction" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Dataset that contains the Locus to Gene predictions.</p>
@@ -2530,8 +2711,9 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 confidence of the prediction that a gene is causal to an association.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/l2g_prediction.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">25</span>
+              <summary>Source code in <code>src/gentropy/dataset/l2g_prediction.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">24</span>
+<span class="normal">25</span>
 <span class="normal">26</span>
 <span class="normal">27</span>
 <span class="normal">28</span>
@@ -2595,7 +2777,17 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 <span class="normal">86</span>
 <span class="normal">87</span>
 <span class="normal">88</span>
-<span class="normal">89</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">89</span>
+<span class="normal">90</span>
+<span class="normal">91</span>
+<span class="normal">92</span>
+<span class="normal">93</span>
+<span class="normal">94</span>
+<span class="normal">95</span>
+<span class="normal">96</span>
+<span class="normal">97</span>
+<span class="normal">98</span>
+<span class="normal">99</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">L2GPrediction</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Dataset that contains the Locus to Gene predictions.</span>
 
@@ -2621,9 +2813,9 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
         <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
         <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span>
         <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span>
-        <span class="c1"># coloc: Colocalisation,</span>
+        <span class="n">coloc</span><span class="p">:</span> <span class="n">Colocalisation</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GPrediction</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Initialise L2G from feature matrix.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Extract L2G predictions for a set of credible sets derived from GWAS.</span>
 
 <span class="sd">        Args:</span>
 <span class="sd">            model_path (str): Path to the fitted model</span>
@@ -2631,6 +2823,7 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 <span class="sd">            study_locus (StudyLocus): Study locus dataset</span>
 <span class="sd">            study_index (StudyIndex): Study index dataset</span>
 <span class="sd">            v2g (V2G): Variant to gene dataset</span>
+<span class="sd">            coloc (Colocalisation): Colocalisation dataset</span>
 
 <span class="sd">        Returns:</span>
 <span class="sd">            L2GPrediction: L2G dataset</span>
@@ -2640,8 +2833,18 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
             <span class="n">study_locus</span><span class="o">=</span><span class="n">study_locus</span><span class="p">,</span>
             <span class="n">study_index</span><span class="o">=</span><span class="n">study_index</span><span class="p">,</span>
             <span class="n">variant_gene</span><span class="o">=</span><span class="n">v2g</span><span class="p">,</span>
-            <span class="c1"># colocalisation=coloc,</span>
+            <span class="n">colocalisation</span><span class="o">=</span><span class="n">coloc</span><span class="p">,</span>
         <span class="p">)</span><span class="o">.</span><span class="n">fill_na</span><span class="p">()</span>
+
+        <span class="n">gwas_fm</span> <span class="o">=</span> <span class="n">L2GFeatureMatrix</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
+                <span class="n">fm</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="n">study_locus</span><span class="o">.</span><span class="n">filter_by_study_type</span><span class="p">(</span><span class="s2">&quot;gwas&quot;</span><span class="p">,</span> <span class="n">study_index</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
+                    <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
+                <span class="p">)</span>
+            <span class="p">),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span>
         <span class="k">return</span> <span class="n">L2GPrediction</span><span class="p">(</span>
             <span class="c1"># Load and apply fitted model</span>
             <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
@@ -2649,7 +2852,7 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
                     <span class="n">model_path</span><span class="p">,</span>
                     <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
                 <span class="p">)</span>
-                <span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">fm</span><span class="p">)</span>
+                <span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">gwas_fm</span><span class="p">)</span>
                 <span class="c1"># the probability of the positive class is the second element inside the probability array</span>
                 <span class="c1"># - this is selected as the L2G probability</span>
                 <span class="o">.</span><span class="n">select</span><span class="p">(</span>
@@ -2680,20 +2883,19 @@ <h2 id="otg.dataset.l2g_prediction.L2GPrediction" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">from_credible_set</span><span class="p">(</span><span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GPrediction</span></code>
+<h3 id="gentropy.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">from_credible_set</span><span class="p">(</span><span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span> <span class="n">coloc</span><span class="p">:</span> <span class="n">Colocalisation</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GPrediction</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
   
-      <p>Initialise L2G from feature matrix.</p>
+      <p>Extract L2G predictions for a set of credible sets derived from GWAS.</p>
 
 
 
@@ -2739,7 +2941,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
         <tr>
           <td><code>study_locus</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2753,7 +2955,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
         <tr>
           <td><code>study_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2767,7 +2969,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
         <tr>
           <td><code>v2g</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2778,6 +2980,20 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
               <em>required</em>
           </td>
         </tr>
+        <tr>
+          <td><code>coloc</code></td>
+          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.colocalisation.Colocalisation" href="../colocalisation/#gentropy.dataset.colocalisation.Colocalisation">Colocalisation</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Colocalisation dataset</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
     </tbody>
   </table>
 
@@ -2794,7 +3010,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
     <tbody>
         <tr>
 <td><code>L2GPrediction</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_prediction.L2GPrediction" href="#otg.dataset.l2g_prediction.L2GPrediction">L2GPrediction</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_prediction.L2GPrediction" href="#gentropy.dataset.l2g_prediction.L2GPrediction">L2GPrediction</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2806,8 +3022,9 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_prediction.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">43</span>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_prediction.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">42</span>
+<span class="normal">43</span>
 <span class="normal">44</span>
 <span class="normal">45</span>
 <span class="normal">46</span>
@@ -2853,7 +3070,17 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
 <span class="normal">86</span>
 <span class="normal">87</span>
 <span class="normal">88</span>
-<span class="normal">89</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">89</span>
+<span class="normal">90</span>
+<span class="normal">91</span>
+<span class="normal">92</span>
+<span class="normal">93</span>
+<span class="normal">94</span>
+<span class="normal">95</span>
+<span class="normal">96</span>
+<span class="normal">97</span>
+<span class="normal">98</span>
+<span class="normal">99</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">from_credible_set</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">L2GPrediction</span><span class="p">],</span>
     <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
@@ -2861,9 +3088,9 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
     <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
     <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span>
     <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span>
-    <span class="c1"># coloc: Colocalisation,</span>
+    <span class="n">coloc</span><span class="p">:</span> <span class="n">Colocalisation</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GPrediction</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Initialise L2G from feature matrix.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Extract L2G predictions for a set of credible sets derived from GWAS.</span>
 
 <span class="sd">    Args:</span>
 <span class="sd">        model_path (str): Path to the fitted model</span>
@@ -2871,6 +3098,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
 <span class="sd">        study_locus (StudyLocus): Study locus dataset</span>
 <span class="sd">        study_index (StudyIndex): Study index dataset</span>
 <span class="sd">        v2g (V2G): Variant to gene dataset</span>
+<span class="sd">        coloc (Colocalisation): Colocalisation dataset</span>
 
 <span class="sd">    Returns:</span>
 <span class="sd">        L2GPrediction: L2G dataset</span>
@@ -2880,8 +3108,18 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
         <span class="n">study_locus</span><span class="o">=</span><span class="n">study_locus</span><span class="p">,</span>
         <span class="n">study_index</span><span class="o">=</span><span class="n">study_index</span><span class="p">,</span>
         <span class="n">variant_gene</span><span class="o">=</span><span class="n">v2g</span><span class="p">,</span>
-        <span class="c1"># colocalisation=coloc,</span>
+        <span class="n">colocalisation</span><span class="o">=</span><span class="n">coloc</span><span class="p">,</span>
     <span class="p">)</span><span class="o">.</span><span class="n">fill_na</span><span class="p">()</span>
+
+    <span class="n">gwas_fm</span> <span class="o">=</span> <span class="n">L2GFeatureMatrix</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
+            <span class="n">fm</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">study_locus</span><span class="o">.</span><span class="n">filter_by_study_type</span><span class="p">(</span><span class="s2">&quot;gwas&quot;</span><span class="p">,</span> <span class="n">study_index</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
+                <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">),</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="bp">cls</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+    <span class="p">)</span>
     <span class="k">return</span> <span class="n">L2GPrediction</span><span class="p">(</span>
         <span class="c1"># Load and apply fitted model</span>
         <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
@@ -2889,7 +3127,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
                 <span class="n">model_path</span><span class="p">,</span>
                 <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
             <span class="p">)</span>
-            <span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">fm</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">predict</span><span class="p">(</span><span class="n">gwas_fm</span><span class="p">)</span>
             <span class="c1"># the probability of the positive class is the second element inside the probability array</span>
             <span class="c1"># - this is selected as the L2G probability</span>
             <span class="o">.</span><span class="n">select</span><span class="p">(</span>
@@ -2911,15 +3149,14 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.from_credible_set" class="doc d
 
 
 
-
-<h3 id="otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.l2g_prediction.L2GPrediction.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.l2g_prediction.L2GPrediction.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2951,15 +3188,15 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="doc doc-head
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/l2g_prediction.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">34</span>
+            <summary>Source code in <code>src/gentropy/dataset/l2g_prediction.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">33</span>
+<span class="normal">34</span>
 <span class="normal">35</span>
 <span class="normal">36</span>
 <span class="normal">37</span>
 <span class="normal">38</span>
 <span class="normal">39</span>
-<span class="normal">40</span>
-<span class="normal">41</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">40</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">get_schema</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">L2GPrediction</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">StructType</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Provides the schema for the L2GPrediction dataset.</span>
 
@@ -2979,6 +3216,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="doc doc-head
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <hr />
 <div class="md-source-file">
@@ -3002,7 +3240,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="doc doc-head
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3021,14 +3259,6 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="doc doc-head
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
           </li></ul>
       </li>
     </ul>
@@ -3077,7 +3307,7 @@ <h3 id="otg.dataset.l2g_prediction.L2GPrediction.get_schema" class="doc doc-head
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/dataset/ld_index/index.html b/python_api/datasets/ld_index/index.html
similarity index 81%
rename from python_api/dataset/ld_index/index.html
rename to python_api/datasets/ld_index/index.html
index 40e101efa..79a4c78f7 100644
--- a/python_api/dataset/ld_index/index.html
+++ b/python_api/datasets/ld_index/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>LD Index - Open Targets Genetics</title>
+        <title>LD Index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.ld_index.LDIndex" class="md-skip">
+        <a href="#gentropy.dataset.ld_index.LDIndex" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
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+          <ul class="md-nav__list" data-md-scrollfix>
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
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+  
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+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
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+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -803,7 +954,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.ld_index.LDIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.ld_index.LDIndex" class="md-nav__link">
     <span class="md-ellipsis">
       LDIndex
     </span>
@@ -813,9 +964,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.ld_index.LDIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.ld_index.LDIndex.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -1015,32 +1166,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1060,12 +1211,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1076,14 +1227,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1096,7 +1247,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1134,12 +1306,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1150,14 +1322,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1170,7 +1342,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1208,12 +1401,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1224,14 +1417,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1244,7 +1437,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1265,7 +1458,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1303,12 +1496,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1319,14 +1512,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1339,7 +1532,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1360,7 +1553,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1381,7 +1574,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1402,7 +1595,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1440,12 +1633,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1456,14 +1649,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1476,7 +1669,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1497,7 +1690,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1518,7 +1711,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1539,7 +1732,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1577,12 +1770,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1593,14 +1786,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1613,7 +1806,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1634,7 +1827,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1656,80 +1849,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1754,32 +1873,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1790,11 +1909,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1811,11 +1930,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1832,11 +1951,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1853,11 +1972,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1874,11 +1993,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1895,11 +2014,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1925,12 +2044,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1941,14 +2060,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1961,7 +2080,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1982,7 +2101,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2003,7 +2122,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2024,7 +2143,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2070,32 +2189,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2106,11 +2225,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2127,11 +2246,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2148,11 +2267,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2169,11 +2288,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2190,11 +2309,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2211,11 +2330,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2232,11 +2351,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2253,11 +2372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2274,11 +2393,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2295,11 +2414,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2316,11 +2435,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2337,11 +2456,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2358,11 +2477,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2379,11 +2498,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2433,7 +2615,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.ld_index.LDIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.ld_index.LDIndex" class="md-nav__link">
     <span class="md-ellipsis">
       LDIndex
     </span>
@@ -2443,9 +2625,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.ld_index.LDIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.ld_index.LDIndex.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -2489,27 +2671,26 @@ <h1>LD Index</h1>
 
 
 
-
-<h2 id="otg.dataset.ld_index.LDIndex" class="doc doc-heading">
-          <code>otg.dataset.ld_index.LDIndex</code>
+<h2 id="gentropy.dataset.ld_index.LDIndex" class="doc doc-heading">
+          <code>gentropy.dataset.ld_index.LDIndex</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.ld_index.LDIndex" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.ld_index.LDIndex" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Dataset containing linkage desequilibrium information between variants.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/ld_index.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/ld_index.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
@@ -2553,15 +2734,14 @@ <h2 id="otg.dataset.ld_index.LDIndex" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.ld_index.LDIndex.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.ld_index.LDIndex.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.ld_index.LDIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.ld_index.LDIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2593,7 +2773,7 @@ <h3 id="otg.dataset.ld_index.LDIndex.get_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/ld_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/ld_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">18</span>
 <span class="normal">19</span>
 <span class="normal">20</span>
@@ -2621,6 +2801,7 @@ <h3 id="otg.dataset.ld_index.LDIndex.get_schema" class="doc doc-heading">
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- variantId: string (nullable = false)
@@ -2655,7 +2836,7 @@ <h3 id="otg.dataset.ld_index.LDIndex.get_schema" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2722,7 +2903,7 @@ <h3 id="otg.dataset.ld_index.LDIndex.get_schema" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/study_index/index.html b/python_api/datasets/study_index/index.html
similarity index 69%
rename from python_api/dataset/study_index/index.html
rename to python_api/datasets/study_index/index.html
index bcba951ff..dabfb2f9d 100644
--- a/python_api/dataset/study_index/index.html
+++ b/python_api/datasets/study_index/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Study Index - Open Targets Genetics</title>
+        <title>Study Index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.study_index.StudyIndex" class="md-skip">
+        <a href="#gentropy.dataset.study_index.StudyIndex" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -824,7 +975,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex" class="md-nav__link">
     <span class="md-ellipsis">
       StudyIndex
     </span>
@@ -834,27 +985,72 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="md-nav__link">
+    <span class="md-ellipsis">
+      aggregate_and_map_ancestries
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.get_schema" class="md-nav__link">
+    <span class="md-ellipsis">
+      get_schema
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.has_mapped_trait" class="md-nav__link">
+    <span class="md-ellipsis">
+      has_mapped_trait
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.has_summarystats" class="md-nav__link">
+    <span class="md-ellipsis">
+      has_summarystats
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.is_gwas" class="md-nav__link">
+    <span class="md-ellipsis">
+      is_gwas
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.is_qtl" class="md-nav__link">
     <span class="md-ellipsis">
-      aggregate_and_map_ancestries()
+      is_qtl
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex.is_quality_flagged" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      is_quality_flagged
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex.study_type_lut" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex.study_type_lut" class="md-nav__link">
     <span class="md-ellipsis">
-      study_type_lut()
+      study_type_lut
     </span>
   </a>
   
@@ -1033,32 +1229,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1078,12 +1274,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1094,14 +1290,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1114,7 +1310,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1152,12 +1369,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1168,14 +1385,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1188,7 +1405,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1226,12 +1464,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1242,14 +1480,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1262,7 +1500,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1283,7 +1521,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1321,12 +1559,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1337,14 +1575,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1357,7 +1595,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1378,7 +1616,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1399,7 +1637,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1420,7 +1658,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1458,12 +1696,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1474,14 +1712,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1494,7 +1732,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1515,7 +1753,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1536,7 +1774,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1557,7 +1795,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1595,12 +1833,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1611,14 +1849,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1631,7 +1869,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1652,7 +1890,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1674,6 +1912,14 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
@@ -1690,32 +1936,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1726,11 +1972,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1740,83 +1986,22 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
   
 
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Clumping
-  </span>
-  
-
-      </a>
+      </a>
     </li>
   
 
@@ -1829,7 +2014,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1850,7 +2035,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1871,7 +2056,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1892,7 +2077,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1912,27 +2097,6 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     
     
     
@@ -1943,12 +2107,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1959,14 +2123,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1979,7 +2143,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2000,7 +2164,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2021,7 +2185,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2042,7 +2206,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2088,32 +2252,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2124,11 +2288,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2145,11 +2309,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2166,11 +2330,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2187,11 +2351,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2208,11 +2372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2229,11 +2393,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2250,11 +2414,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2271,11 +2435,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2292,11 +2456,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2313,11 +2477,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2334,11 +2498,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2355,11 +2519,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2376,11 +2540,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2397,11 +2561,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2451,7 +2678,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex" class="md-nav__link">
     <span class="md-ellipsis">
       StudyIndex
     </span>
@@ -2461,27 +2688,72 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="md-nav__link">
+    <span class="md-ellipsis">
+      aggregate_and_map_ancestries
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.get_schema" class="md-nav__link">
+    <span class="md-ellipsis">
+      get_schema
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.has_mapped_trait" class="md-nav__link">
+    <span class="md-ellipsis">
+      has_mapped_trait
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.has_summarystats" class="md-nav__link">
+    <span class="md-ellipsis">
+      has_summarystats
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.is_gwas" class="md-nav__link">
     <span class="md-ellipsis">
-      aggregate_and_map_ancestries()
+      is_gwas
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex.is_qtl" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      is_qtl
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_index.StudyIndex.study_type_lut" class="md-nav__link">
+  <a href="#gentropy.dataset.study_index.StudyIndex.is_quality_flagged" class="md-nav__link">
     <span class="md-ellipsis">
-      study_type_lut()
+      is_quality_flagged
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_index.StudyIndex.study_type_lut" class="md-nav__link">
+    <span class="md-ellipsis">
+      study_type_lut
     </span>
   </a>
   
@@ -2525,28 +2797,27 @@ <h1>Study Index</h1>
 
 
 
-
-<h2 id="otg.dataset.study_index.StudyIndex" class="doc doc-heading">
-          <code>otg.dataset.study_index.StudyIndex</code>
+<h2 id="gentropy.dataset.study_index.StudyIndex" class="doc doc-heading">
+          <code>gentropy.dataset.study_index.StudyIndex</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.study_index.StudyIndex" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.study_index.StudyIndex" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Study index dataset.</p>
 <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/study_index.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 21</span>
 <span class="normal"> 22</span>
 <span class="normal"> 23</span>
@@ -2667,7 +2938,51 @@ <h2 id="otg.dataset.study_index.StudyIndex" class="doc doc-heading">
 <span class="normal">138</span>
 <span class="normal">139</span>
 <span class="normal">140</span>
-<span class="normal">141</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">141</span>
+<span class="normal">142</span>
+<span class="normal">143</span>
+<span class="normal">144</span>
+<span class="normal">145</span>
+<span class="normal">146</span>
+<span class="normal">147</span>
+<span class="normal">148</span>
+<span class="normal">149</span>
+<span class="normal">150</span>
+<span class="normal">151</span>
+<span class="normal">152</span>
+<span class="normal">153</span>
+<span class="normal">154</span>
+<span class="normal">155</span>
+<span class="normal">156</span>
+<span class="normal">157</span>
+<span class="normal">158</span>
+<span class="normal">159</span>
+<span class="normal">160</span>
+<span class="normal">161</span>
+<span class="normal">162</span>
+<span class="normal">163</span>
+<span class="normal">164</span>
+<span class="normal">165</span>
+<span class="normal">166</span>
+<span class="normal">167</span>
+<span class="normal">168</span>
+<span class="normal">169</span>
+<span class="normal">170</span>
+<span class="normal">171</span>
+<span class="normal">172</span>
+<span class="normal">173</span>
+<span class="normal">174</span>
+<span class="normal">175</span>
+<span class="normal">176</span>
+<span class="normal">177</span>
+<span class="normal">178</span>
+<span class="normal">179</span>
+<span class="normal">180</span>
+<span class="normal">181</span>
+<span class="normal">182</span>
+<span class="normal">183</span>
+<span class="normal">184</span>
+<span class="normal">185</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">StudyIndex</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study index dataset.</span>
 
@@ -2788,6 +3103,50 @@ <h2 id="otg.dataset.study_index.StudyIndex" class="doc doc-heading">
 <span class="sd">            DataFrame: A dataframe containing `studyId` and `studyType` columns.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;studyType&quot;</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">is_qtl</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return a boolean column with true values for QTL studies.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: True if the study is a QTL study.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">studyType</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">&quot;qtl&quot;</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">is_gwas</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return a boolean column with true values for GWAS studies.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: True if the study is a GWAS study.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">studyType</span> <span class="o">==</span> <span class="s2">&quot;gwas&quot;</span>
+
+    <span class="k">def</span> <span class="nf">has_mapped_trait</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return a boolean column indicating if a study has mapped disease.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: True if the study has mapped disease.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">traitFromSourceMappedIds</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span>
+
+    <span class="k">def</span> <span class="nf">is_quality_flagged</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return a boolean column indicating if a study is flagged due to quality issues.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: True if the study is flagged.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Testing for the presence of the qualityControls column:</span>
+        <span class="k">if</span> <span class="s2">&quot;qualityControls&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">qualityControls</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span>
+
+    <span class="k">def</span> <span class="nf">has_summarystats</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return a boolean column indicating if a study has harmonized summary statistics.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: True if the study has harmonized summary statistics.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">hasSumstats</span>
 </code></pre></div></td></tr></table></div>
             </details>
 
@@ -2808,15 +3167,14 @@ <h2 id="otg.dataset.study_index.StudyIndex" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">aggregate_and_map_ancestries</span><span class="p">(</span><span class="n">discovery_samples</span><span class="p">:</span> <span class="n">Column</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2878,7 +3236,7 @@ <h3 id="otg.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 89</span>
 <span class="normal"> 90</span>
 <span class="normal"> 91</span>
@@ -2979,15 +3337,14 @@ <h3 id="otg.dataset.study_index.StudyIndex.aggregate_and_map_ancestries" class="
 
 
 
-
-<h3 id="otg.dataset.study_index.StudyIndex.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_index.StudyIndex.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.study_index.StudyIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_index.StudyIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3019,7 +3376,7 @@ <h3 id="otg.dataset.study_index.StudyIndex.get_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">80</span>
 <span class="normal">81</span>
 <span class="normal">82</span>
@@ -3046,11 +3403,318 @@ <h3 id="otg.dataset.study_index.StudyIndex.get_schema" class="doc doc-heading">
 
 
 
+<h3 id="gentropy.dataset.study_index.StudyIndex.has_mapped_trait" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">has_mapped_trait</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
+
+<a href="#gentropy.dataset.study_index.StudyIndex.has_mapped_trait" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Return a boolean column indicating if a study has mapped disease.</p>
+
+
 
-<h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-heading">
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>Column</code></td>          <td>
+                <code><span title="pyspark.sql.Column">Column</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>True if the study has mapped disease.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">159</span>
+<span class="normal">160</span>
+<span class="normal">161</span>
+<span class="normal">162</span>
+<span class="normal">163</span>
+<span class="normal">164</span>
+<span class="normal">165</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">has_mapped_trait</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a boolean column indicating if a study has mapped disease.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        Column: True if the study has mapped disease.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">traitFromSourceMappedIds</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.dataset.study_index.StudyIndex.has_summarystats" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">has_summarystats</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
+
+<a href="#gentropy.dataset.study_index.StudyIndex.has_summarystats" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Return a boolean column indicating if a study has harmonized summary statistics.</p>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>Column</code></td>          <td>
+                <code><span title="pyspark.sql.Column">Column</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>True if the study has harmonized summary statistics.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">179</span>
+<span class="normal">180</span>
+<span class="normal">181</span>
+<span class="normal">182</span>
+<span class="normal">183</span>
+<span class="normal">184</span>
+<span class="normal">185</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">has_summarystats</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a boolean column indicating if a study has harmonized summary statistics.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        Column: True if the study has harmonized summary statistics.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">hasSumstats</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.dataset.study_index.StudyIndex.is_gwas" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">is_gwas</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
+
+<a href="#gentropy.dataset.study_index.StudyIndex.is_gwas" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Return a boolean column with true values for GWAS studies.</p>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>Column</code></td>          <td>
+                <code><span title="pyspark.sql.Column">Column</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>True if the study is a GWAS study.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">151</span>
+<span class="normal">152</span>
+<span class="normal">153</span>
+<span class="normal">154</span>
+<span class="normal">155</span>
+<span class="normal">156</span>
+<span class="normal">157</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">is_gwas</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a boolean column with true values for GWAS studies.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        Column: True if the study is a GWAS study.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">studyType</span> <span class="o">==</span> <span class="s2">&quot;gwas&quot;</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.dataset.study_index.StudyIndex.is_qtl" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">is_qtl</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
+
+<a href="#gentropy.dataset.study_index.StudyIndex.is_qtl" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Return a boolean column with true values for QTL studies.</p>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>Column</code></td>          <td>
+                <code><span title="pyspark.sql.Column">Column</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>True if the study is a QTL study.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">143</span>
+<span class="normal">144</span>
+<span class="normal">145</span>
+<span class="normal">146</span>
+<span class="normal">147</span>
+<span class="normal">148</span>
+<span class="normal">149</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">is_qtl</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a boolean column with true values for QTL studies.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        Column: True if the study is a QTL study.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">studyType</span><span class="o">.</span><span class="n">endswith</span><span class="p">(</span><span class="s2">&quot;qtl&quot;</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.dataset.study_index.StudyIndex.is_quality_flagged" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">is_quality_flagged</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
+
+<a href="#gentropy.dataset.study_index.StudyIndex.is_quality_flagged" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Return a boolean column indicating if a study is flagged due to quality issues.</p>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>Column</code></td>          <td>
+                <code><span title="pyspark.sql.Column">Column</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>True if the study is flagged.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">167</span>
+<span class="normal">168</span>
+<span class="normal">169</span>
+<span class="normal">170</span>
+<span class="normal">171</span>
+<span class="normal">172</span>
+<span class="normal">173</span>
+<span class="normal">174</span>
+<span class="normal">175</span>
+<span class="normal">176</span>
+<span class="normal">177</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">is_quality_flagged</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a boolean column indicating if a study is flagged due to quality issues.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        Column: True if the study is flagged.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># Testing for the presence of the qualityControls column:</span>
+    <span class="k">if</span> <span class="s2">&quot;qualityControls&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">qualityControls</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">study_type_lut</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
 
-<a href="#otg.dataset.study_index.StudyIndex.study_type_lut" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_index.StudyIndex.study_type_lut" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3082,7 +3746,7 @@ <h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-headin
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/study_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">135</span>
 <span class="normal">136</span>
 <span class="normal">137</span>
@@ -3108,6 +3772,7 @@ <h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-headin
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- studyId: string (nullable = false)
@@ -3125,9 +3790,9 @@ <h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-headin
  |-- backgroundTraitFromSourceMappedIds: array (nullable = true)
  |    |-- element: string (containsNull = true)
  |-- initialSampleSize: string (nullable = true)
- |-- nCases: long (nullable = true)
- |-- nControls: long (nullable = true)
- |-- nSamples: long (nullable = true)
+ |-- nCases: integer (nullable = true)
+ |-- nControls: integer (nullable = true)
+ |-- nSamples: integer (nullable = true)
  |-- cohorts: array (nullable = true)
  |    |-- element: string (containsNull = true)
  |-- ldPopulationStructure: array (nullable = true)
@@ -3136,12 +3801,16 @@ <h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-headin
  |    |    |-- relativeSampleSize: double (nullable = true)
  |-- discoverySamples: array (nullable = true)
  |    |-- element: struct (containsNull = false)
- |    |    |-- sampleSize: long (nullable = true)
+ |    |    |-- sampleSize: integer (nullable = true)
  |    |    |-- ancestry: string (nullable = true)
  |-- replicationSamples: array (nullable = true)
  |    |-- element: struct (containsNull = false)
- |    |    |-- sampleSize: long (nullable = true)
+ |    |    |-- sampleSize: integer (nullable = true)
  |    |    |-- ancestry: string (nullable = true)
+ |-- qualityControls: array (nullable = true)
+ |    |-- element: string (containsNull = true)
+ |-- analysisFlags: array (nullable = true)
+ |    |-- element: string (containsNull = true)
  |-- summarystatsLocation: string (nullable = true)
  |-- hasSumstats: boolean (nullable = true)
 </code></pre></div>
@@ -3167,7 +3836,7 @@ <h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-headin
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3186,14 +3855,6 @@ <h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-headin
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
           </li></ul>
       </li>
     </ul>
@@ -3242,7 +3903,7 @@ <h3 id="otg.dataset.study_index.StudyIndex.study_type_lut" class="doc doc-headin
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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     </a>
   
diff --git a/python_api/dataset/study_locus/index.html b/python_api/datasets/study_locus/index.html
similarity index 83%
rename from python_api/dataset/study_locus/index.html
rename to python_api/datasets/study_locus/index.html
index 9cfb8fbcf..ea04ae947 100644
--- a/python_api/dataset/study_locus/index.html
+++ b/python_api/datasets/study_locus/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Study Locus - Open Targets Genetics</title>
+        <title>Study Locus - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.study_locus.StudyLocus" class="md-skip">
+        <a href="#gentropy.dataset.study_locus.StudyLocus" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
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+      
+        
+  
+  
+  
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       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
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       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
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@@ -338,11 +372,11 @@
   
   
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-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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+    Home
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@@ -358,11 +392,11 @@
   
   
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+      <a href="../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +429,11 @@
           
           
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+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -845,7 +996,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocus
     </span>
@@ -855,90 +1006,99 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.annotate_credible_sets" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_credible_sets()
+      annotate_credible_sets
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.annotate_ld" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.annotate_ld" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_ld()
+      annotate_ld
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.assign_study_locus_id" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.assign_study_locus_id" class="md-nav__link">
     <span class="md-ellipsis">
-      assign_study_locus_id()
+      assign_study_locus_id
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.clump" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.clump" class="md-nav__link">
     <span class="md-ellipsis">
-      clump()
+      clump
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.filter_credible_set" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.filter_by_study_type" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_credible_set()
+      filter_by_study_type
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.find_overlaps" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.filter_credible_set" class="md-nav__link">
     <span class="md-ellipsis">
-      find_overlaps()
+      filter_credible_set
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.find_overlaps" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      find_overlaps
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.neglog_pvalue" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      neglog_pvalue()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.neglog_pvalue" class="md-nav__link">
     <span class="md-ellipsis">
-      unique_variants_in_locus()
+      neglog_pvalue
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.update_quality_flag" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="md-nav__link">
     <span class="md-ellipsis">
-      update_quality_flag()
+      unique_variants_in_locus
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.update_quality_flag" class="md-nav__link">
+    <span class="md-ellipsis">
+      update_quality_flag
     </span>
   </a>
   
@@ -950,7 +1110,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocusQualityCheck" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocusQualityCheck" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocusQualityCheck
     </span>
@@ -959,7 +1119,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.CredibleInterval" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.CredibleInterval" class="md-nav__link">
     <span class="md-ellipsis">
       CredibleInterval
     </span>
@@ -1114,32 +1274,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1159,12 +1319,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1175,14 +1335,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1195,7 +1355,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1233,12 +1414,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1249,14 +1430,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1269,7 +1450,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1307,12 +1509,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1323,14 +1525,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1343,7 +1545,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1364,7 +1566,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1402,12 +1604,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1418,14 +1620,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1438,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1459,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1480,7 +1682,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1501,7 +1703,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1539,12 +1741,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1555,14 +1757,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1575,7 +1777,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1596,7 +1798,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1617,7 +1819,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1638,7 +1840,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1676,12 +1878,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1692,14 +1894,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1712,7 +1914,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1733,7 +1935,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1755,6 +1957,14 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
@@ -1771,32 +1981,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1807,11 +2017,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1821,67 +2031,6 @@
 
               
             
-          </ul>
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-      
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-  
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-              
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-        
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-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
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-            </a>
-            
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-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
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-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1889,7 +2038,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1910,7 +2059,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1931,7 +2080,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1952,7 +2101,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1973,7 +2122,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1993,27 +2142,6 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     
     
     
@@ -2024,12 +2152,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -2040,14 +2168,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2060,7 +2188,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2081,7 +2209,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2102,7 +2230,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2123,7 +2251,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2169,32 +2297,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2205,11 +2333,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2226,11 +2354,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2247,11 +2375,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2268,11 +2396,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2289,11 +2417,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2310,11 +2438,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2331,11 +2459,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2352,11 +2480,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2373,11 +2501,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2394,11 +2522,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2415,11 +2543,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2436,11 +2564,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2457,11 +2585,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2478,11 +2606,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2532,7 +2723,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocus
     </span>
@@ -2542,90 +2733,99 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.annotate_credible_sets" class="md-nav__link">
+    <span class="md-ellipsis">
+      annotate_credible_sets
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.annotate_ld" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_credible_sets()
+      annotate_ld
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.annotate_ld" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.assign_study_locus_id" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_ld()
+      assign_study_locus_id
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.assign_study_locus_id" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.clump" class="md-nav__link">
     <span class="md-ellipsis">
-      assign_study_locus_id()
+      clump
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.clump" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.filter_by_study_type" class="md-nav__link">
     <span class="md-ellipsis">
-      clump()
+      filter_by_study_type
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.filter_credible_set" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.filter_credible_set" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_credible_set()
+      filter_credible_set
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.find_overlaps" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.find_overlaps" class="md-nav__link">
     <span class="md-ellipsis">
-      find_overlaps()
+      find_overlaps
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.neglog_pvalue" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.neglog_pvalue" class="md-nav__link">
     <span class="md-ellipsis">
-      neglog_pvalue()
+      neglog_pvalue
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="md-nav__link">
     <span class="md-ellipsis">
-      unique_variants_in_locus()
+      unique_variants_in_locus
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocus.update_quality_flag" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocus.update_quality_flag" class="md-nav__link">
     <span class="md-ellipsis">
-      update_quality_flag()
+      update_quality_flag
     </span>
   </a>
   
@@ -2637,7 +2837,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.StudyLocusQualityCheck" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.StudyLocusQualityCheck" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocusQualityCheck
     </span>
@@ -2646,7 +2846,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus.CredibleInterval" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus.CredibleInterval" class="md-nav__link">
     <span class="md-ellipsis">
       CredibleInterval
     </span>
@@ -2687,33 +2887,28 @@ <h1>Study Locus</h1>
 
 
 
-
-<h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
-          <code>otg.dataset.study_locus.StudyLocus</code>
+<h2 id="gentropy.dataset.study_locus.StudyLocus" class="doc doc-heading">
+          <code>gentropy.dataset.study_locus.StudyLocus</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.study_locus.StudyLocus" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.study_locus.StudyLocus" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Study-Locus dataset.</p>
 <p>This dataset captures associations between study/traits and a genetic loci as provided by finemapping methods.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 68</span>
-<span class="normal"> 69</span>
-<span class="normal"> 70</span>
-<span class="normal"> 71</span>
-<span class="normal"> 72</span>
+              <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 72</span>
 <span class="normal"> 73</span>
 <span class="normal"> 74</span>
 <span class="normal"> 75</span>
@@ -3100,7 +3295,40 @@ <h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
 <span class="normal">456</span>
 <span class="normal">457</span>
 <span class="normal">458</span>
-<span class="normal">459</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">459</span>
+<span class="normal">460</span>
+<span class="normal">461</span>
+<span class="normal">462</span>
+<span class="normal">463</span>
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+<span class="normal">492</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">StudyLocus</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study-Locus dataset.</span>
 
@@ -3152,7 +3380,7 @@ <h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Align overlapping tags in pairs of overlapping study-locus, keeping all tags in both loci.</span>
 
 <span class="sd">        Args:</span>
-<span class="sd">            loci_to_overlap (DataFrame): containing `studyLocusId`, `studyType`, `chromosome`, `tagVariantId`, `logABF` and `posteriorProbability` columns.</span>
+<span class="sd">            loci_to_overlap (DataFrame): containing `studyLocusId`, `studyType`, `chromosome`, `tagVariantId`, `logBF` and `posteriorProbability` columns.</span>
 <span class="sd">            peak_overlaps (DataFrame): containing `leftStudyLocusId`, `rightStudyLocusId` and `chromosome` columns.</span>
 
 <span class="sd">        Returns:</span>
@@ -3160,7 +3388,7 @@ <h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c1"># Complete information about all tags in the left study-locus of the overlap</span>
         <span class="n">stats_cols</span> <span class="o">=</span> <span class="p">[</span>
-            <span class="s2">&quot;logABF&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;logBF&quot;</span><span class="p">,</span>
             <span class="s2">&quot;posteriorProbability&quot;</span><span class="p">,</span>
             <span class="s2">&quot;beta&quot;</span><span class="p">,</span>
             <span class="s2">&quot;pValueMantissa&quot;</span><span class="p">,</span>
@@ -3259,6 +3487,35 @@ <h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="n">parse_spark_schema</span><span class="p">(</span><span class="s2">&quot;study_locus.json&quot;</span><span class="p">)</span>
 
+    <span class="k">def</span> <span class="nf">filter_by_study_type</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Creates a new StudyLocus dataset filtered by study type.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            study_type (str): Study type to filter for. Can be one of `gwas`, `eqtl`, `pqtl`, `eqtl`.</span>
+<span class="sd">            study_index (StudyIndex): Study index to resolve study types.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            StudyLocus: Filtered study-locus dataset.</span>
+
+<span class="sd">        Raises:</span>
+<span class="sd">            ValueError: If study type is not supported.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">study_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;gwas&quot;</span><span class="p">,</span> <span class="s2">&quot;eqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;pqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;sqtl&quot;</span><span class="p">]:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s2">&quot;Study type </span><span class="si">{</span><span class="n">study_type</span><span class="si">}</span><span class="s2"> not supported. Supported types are: gwas, eqtl, pqtl, sqtl.&quot;</span>
+            <span class="p">)</span>
+        <span class="n">new_df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">study_index</span><span class="o">.</span><span class="n">study_type_lut</span><span class="p">(),</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">)</span> <span class="o">==</span> <span class="n">study_type</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">return</span> <span class="n">StudyLocus</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">new_df</span><span class="p">,</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_schema</span><span class="p">,</span>
+        <span class="p">)</span>
+
     <span class="k">def</span> <span class="nf">filter_credible_set</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
         <span class="n">credible_interval</span><span class="p">:</span> <span class="n">CredibleInterval</span><span class="p">,</span>
@@ -3300,7 +3557,7 @@ <h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
                 <span class="s2">&quot;studyType&quot;</span><span class="p">,</span>
                 <span class="s2">&quot;chromosome&quot;</span><span class="p">,</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.variantId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;tagVariantId&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.logABF&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;logABF&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.logBF&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;logBF&quot;</span><span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.posteriorProbability&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;posteriorProbability&quot;</span><span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.pValueMantissa&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;pValueMantissa&quot;</span><span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.pValueExponent&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;pValueExponent&quot;</span><span class="p">),</span>
@@ -3416,7 +3673,7 @@ <h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
 <span class="sd">        Returns:</span>
 <span class="sd">            StudyLocus: Study locus annotated with ld information from LD index.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">otg.method.ld</span> <span class="kn">import</span> <span class="n">LDAnnotator</span>
+        <span class="kn">from</span> <span class="nn">gentropy.method.ld</span> <span class="kn">import</span> <span class="n">LDAnnotator</span>
 
         <span class="k">return</span> <span class="n">LDAnnotator</span><span class="o">.</span><span class="n">ld_annotate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">study_index</span><span class="p">,</span> <span class="n">ld_index</span><span class="p">)</span>
 
@@ -3512,11 +3769,10 @@ <h2 id="otg.dataset.study_locus.StudyLocus" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.annotate_credible_sets" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">annotate_credible_sets</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
 
-<a href="#otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.annotate_credible_sets" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3539,7 +3795,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="doc do
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3575,41 +3831,8 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="doc do
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">317</span>
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+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">350</span>
 <span class="normal">351</span>
 <span class="normal">352</span>
 <span class="normal">353</span>
@@ -3629,7 +3852,40 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="doc do
 <span class="normal">367</span>
 <span class="normal">368</span>
 <span class="normal">369</span>
-<span class="normal">370</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_credible_sets</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
+<span class="normal">370</span>
+<span class="normal">371</span>
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+<span class="normal">401</span>
+<span class="normal">402</span>
+<span class="normal">403</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_credible_sets</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Annotate study-locus dataset with credible set flags.</span>
 
 <span class="sd">    Sorts the array in the `locus` column elements by their `posteriorProbability` values in descending order and adds</span>
@@ -3694,11 +3950,10 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_credible_sets" class="doc do
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">annotate_ld</span><span class="p">(</span><span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">ld_index</span><span class="p">:</span> <span class="n">LDIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
 
-<a href="#otg.dataset.study_locus.StudyLocus.annotate_ld" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.annotate_ld" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3721,7 +3976,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
         <tr>
           <td><code>study_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3735,7 +3990,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
         <tr>
           <td><code>ld_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.ld_index.LDIndex" href="../ld_index/#otg.dataset.ld_index.LDIndex">LDIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.ld_index.LDIndex" href="../ld_index/#gentropy.dataset.ld_index.LDIndex">LDIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3762,7 +4017,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3774,22 +4029,22 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">372</span>
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-<span class="normal">386</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_ld</span><span class="p">(</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">405</span>
+<span class="normal">406</span>
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+<span class="normal">409</span>
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+<span class="normal">418</span>
+<span class="normal">419</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_ld</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">ld_index</span><span class="p">:</span> <span class="n">LDIndex</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Annotate LD information to study-locus.</span>
@@ -3801,7 +4056,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
 <span class="sd">    Returns:</span>
 <span class="sd">        StudyLocus: Study locus annotated with ld information from LD index.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">otg.method.ld</span> <span class="kn">import</span> <span class="n">LDAnnotator</span>
+    <span class="kn">from</span> <span class="nn">gentropy.method.ld</span> <span class="kn">import</span> <span class="n">LDAnnotator</span>
 
     <span class="k">return</span> <span class="n">LDAnnotator</span><span class="o">.</span><span class="n">ld_annotate</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">study_index</span><span class="p">,</span> <span class="n">ld_index</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
@@ -3815,15 +4070,14 @@ <h3 id="otg.dataset.study_locus.StudyLocus.annotate_ld" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.assign_study_locus_id" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.assign_study_locus_id" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">assign_study_locus_id</span><span class="p">(</span><span class="n">study_id_col</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span> <span class="n">variant_id_col</span><span class="p">:</span> <span class="n">Column</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.dataset.study_locus.StudyLocus.assign_study_locus_id" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.assign_study_locus_id" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3912,12 +4166,8 @@ <h3 id="otg.dataset.study_locus.StudyLocus.assign_study_locus_id" class="doc doc
 </code></pre></div>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">193</span>
-<span class="normal">194</span>
-<span class="normal">195</span>
-<span class="normal">196</span>
-<span class="normal">197</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">197</span>
 <span class="normal">198</span>
 <span class="normal">199</span>
 <span class="normal">200</span>
@@ -3936,7 +4186,11 @@ <h3 id="otg.dataset.study_locus.StudyLocus.assign_study_locus_id" class="doc doc
 <span class="normal">213</span>
 <span class="normal">214</span>
 <span class="normal">215</span>
-<span class="normal">216</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+<span class="normal">216</span>
+<span class="normal">217</span>
+<span class="normal">218</span>
+<span class="normal">219</span>
+<span class="normal">220</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
 <span class="k">def</span> <span class="nf">assign_study_locus_id</span><span class="p">(</span><span class="n">study_id_col</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span> <span class="n">variant_id_col</span><span class="p">:</span> <span class="n">Column</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Hashes a column with a variant ID and a study ID to extract a consistent studyLocusId.</span>
 
@@ -3971,11 +4225,10 @@ <h3 id="otg.dataset.study_locus.StudyLocus.assign_study_locus_id" class="doc doc
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.clump" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.clump" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">clump</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
 
-<a href="#otg.dataset.study_locus.StudyLocus.clump" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.clump" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3996,7 +4249,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.clump" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4008,59 +4261,59 @@ <h3 id="otg.dataset.study_locus.StudyLocus.clump" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">388</span>
-<span class="normal">389</span>
-<span class="normal">390</span>
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-<span class="normal">419</span>
-<span class="normal">420</span>
-<span class="normal">421</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">clump</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Perform LD clumping of the studyLocus.</span>
-
-<span class="sd">    Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.</span>
-
-<span class="sd">    Returns:</span>
-<span class="sd">        StudyLocus: with empty credible sets for linked variants and QC flag.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-            <span class="s2">&quot;is_lead_linked&quot;</span><span class="p">,</span>
-            <span class="n">LDclumping</span><span class="o">.</span><span class="n">_is_lead_linked</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">studyId</span><span class="p">,</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">variantId</span><span class="p">,</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">pValueExponent</span><span class="p">,</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">pValueMantissa</span><span class="p">,</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">ldSet</span><span class="p">,</span>
-            <span class="p">),</span>
-        <span class="p">)</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">421</span>
+<span class="normal">422</span>
+<span class="normal">423</span>
+<span class="normal">424</span>
+<span class="normal">425</span>
+<span class="normal">426</span>
+<span class="normal">427</span>
+<span class="normal">428</span>
+<span class="normal">429</span>
+<span class="normal">430</span>
+<span class="normal">431</span>
+<span class="normal">432</span>
+<span class="normal">433</span>
+<span class="normal">434</span>
+<span class="normal">435</span>
+<span class="normal">436</span>
+<span class="normal">437</span>
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+<span class="normal">440</span>
+<span class="normal">441</span>
+<span class="normal">442</span>
+<span class="normal">443</span>
+<span class="normal">444</span>
+<span class="normal">445</span>
+<span class="normal">446</span>
+<span class="normal">447</span>
+<span class="normal">448</span>
+<span class="normal">449</span>
+<span class="normal">450</span>
+<span class="normal">451</span>
+<span class="normal">452</span>
+<span class="normal">453</span>
+<span class="normal">454</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">clump</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Perform LD clumping of the studyLocus.</span>
+
+<span class="sd">    Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        StudyLocus: with empty credible sets for linked variants and QC flag.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+            <span class="s2">&quot;is_lead_linked&quot;</span><span class="p">,</span>
+            <span class="n">LDclumping</span><span class="o">.</span><span class="n">_is_lead_linked</span><span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">studyId</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">variantId</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">pValueExponent</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">pValueMantissa</span><span class="p">,</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">ldSet</span><span class="p">,</span>
+            <span class="p">),</span>
+        <span class="p">)</span>
         <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
             <span class="s2">&quot;ldSet&quot;</span><span class="p">,</span>
             <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;is_lead_linked&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">())</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ldSet&quot;</span><span class="p">)),</span>
@@ -4087,16 +4340,15 @@ <h3 id="otg.dataset.study_locus.StudyLocus.clump" class="doc doc-heading">
 
 
 
+<h3 id="gentropy.dataset.study_locus.StudyLocus.filter_by_study_type" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">filter_by_study_type</span><span class="p">(</span><span class="n">study_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
 
-<h3 id="otg.dataset.study_locus.StudyLocus.filter_credible_set" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">filter_credible_set</span><span class="p">(</span><span class="n">credible_interval</span><span class="p">:</span> <span class="n">CredibleInterval</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
-
-<a href="#otg.dataset.study_locus.StudyLocus.filter_credible_set" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.filter_by_study_type" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
   
-      <p>Filter study-locus tag variants based on given credible interval.</p>
+      <p>Creates a new StudyLocus dataset filtered by study type.</p>
 
 
 
@@ -4112,13 +4364,27 @@ <h3 id="otg.dataset.study_locus.StudyLocus.filter_credible_set" class="doc doc-h
     </thead>
     <tbody>
         <tr>
-          <td><code>credible_interval</code></td>
+          <td><code>study_type</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.CredibleInterval" href="#otg.dataset.study_locus.CredibleInterval">CredibleInterval</a></code>
+                <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Credible interval to filter for.</p>
+              <p>Study type to filter for. Can be one of <code>gwas</code>, <code>eqtl</code>, <code>pqtl</code>, <code>eqtl</code>.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>study_index</code></td>
+          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Study index to resolve study types.</p>
             </div>
           </td>
           <td>
@@ -4141,7 +4407,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.filter_credible_set" class="doc doc-h
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4152,13 +4418,33 @@ <h3 id="otg.dataset.study_locus.StudyLocus.filter_credible_set" class="doc doc-h
     </tbody>
   </table>
 
+
+
+  <p><strong>Raises:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td>
+                <code>ValueError</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>If study type is not supported.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">227</span>
-<span class="normal">228</span>
-<span class="normal">229</span>
-<span class="normal">230</span>
-<span class="normal">231</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">231</span>
 <span class="normal">232</span>
 <span class="normal">233</span>
 <span class="normal">234</span>
@@ -4173,7 +4459,143 @@ <h3 id="otg.dataset.study_locus.StudyLocus.filter_credible_set" class="doc doc-h
 <span class="normal">243</span>
 <span class="normal">244</span>
 <span class="normal">245</span>
-<span class="normal">246</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">filter_credible_set</span><span class="p">(</span>
+<span class="normal">246</span>
+<span class="normal">247</span>
+<span class="normal">248</span>
+<span class="normal">249</span>
+<span class="normal">250</span>
+<span class="normal">251</span>
+<span class="normal">252</span>
+<span class="normal">253</span>
+<span class="normal">254</span>
+<span class="normal">255</span>
+<span class="normal">256</span>
+<span class="normal">257</span>
+<span class="normal">258</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">filter_by_study_type</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_type</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Creates a new StudyLocus dataset filtered by study type.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        study_type (str): Study type to filter for. Can be one of `gwas`, `eqtl`, `pqtl`, `eqtl`.</span>
+<span class="sd">        study_index (StudyIndex): Study index to resolve study types.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        StudyLocus: Filtered study-locus dataset.</span>
+
+<span class="sd">    Raises:</span>
+<span class="sd">        ValueError: If study type is not supported.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">study_type</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;gwas&quot;</span><span class="p">,</span> <span class="s2">&quot;eqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;pqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;sqtl&quot;</span><span class="p">]:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="sa">f</span><span class="s2">&quot;Study type </span><span class="si">{</span><span class="n">study_type</span><span class="si">}</span><span class="s2"> not supported. Supported types are: gwas, eqtl, pqtl, sqtl.&quot;</span>
+        <span class="p">)</span>
+    <span class="n">new_df</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">study_index</span><span class="o">.</span><span class="n">study_type_lut</span><span class="p">(),</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">)</span> <span class="o">==</span> <span class="n">study_type</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">)</span>
+    <span class="p">)</span>
+    <span class="k">return</span> <span class="n">StudyLocus</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="n">new_df</span><span class="p">,</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">_schema</span><span class="p">,</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.dataset.study_locus.StudyLocus.filter_credible_set" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">filter_credible_set</span><span class="p">(</span><span class="n">credible_interval</span><span class="p">:</span> <span class="n">CredibleInterval</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
+
+<a href="#gentropy.dataset.study_locus.StudyLocus.filter_credible_set" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Filter study-locus tag variants based on given credible interval.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>credible_interval</code></td>
+          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.CredibleInterval" href="#gentropy.dataset.study_locus.CredibleInterval">CredibleInterval</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Credible interval to filter for.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>StudyLocus</code></td>          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Filtered study-locus dataset.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">260</span>
+<span class="normal">261</span>
+<span class="normal">262</span>
+<span class="normal">263</span>
+<span class="normal">264</span>
+<span class="normal">265</span>
+<span class="normal">266</span>
+<span class="normal">267</span>
+<span class="normal">268</span>
+<span class="normal">269</span>
+<span class="normal">270</span>
+<span class="normal">271</span>
+<span class="normal">272</span>
+<span class="normal">273</span>
+<span class="normal">274</span>
+<span class="normal">275</span>
+<span class="normal">276</span>
+<span class="normal">277</span>
+<span class="normal">278</span>
+<span class="normal">279</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">filter_credible_set</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
     <span class="n">credible_interval</span><span class="p">:</span> <span class="n">CredibleInterval</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
@@ -4204,11 +4626,10 @@ <h3 id="otg.dataset.study_locus.StudyLocus.filter_credible_set" class="doc doc-h
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.find_overlaps" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.find_overlaps" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">find_overlaps</span><span class="p">(</span><span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusOverlap</span></code>
 
-<a href="#otg.dataset.study_locus.StudyLocus.find_overlaps" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.find_overlaps" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4233,7 +4654,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.find_overlaps" class="doc doc-heading
         <tr>
           <td><code>study_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4260,7 +4681,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.find_overlaps" class="doc doc-heading
     <tbody>
         <tr>
 <td><code>StudyLocusOverlap</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus_overlap.StudyLocusOverlap" href="../study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus_overlap.StudyLocusOverlap" href="../study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4272,41 +4693,41 @@ <h3 id="otg.dataset.study_locus.StudyLocus.find_overlaps" class="doc doc-heading
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">248</span>
-<span class="normal">249</span>
-<span class="normal">250</span>
-<span class="normal">251</span>
-<span class="normal">252</span>
-<span class="normal">253</span>
-<span class="normal">254</span>
-<span class="normal">255</span>
-<span class="normal">256</span>
-<span class="normal">257</span>
-<span class="normal">258</span>
-<span class="normal">259</span>
-<span class="normal">260</span>
-<span class="normal">261</span>
-<span class="normal">262</span>
-<span class="normal">263</span>
-<span class="normal">264</span>
-<span class="normal">265</span>
-<span class="normal">266</span>
-<span class="normal">267</span>
-<span class="normal">268</span>
-<span class="normal">269</span>
-<span class="normal">270</span>
-<span class="normal">271</span>
-<span class="normal">272</span>
-<span class="normal">273</span>
-<span class="normal">274</span>
-<span class="normal">275</span>
-<span class="normal">276</span>
-<span class="normal">277</span>
-<span class="normal">278</span>
-<span class="normal">279</span>
-<span class="normal">280</span>
-<span class="normal">281</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">find_overlaps</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusOverlap</span><span class="p">:</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">281</span>
+<span class="normal">282</span>
+<span class="normal">283</span>
+<span class="normal">284</span>
+<span class="normal">285</span>
+<span class="normal">286</span>
+<span class="normal">287</span>
+<span class="normal">288</span>
+<span class="normal">289</span>
+<span class="normal">290</span>
+<span class="normal">291</span>
+<span class="normal">292</span>
+<span class="normal">293</span>
+<span class="normal">294</span>
+<span class="normal">295</span>
+<span class="normal">296</span>
+<span class="normal">297</span>
+<span class="normal">298</span>
+<span class="normal">299</span>
+<span class="normal">300</span>
+<span class="normal">301</span>
+<span class="normal">302</span>
+<span class="normal">303</span>
+<span class="normal">304</span>
+<span class="normal">305</span>
+<span class="normal">306</span>
+<span class="normal">307</span>
+<span class="normal">308</span>
+<span class="normal">309</span>
+<span class="normal">310</span>
+<span class="normal">311</span>
+<span class="normal">312</span>
+<span class="normal">313</span>
+<span class="normal">314</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">find_overlaps</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusOverlap</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Calculate overlapping study-locus.</span>
 
 <span class="sd">    Find overlapping study-locus that share at least one tagging variant. All GWAS-GWAS and all GWAS-Molecular traits are computed with the Molecular traits always</span>
@@ -4326,7 +4747,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.find_overlaps" class="doc doc-heading
             <span class="s2">&quot;studyType&quot;</span><span class="p">,</span>
             <span class="s2">&quot;chromosome&quot;</span><span class="p">,</span>
             <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.variantId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;tagVariantId&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.logABF&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;logABF&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.logBF&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;logBF&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.posteriorProbability&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;posteriorProbability&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.pValueMantissa&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;pValueMantissa&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.pValueExponent&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;pValueExponent&quot;</span><span class="p">),</span>
@@ -4351,15 +4772,14 @@ <h3 id="otg.dataset.study_locus.StudyLocus.find_overlaps" class="doc doc-heading
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.study_locus.StudyLocus.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4391,15 +4811,15 @@ <h3 id="otg.dataset.study_locus.StudyLocus.get_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">218</span>
-<span class="normal">219</span>
-<span class="normal">220</span>
-<span class="normal">221</span>
-<span class="normal">222</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">222</span>
 <span class="normal">223</span>
 <span class="normal">224</span>
-<span class="normal">225</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">225</span>
+<span class="normal">226</span>
+<span class="normal">227</span>
+<span class="normal">228</span>
+<span class="normal">229</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">get_schema</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">StudyLocus</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">StructType</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Provides the schema for the StudyLocus dataset.</span>
 
@@ -4418,11 +4838,10 @@ <h3 id="otg.dataset.study_locus.StudyLocus.get_schema" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.neglog_pvalue" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.neglog_pvalue" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">neglog_pvalue</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
 
-<a href="#otg.dataset.study_locus.StudyLocus.neglog_pvalue" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.neglog_pvalue" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4454,17 +4873,17 @@ <h3 id="otg.dataset.study_locus.StudyLocus.neglog_pvalue" class="doc doc-heading
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">306</span>
-<span class="normal">307</span>
-<span class="normal">308</span>
-<span class="normal">309</span>
-<span class="normal">310</span>
-<span class="normal">311</span>
-<span class="normal">312</span>
-<span class="normal">313</span>
-<span class="normal">314</span>
-<span class="normal">315</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">neglog_pvalue</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">339</span>
+<span class="normal">340</span>
+<span class="normal">341</span>
+<span class="normal">342</span>
+<span class="normal">343</span>
+<span class="normal">344</span>
+<span class="normal">345</span>
+<span class="normal">346</span>
+<span class="normal">347</span>
+<span class="normal">348</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">neglog_pvalue</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Returns the negative log p-value.</span>
 
 <span class="sd">    Returns:</span>
@@ -4485,11 +4904,10 @@ <h3 id="otg.dataset.study_locus.StudyLocus.neglog_pvalue" class="doc doc-heading
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">unique_variants_in_locus</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
 
-<a href="#otg.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4521,29 +4939,29 @@ <h3 id="otg.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">283</span>
-<span class="normal">284</span>
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-<span class="normal">303</span>
-<span class="normal">304</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">unique_variants_in_locus</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">316</span>
+<span class="normal">317</span>
+<span class="normal">318</span>
+<span class="normal">319</span>
+<span class="normal">320</span>
+<span class="normal">321</span>
+<span class="normal">322</span>
+<span class="normal">323</span>
+<span class="normal">324</span>
+<span class="normal">325</span>
+<span class="normal">326</span>
+<span class="normal">327</span>
+<span class="normal">328</span>
+<span class="normal">329</span>
+<span class="normal">330</span>
+<span class="normal">331</span>
+<span class="normal">332</span>
+<span class="normal">333</span>
+<span class="normal">334</span>
+<span class="normal">335</span>
+<span class="normal">336</span>
+<span class="normal">337</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">unique_variants_in_locus</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;All unique variants collected in a `StudyLocus` dataframe.</span>
 
 <span class="sd">    Returns:</span>
@@ -4576,15 +4994,14 @@ <h3 id="otg.dataset.study_locus.StudyLocus.unique_variants_in_locus" class="doc
 
 
 
-
-<h3 id="otg.dataset.study_locus.StudyLocus.update_quality_flag" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus.StudyLocus.update_quality_flag" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">update_quality_flag</span><span class="p">(</span><span class="n">qc</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span> <span class="n">flag_condition</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span> <span class="n">flag_text</span><span class="p">:</span> <span class="n">StudyLocusQualityCheck</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.dataset.study_locus.StudyLocus.update_quality_flag" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus.StudyLocus.update_quality_flag" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4635,7 +5052,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.update_quality_flag" class="doc doc-h
         <tr>
           <td><code>flag_text</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocusQualityCheck" href="#otg.dataset.study_locus.StudyLocusQualityCheck">StudyLocusQualityCheck</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocusQualityCheck" href="#gentropy.dataset.study_locus.StudyLocusQualityCheck">StudyLocusQualityCheck</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4674,12 +5091,8 @@ <h3 id="otg.dataset.study_locus.StudyLocus.update_quality_flag" class="doc doc-h
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">173</span>
-<span class="normal">174</span>
-<span class="normal">175</span>
-<span class="normal">176</span>
-<span class="normal">177</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">177</span>
 <span class="normal">178</span>
 <span class="normal">179</span>
 <span class="normal">180</span>
@@ -4693,7 +5106,11 @@ <h3 id="otg.dataset.study_locus.StudyLocus.update_quality_flag" class="doc doc-h
 <span class="normal">188</span>
 <span class="normal">189</span>
 <span class="normal">190</span>
-<span class="normal">191</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+<span class="normal">191</span>
+<span class="normal">192</span>
+<span class="normal">193</span>
+<span class="normal">194</span>
+<span class="normal">195</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
 <span class="k">def</span> <span class="nf">update_quality_flag</span><span class="p">(</span>
     <span class="n">qc</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span> <span class="n">flag_condition</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span> <span class="n">flag_text</span><span class="p">:</span> <span class="n">StudyLocusQualityCheck</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
@@ -4724,6 +5141,7 @@ <h3 id="otg.dataset.study_locus.StudyLocus.update_quality_flag" class="doc doc-h
 
   </div>
 
+
 </div><hr />
 
 
@@ -4731,12 +5149,11 @@ <h3 id="otg.dataset.study_locus.StudyLocus.update_quality_flag" class="doc doc-h
 
 
 
-
-<h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
-          <code>otg.dataset.study_locus.StudyLocusQualityCheck</code>
+<h2 id="gentropy.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
+          <code>gentropy.dataset.study_locus.StudyLocusQualityCheck</code>
 
 
-<a href="#otg.dataset.study_locus.StudyLocusQualityCheck" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.study_locus.StudyLocusQualityCheck" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -4759,7 +5176,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
     </thead>
     <tbody>
         <tr>
-          <td><code>SUBSIGNIFICANT_FLAG</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.SUBSIGNIFICANT_FLAG">SUBSIGNIFICANT_FLAG</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4770,7 +5187,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>NO_GENOMIC_LOCATION_FLAG</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.NO_GENOMIC_LOCATION_FLAG">NO_GENOMIC_LOCATION_FLAG</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4781,7 +5198,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>COMPOSITE_FLAG</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.COMPOSITE_FLAG">COMPOSITE_FLAG</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4792,7 +5209,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>VARIANT_INCONSISTENCY_FLAG</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.VARIANT_INCONSISTENCY_FLAG">VARIANT_INCONSISTENCY_FLAG</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4803,7 +5220,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>NON_MAPPED_VARIANT_FLAG</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.NON_MAPPED_VARIANT_FLAG">NON_MAPPED_VARIANT_FLAG</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4814,7 +5231,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>PALINDROMIC_ALLELE_FLAG</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.PALINDROMIC_ALLELE_FLAG">PALINDROMIC_ALLELE_FLAG</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4825,7 +5242,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>AMBIGUOUS_STUDY</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.AMBIGUOUS_STUDY">AMBIGUOUS_STUDY</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4836,7 +5253,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>UNRESOLVED_LD</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.UNRESOLVED_LD">UNRESOLVED_LD</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4847,7 +5264,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>LD_CLUMPED</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.LD_CLUMPED">LD_CLUMPED</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4857,11 +5274,22 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
             </div>
           </td>
         </tr>
+        <tr>
+          <td><code><span title="gentropy.dataset.study_locus.StudyLocusQualityCheck.UNPICSABLE">UNPICSABLE</span></code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Unable to calculate PIPs with the provided data</p>
+            </div>
+          </td>
+        </tr>
     </tbody>
   </table>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">27</span>
 <span class="normal">28</span>
 <span class="normal">29</span>
@@ -4886,7 +5314,11 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
 <span class="normal">48</span>
 <span class="normal">49</span>
 <span class="normal">50</span>
-<span class="normal">51</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">StudyLocusQualityCheck</span><span class="p">(</span><span class="n">Enum</span><span class="p">):</span>
+<span class="normal">51</span>
+<span class="normal">52</span>
+<span class="normal">53</span>
+<span class="normal">54</span>
+<span class="normal">55</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">StudyLocusQualityCheck</span><span class="p">(</span><span class="n">Enum</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study-Locus quality control options listing concerns on the quality of the association.</span>
 
 <span class="sd">    Attributes:</span>
@@ -4899,6 +5331,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
 <span class="sd">        AMBIGUOUS_STUDY (str): Association with ambiguous study</span>
 <span class="sd">        UNRESOLVED_LD (str): Variant not found in LD reference</span>
 <span class="sd">        LD_CLUMPED (str): Explained by a more significant variant in high LD (clumped)</span>
+<span class="sd">        UNPICSABLE (str): Unable to calculate PIPs with the provided data</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="n">SUBSIGNIFICANT_FLAG</span> <span class="o">=</span> <span class="s2">&quot;Subsignificant p-value&quot;</span>
@@ -4911,6 +5344,9 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
     <span class="n">UNRESOLVED_LD</span> <span class="o">=</span> <span class="s2">&quot;Variant not found in LD reference&quot;</span>
     <span class="n">LD_CLUMPED</span> <span class="o">=</span> <span class="s2">&quot;Explained by a more significant variant in high LD (clumped)&quot;</span>
     <span class="n">NO_POPULATION</span> <span class="o">=</span> <span class="s2">&quot;Study does not have population annotation to resolve LD&quot;</span>
+    <span class="n">NOT_QUALIFYING_LD_BLOCK</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s2">&quot;LD block does not contain variants at the required R^2 threshold&quot;</span>
+    <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
             </details>
 
@@ -4932,6 +5368,7 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
 
   </div>
 
+
 </div><hr />
 
 
@@ -4939,12 +5376,11 @@ <h2 id="otg.dataset.study_locus.StudyLocusQualityCheck" class="doc doc-heading">
 
 
 
-
-<h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
-          <code>otg.dataset.study_locus.CredibleInterval</code>
+<h2 id="gentropy.dataset.study_locus.CredibleInterval" class="doc doc-heading">
+          <code>gentropy.dataset.study_locus.CredibleInterval</code>
 
 
-<a href="#otg.dataset.study_locus.CredibleInterval" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.study_locus.CredibleInterval" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -4968,7 +5404,7 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
     </thead>
     <tbody>
         <tr>
-          <td><code>IS95</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.CredibleInterval.IS95">IS95</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4979,7 +5415,7 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>IS99</code></td>
+          <td><code><span title="gentropy.dataset.study_locus.CredibleInterval.IS99">IS99</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -4993,19 +5429,19 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
   </table>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/study_locus.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">54</span>
-<span class="normal">55</span>
-<span class="normal">56</span>
-<span class="normal">57</span>
-<span class="normal">58</span>
+              <summary>Source code in <code>src/gentropy/dataset/study_locus.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">58</span>
 <span class="normal">59</span>
 <span class="normal">60</span>
 <span class="normal">61</span>
 <span class="normal">62</span>
 <span class="normal">63</span>
 <span class="normal">64</span>
-<span class="normal">65</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">CredibleInterval</span><span class="p">(</span><span class="n">Enum</span><span class="p">):</span>
+<span class="normal">65</span>
+<span class="normal">66</span>
+<span class="normal">67</span>
+<span class="normal">68</span>
+<span class="normal">69</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">CredibleInterval</span><span class="p">(</span><span class="n">Enum</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Credible interval enum.</span>
 
 <span class="sd">    Interval within which an unobserved parameter value falls with a particular probability.</span>
@@ -5038,6 +5474,7 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- studyLocusId: long (nullable = false)
@@ -5063,17 +5500,13 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
  |    |-- element: struct (containsNull = true)
  |    |    |-- is95CredibleSet: boolean (nullable = true)
  |    |    |-- is99CredibleSet: boolean (nullable = true)
- |    |    |-- logABF: double (nullable = true)
+ |    |    |-- logBF: double (nullable = true)
  |    |    |-- posteriorProbability: double (nullable = true)
  |    |    |-- variantId: string (nullable = true)
  |    |    |-- pValueMantissa: float (nullable = true)
  |    |    |-- pValueExponent: integer (nullable = true)
- |    |    |-- pValueMantissaConditioned: float (nullable = true)
- |    |    |-- pValueExponentConditioned: integer (nullable = true)
  |    |    |-- beta: double (nullable = true)
  |    |    |-- standardError: double (nullable = true)
- |    |    |-- betaConditioned: double (nullable = true)
- |    |    |-- standardErrorConditioned: double (nullable = true)
  |    |    |-- r2Overall: double (nullable = true)
 </code></pre></div>
 <hr />
@@ -5098,7 +5531,7 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -5117,14 +5550,6 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
           </li></ul>
       </li>
     </ul>
@@ -5173,7 +5598,7 @@ <h2 id="otg.dataset.study_locus.CredibleInterval" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/dataset/study_locus_overlap/index.html b/python_api/datasets/study_locus_overlap/index.html
similarity index 82%
rename from python_api/dataset/study_locus_overlap/index.html
rename to python_api/datasets/study_locus_overlap/index.html
index dfea7e32d..68c31b565 100644
--- a/python_api/dataset/study_locus_overlap/index.html
+++ b/python_api/datasets/study_locus_overlap/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Study Locus Overlap - Open Targets Genetics</title>
+        <title>Study Locus Overlap - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap" class="md-skip">
+        <a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
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+                <span class="md-nav__icon md-icon"></span>
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+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+    Datasets
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+            Datasets
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         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap" class="md-nav__link">
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       StudyLocusOverlap
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           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="md-nav__link">
     <span class="md-ellipsis">
-      from_associations()
+      from_associations
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   </a>
   
 </li>
         
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-  <a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="md-nav__link">
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-      get_schema()
+      get_schema
     </span>
   </a>
   
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1085,14 +1236,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
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@@ -1105,7 +1256,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1143,12 +1315,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1159,14 +1331,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1179,7 +1351,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1217,12 +1410,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1233,14 +1426,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1253,7 +1446,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1274,7 +1467,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
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@@ -1312,12 +1505,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1328,14 +1521,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1348,7 +1541,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,7 +1562,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1390,7 +1583,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1411,7 +1604,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1449,12 +1642,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1465,14 +1658,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1485,7 +1678,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
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@@ -1506,7 +1699,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
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@@ -1527,7 +1720,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
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@@ -1548,7 +1741,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
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@@ -1586,12 +1779,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
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@@ -1602,14 +1795,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1622,7 +1815,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1643,7 +1836,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
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@@ -1665,80 +1858,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
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-    
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-      
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-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1763,32 +1882,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1799,11 +1918,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1820,11 +1939,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1841,11 +1960,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1862,11 +1981,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1883,11 +2002,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1904,11 +2023,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1934,12 +2053,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1950,14 +2069,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1970,7 +2089,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1991,7 +2110,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2012,7 +2131,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2033,7 +2152,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2079,32 +2198,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2115,11 +2234,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2136,11 +2255,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2157,11 +2276,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2178,11 +2297,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2199,11 +2318,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2220,11 +2339,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2241,11 +2360,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2262,11 +2381,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2283,11 +2402,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2304,11 +2423,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2325,11 +2444,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2346,11 +2465,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2367,11 +2486,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2388,11 +2507,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2442,7 +2624,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocusOverlap
     </span>
@@ -2452,18 +2634,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="md-nav__link">
     <span class="md-ellipsis">
-      from_associations()
+      from_associations
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -2507,21 +2689,20 @@ <h1>Study Locus Overlap</h1>
 
 
 
-
-<h2 id="otg.dataset.study_locus_overlap.StudyLocusOverlap" class="doc doc-heading">
-          <code>otg.dataset.study_locus_overlap.StudyLocusOverlap</code>
+<h2 id="gentropy.dataset.study_locus_overlap.StudyLocusOverlap" class="doc doc-heading">
+          <code>gentropy.dataset.study_locus_overlap.StudyLocusOverlap</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Study-Locus overlap.</p>
@@ -2532,7 +2713,7 @@ <h2 id="otg.dataset.study_locus_overlap.StudyLocusOverlap" class="doc doc-headin
 </div>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/study_locus_overlap.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/study_locus_overlap.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">17</span>
 <span class="normal">18</span>
 <span class="normal">19</span>
@@ -2582,13 +2763,15 @@ <h2 id="otg.dataset.study_locus_overlap.StudyLocusOverlap" class="doc doc-headin
 <span class="normal">63</span>
 <span class="normal">64</span>
 <span class="normal">65</span>
-<span class="normal">66</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">66</span>
+<span class="normal">67</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">StudyLocusOverlap</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study-Locus overlap.</span>
 
 <span class="sd">    This dataset captures pairs of overlapping `StudyLocus`: that is associations whose credible sets share at least one tagging variant.</span>
 
 <span class="sd">    !!! note</span>
+
 <span class="sd">        This is a helpful dataset for other downstream analyses, such as colocalisation. This dataset will contain the overlapping signals between studyLocus associations once they have been clumped and fine-mapped.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
@@ -2652,15 +2835,14 @@ <h2 id="otg.dataset.study_locus_overlap.StudyLocusOverlap" class="doc doc-headin
 
 
 
-
-<h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_associations</span><span class="p">(</span><span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusOverlap</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2683,7 +2865,7 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" cla
         <tr>
           <td><code>study_locus</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2697,7 +2879,7 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" cla
         <tr>
           <td><code>study_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2724,7 +2906,7 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" cla
     <tbody>
         <tr>
 <td><code>StudyLocusOverlap</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus_overlap.StudyLocusOverlap" href="#otg.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus_overlap.StudyLocusOverlap" href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2736,9 +2918,8 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" cla
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus_overlap.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">36</span>
-<span class="normal">37</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus_overlap.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">37</span>
 <span class="normal">38</span>
 <span class="normal">39</span>
 <span class="normal">40</span>
@@ -2750,7 +2931,8 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" cla
 <span class="normal">46</span>
 <span class="normal">47</span>
 <span class="normal">48</span>
-<span class="normal">49</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">49</span>
+<span class="normal">50</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">from_associations</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">StudyLocusOverlap</span><span class="p">],</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndex</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusOverlap</span><span class="p">:</span>
@@ -2775,15 +2957,14 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations" cla
 
 
 
-
-<h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2815,15 +2996,15 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/study_locus_overlap.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">27</span>
-<span class="normal">28</span>
+            <summary>Source code in <code>src/gentropy/dataset/study_locus_overlap.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">28</span>
 <span class="normal">29</span>
 <span class="normal">30</span>
 <span class="normal">31</span>
 <span class="normal">32</span>
 <span class="normal">33</span>
-<span class="normal">34</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">34</span>
+<span class="normal">35</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">get_schema</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">StudyLocusOverlap</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">StructType</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Provides the schema for the StudyLocusOverlap dataset.</span>
 
@@ -2843,6 +3024,7 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="doc
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- leftStudyLocusId: long (nullable = false)
@@ -2856,8 +3038,8 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="doc
  |    |-- right_pValueExponent: integer (nullable = true)
  |    |-- left_beta: double (nullable = true)
  |    |-- right_beta: double (nullable = true)
- |    |-- left_logABF: double (nullable = true)
- |    |-- right_logABF: double (nullable = true)
+ |    |-- left_logBF: double (nullable = true)
+ |    |-- right_logBF: double (nullable = true)
  |    |-- left_posteriorProbability: double (nullable = true)
  |    |-- right_posteriorProbability: double (nullable = true)
 </code></pre></div>
@@ -2883,7 +3065,7 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="doc
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2950,7 +3132,7 @@ <h3 id="otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema" class="doc
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/summary_statistics/index.html b/python_api/datasets/summary_statistics/index.html
similarity index 85%
rename from python_api/dataset/summary_statistics/index.html
rename to python_api/datasets/summary_statistics/index.html
index 2a6482699..d64f77abd 100644
--- a/python_api/dataset/summary_statistics/index.html
+++ b/python_api/datasets/summary_statistics/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Summary Statistics - Open Targets Genetics</title>
+        <title>Summary Statistics - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.summary_statistics.SummaryStatistics" class="md-skip">
+        <a href="#gentropy.dataset.summary_statistics.SummaryStatistics" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
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+
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@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -338,11 +372,11 @@
   
   
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-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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+      <a href="../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +429,11 @@
           
           
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+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -887,7 +1038,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics" class="md-nav__link">
     <span class="md-ellipsis">
       SummaryStatistics
     </span>
@@ -897,36 +1048,36 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.exclude_region" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.exclude_region" class="md-nav__link">
     <span class="md-ellipsis">
-      exclude_region()
+      exclude_region
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="md-nav__link">
     <span class="md-ellipsis">
-      pvalue_filter()
+      pvalue_filter
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="md-nav__link">
     <span class="md-ellipsis">
-      window_based_clumping()
+      window_based_clumping
     </span>
   </a>
   
@@ -1042,32 +1193,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1087,12 +1238,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1103,14 +1254,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1123,7 +1274,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1161,12 +1333,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1177,14 +1349,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1197,7 +1369,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1235,12 +1428,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1251,14 +1444,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1271,7 +1464,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1292,7 +1485,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1330,12 +1523,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1346,14 +1539,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1366,7 +1559,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1387,7 +1580,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1408,7 +1601,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1429,7 +1622,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1467,12 +1660,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1483,14 +1676,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1503,7 +1696,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1524,7 +1717,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1545,7 +1738,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1566,7 +1759,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1604,12 +1797,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1620,14 +1813,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1640,7 +1833,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1661,7 +1854,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1683,80 +1876,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1781,32 +1900,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1817,11 +1936,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1838,11 +1957,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1859,11 +1978,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1880,11 +1999,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1901,11 +2020,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1922,11 +2041,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1952,12 +2071,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1968,14 +2087,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1988,7 +2107,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2009,7 +2128,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2030,7 +2149,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2051,7 +2170,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2097,32 +2216,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2133,11 +2252,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2154,11 +2273,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2175,11 +2294,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2196,11 +2315,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2217,11 +2336,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2238,11 +2357,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2259,11 +2378,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2280,11 +2399,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2301,11 +2420,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2322,11 +2441,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2343,11 +2462,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2364,11 +2483,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2385,11 +2504,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2406,11 +2525,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2460,7 +2642,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics" class="md-nav__link">
     <span class="md-ellipsis">
       SummaryStatistics
     </span>
@@ -2470,36 +2652,36 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.exclude_region" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.exclude_region" class="md-nav__link">
     <span class="md-ellipsis">
-      exclude_region()
+      exclude_region
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="md-nav__link">
     <span class="md-ellipsis">
-      pvalue_filter()
+      pvalue_filter
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="md-nav__link">
+  <a href="#gentropy.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="md-nav__link">
     <span class="md-ellipsis">
-      window_based_clumping()
+      window_based_clumping
     </span>
   </a>
   
@@ -2543,28 +2725,27 @@ <h1>Summary Statistics</h1>
 
 
 
-
-<h2 id="otg.dataset.summary_statistics.SummaryStatistics" class="doc doc-heading">
-          <code>otg.dataset.summary_statistics.SummaryStatistics</code>
+<h2 id="gentropy.dataset.summary_statistics.SummaryStatistics" class="doc doc-heading">
+          <code>gentropy.dataset.summary_statistics.SummaryStatistics</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.summary_statistics.SummaryStatistics" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.summary_statistics.SummaryStatistics" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Summary Statistics dataset.</p>
 <p>A summary statistics dataset contains all single point statistics resulting from a GWAS.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/summary_statistics.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 20</span>
 <span class="normal"> 21</span>
 <span class="normal"> 22</span>
@@ -2778,11 +2959,10 @@ <h2 id="otg.dataset.summary_statistics.SummaryStatistics" class="doc doc-heading
 
 
 
-
-<h3 id="otg.dataset.summary_statistics.SummaryStatistics.exclude_region" class="doc doc-heading">
+<h3 id="gentropy.dataset.summary_statistics.SummaryStatistics.exclude_region" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">exclude_region</span><span class="p">(</span><span class="n">region</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">SummaryStatistics</span></code>
 
-<a href="#otg.dataset.summary_statistics.SummaryStatistics.exclude_region" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.summary_statistics.SummaryStatistics.exclude_region" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2832,7 +3012,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.exclude_region" class="
     <tbody>
         <tr>
 <td><code>SummaryStatistics</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.summary_statistics.SummaryStatistics" href="#gentropy.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2844,7 +3024,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.exclude_region" class="
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/summary_statistics.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 92</span>
 <span class="normal"> 93</span>
 <span class="normal"> 94</span>
@@ -2905,15 +3085,14 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.exclude_region" class="
 
 
 
-
-<h3 id="otg.dataset.summary_statistics.SummaryStatistics.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.summary_statistics.SummaryStatistics.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.summary_statistics.SummaryStatistics.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.summary_statistics.SummaryStatistics.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2945,7 +3124,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.get_schema" class="doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/summary_statistics.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">27</span>
 <span class="normal">28</span>
 <span class="normal">29</span>
@@ -2972,11 +3151,10 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.get_schema" class="doc
 
 
 
-
-<h3 id="otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="doc doc-heading">
+<h3 id="gentropy.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">pvalue_filter</span><span class="p">(</span><span class="n">pvalue</span><span class="p">:</span> <span class="nb">float</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">SummaryStatistics</span></code>
 
-<a href="#otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3026,7 +3204,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="d
     <tbody>
         <tr>
 <td><code>SummaryStatistics</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.summary_statistics.SummaryStatistics" href="#gentropy.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3038,7 +3216,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="d
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/summary_statistics.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">36</span>
 <span class="normal">37</span>
 <span class="normal">38</span>
@@ -3091,11 +3269,10 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter" class="d
 
 
 
-
-<h3 id="otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="doc doc-heading">
+<h3 id="gentropy.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">window_based_clumping</span><span class="p">(</span><span class="n">distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">500000</span><span class="p">,</span> <span class="n">gwas_significance</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">5e-08</span><span class="p">,</span> <span class="n">baseline_significance</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.05</span><span class="p">,</span> <span class="n">locus_collect_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
 
-<a href="#otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.summary_statistics.SummaryStatistics.window_based_clumping" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3187,7 +3364,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping"
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3199,7 +3376,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping"
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/summary_statistics.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/summary_statistics.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">58</span>
 <span class="normal">59</span>
 <span class="normal">60</span>
@@ -3277,6 +3454,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping"
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- studyId: string (nullable = false)
@@ -3312,7 +3490,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping"
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3379,7 +3557,7 @@ <h3 id="otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping"
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/variant_annotation/index.html b/python_api/datasets/variant_annotation/index.html
similarity index 87%
rename from python_api/dataset/variant_annotation/index.html
rename to python_api/datasets/variant_annotation/index.html
index b3b7fc73e..42b7f17f2 100644
--- a/python_api/dataset/variant_annotation/index.html
+++ b/python_api/datasets/variant_annotation/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Variant annotation - Open Targets Genetics</title>
+        <title>Variant annotation - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.variant_annotation.VariantAnnotation" class="md-skip">
+        <a href="#gentropy.dataset.variant_annotation.VariantAnnotation" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -908,7 +1059,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation" class="md-nav__link">
     <span class="md-ellipsis">
       VariantAnnotation
     </span>
@@ -918,63 +1069,63 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_by_variant_df()
+      filter_by_variant_df
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="md-nav__link">
     <span class="md-ellipsis">
-      get_distance_to_tss()
+      get_distance_to_tss
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="md-nav__link">
     <span class="md-ellipsis">
-      get_most_severe_vep_v2g()
+      get_most_severe_vep_v2g
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="md-nav__link">
     <span class="md-ellipsis">
-      get_plof_v2g()
+      get_plof_v2g
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="md-nav__link">
     <span class="md-ellipsis">
-      get_transcript_consequence_df()
+      get_transcript_consequence_df
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.max_maf" class="md-nav__link">
     <span class="md-ellipsis">
-      max_maf()
+      max_maf
     </span>
   </a>
   
@@ -1069,32 +1220,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1114,12 +1265,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1130,14 +1281,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1150,7 +1301,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1188,12 +1360,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1204,14 +1376,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1224,7 +1396,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1262,12 +1455,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1278,14 +1471,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1298,7 +1491,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1319,7 +1512,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1357,12 +1550,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1373,14 +1566,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1393,7 +1586,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1414,7 +1607,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1435,7 +1628,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1456,7 +1649,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1494,12 +1687,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1510,14 +1703,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1530,7 +1723,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1551,7 +1744,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1572,7 +1765,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1593,7 +1786,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1631,12 +1824,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1647,14 +1840,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1667,7 +1860,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1688,7 +1881,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1710,80 +1903,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1808,32 +1927,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1844,11 +1963,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1865,11 +1984,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1886,11 +2005,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1907,11 +2026,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1928,11 +2047,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1949,11 +2068,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1979,12 +2098,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1995,14 +2114,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2015,7 +2134,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2036,7 +2155,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2057,7 +2176,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2078,7 +2197,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2124,32 +2243,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2307,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2328,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2349,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2370,11 +2489,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2391,11 +2510,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2412,11 +2531,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2433,11 +2552,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2487,7 +2669,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation" class="md-nav__link">
     <span class="md-ellipsis">
       VariantAnnotation
     </span>
@@ -2497,63 +2679,63 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_by_variant_df()
+      filter_by_variant_df
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="md-nav__link">
     <span class="md-ellipsis">
-      get_distance_to_tss()
+      get_distance_to_tss
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="md-nav__link">
     <span class="md-ellipsis">
-      get_most_severe_vep_v2g()
+      get_most_severe_vep_v2g
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="md-nav__link">
     <span class="md-ellipsis">
-      get_plof_v2g()
+      get_plof_v2g
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="md-nav__link">
     <span class="md-ellipsis">
-      get_transcript_consequence_df()
+      get_transcript_consequence_df
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_annotation.VariantAnnotation.max_maf" class="md-nav__link">
     <span class="md-ellipsis">
-      max_maf()
+      max_maf
     </span>
   </a>
   
@@ -2597,31 +2779,27 @@ <h1>Variant annotation</h1>
 
 
 
-
-<h2 id="otg.dataset.variant_annotation.VariantAnnotation" class="doc doc-heading">
-          <code>otg.dataset.variant_annotation.VariantAnnotation</code>
+<h2 id="gentropy.dataset.variant_annotation.VariantAnnotation" class="doc doc-heading">
+          <code>gentropy.dataset.variant_annotation.VariantAnnotation</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Dataset with variant-level annotations.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 21</span>
-<span class="normal"> 22</span>
-<span class="normal"> 23</span>
-<span class="normal"> 24</span>
+              <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 24</span>
 <span class="normal"> 25</span>
 <span class="normal"> 26</span>
 <span class="normal"> 27</span>
@@ -2821,7 +2999,10 @@ <h2 id="otg.dataset.variant_annotation.VariantAnnotation" class="doc doc-heading
 <span class="normal">221</span>
 <span class="normal">222</span>
 <span class="normal">223</span>
-<span class="normal">224</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">224</span>
+<span class="normal">225</span>
+<span class="normal">226</span>
+<span class="normal">227</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">VariantAnnotation</span><span class="p">(</span><span class="n">Dataset</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Dataset with variant-level annotations.&quot;&quot;&quot;</span>
 
@@ -3045,11 +3226,10 @@ <h2 id="otg.dataset.variant_annotation.VariantAnnotation" class="doc doc-heading
 
 
 
-
-<h3 id="otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">filter_by_variant_df</span><span class="p">(</span><span class="n">df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">VariantAnnotation</span></code>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3099,7 +3279,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" c
     <tbody>
         <tr>
 <td><code>VariantAnnotation</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.variant_annotation.VariantAnnotation" href="#otg.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.variant_annotation.VariantAnnotation" href="#gentropy.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3111,11 +3291,8 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" c
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">49</span>
-<span class="normal">50</span>
-<span class="normal">51</span>
-<span class="normal">52</span>
+            <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">52</span>
 <span class="normal">53</span>
 <span class="normal">54</span>
 <span class="normal">55</span>
@@ -3128,7 +3305,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" c
 <span class="normal">62</span>
 <span class="normal">63</span>
 <span class="normal">64</span>
-<span class="normal">65</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">filter_by_variant_df</span><span class="p">(</span>
+<span class="normal">65</span>
+<span class="normal">66</span>
+<span class="normal">67</span>
+<span class="normal">68</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">filter_by_variant_df</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span> <span class="n">df</span><span class="p">:</span> <span class="n">DataFrame</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">VariantAnnotation</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Filter variant annotation dataset by a variant dataframe.</span>
@@ -3156,11 +3336,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df" c
 
 
 
-
-<h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_distance_to_tss</span><span class="p">(</span><span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span> <span class="n">max_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">500000</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">V2G</span></code>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3183,7 +3362,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" cl
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3224,7 +3403,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" cl
     <tbody>
         <tr>
 <td><code>V2G</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3236,11 +3415,8 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" cl
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">179</span>
-<span class="normal">180</span>
-<span class="normal">181</span>
-<span class="normal">182</span>
+            <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">182</span>
 <span class="normal">183</span>
 <span class="normal">184</span>
 <span class="normal">185</span>
@@ -3282,7 +3458,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" cl
 <span class="normal">221</span>
 <span class="normal">222</span>
 <span class="normal">223</span>
-<span class="normal">224</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_distance_to_tss</span><span class="p">(</span>
+<span class="normal">224</span>
+<span class="normal">225</span>
+<span class="normal">226</span>
+<span class="normal">227</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_distance_to_tss</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span>
     <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span>
     <span class="n">max_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">500_000</span><span class="p">,</span>
@@ -3339,11 +3518,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss" cl
 
 
 
-
-<h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_most_severe_vep_v2g</span><span class="p">(</span><span class="n">vep_consequences</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">V2G</span></code>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3381,7 +3559,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3408,7 +3586,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g
     <tbody>
         <tr>
 <td><code>V2G</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3420,11 +3598,8 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 97</span>
-<span class="normal"> 98</span>
-<span class="normal"> 99</span>
-<span class="normal">100</span>
+            <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">100</span>
 <span class="normal">101</span>
 <span class="normal">102</span>
 <span class="normal">103</span>
@@ -3461,7 +3636,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g
 <span class="normal">134</span>
 <span class="normal">135</span>
 <span class="normal">136</span>
-<span class="normal">137</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_most_severe_vep_v2g</span><span class="p">(</span>
+<span class="normal">137</span>
+<span class="normal">138</span>
+<span class="normal">139</span>
+<span class="normal">140</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_most_severe_vep_v2g</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span>
     <span class="n">vep_consequences</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
     <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span>
@@ -3513,11 +3691,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g
 
 
 
-
-<h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_plof_v2g</span><span class="p">(</span><span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">V2G</span></code>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3541,7 +3718,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="do
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3568,7 +3745,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="do
     <tbody>
         <tr>
 <td><code>V2G</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3580,11 +3757,8 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="do
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">139</span>
-<span class="normal">140</span>
-<span class="normal">141</span>
-<span class="normal">142</span>
+            <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">142</span>
 <span class="normal">143</span>
 <span class="normal">144</span>
 <span class="normal">145</span>
@@ -3619,7 +3793,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="do
 <span class="normal">174</span>
 <span class="normal">175</span>
 <span class="normal">176</span>
-<span class="normal">177</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_plof_v2g</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">V2G</span><span class="p">:</span>
+<span class="normal">177</span>
+<span class="normal">178</span>
+<span class="normal">179</span>
+<span class="normal">180</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_plof_v2g</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">V2G</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Creates a dataset with variant to gene assignments with a flag indicating if the variant is predicted to be a loss-of-function variant by the LOFTEE algorithm.</span>
 
 <span class="sd">    Optionally the trancript consequences can be reduced to the universe of a gene index.</span>
@@ -3669,15 +3846,14 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g" class="do
 
 
 
-
-<h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_annotation.VariantAnnotation.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3709,15 +3885,15 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_schema" class="doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">25</span>
-<span class="normal">26</span>
-<span class="normal">27</span>
-<span class="normal">28</span>
+            <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">28</span>
 <span class="normal">29</span>
 <span class="normal">30</span>
 <span class="normal">31</span>
-<span class="normal">32</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">32</span>
+<span class="normal">33</span>
+<span class="normal">34</span>
+<span class="normal">35</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">get_schema</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">VariantAnnotation</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">StructType</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Provides the schema for the VariantAnnotation dataset.</span>
 
@@ -3736,11 +3912,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_schema" class="doc
 
 
 
-
-<h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_transcript_consequence_df</span><span class="p">(</span><span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3764,7 +3939,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_transcript_conseque
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a> | None</code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a> | None</code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3803,11 +3978,8 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_transcript_conseque
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">67</span>
-<span class="normal">68</span>
-<span class="normal">69</span>
-<span class="normal">70</span>
+            <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">70</span>
 <span class="normal">71</span>
 <span class="normal">72</span>
 <span class="normal">73</span>
@@ -3832,7 +4004,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_transcript_conseque
 <span class="normal">92</span>
 <span class="normal">93</span>
 <span class="normal">94</span>
-<span class="normal">95</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_transcript_consequence_df</span><span class="p">(</span>
+<span class="normal">95</span>
+<span class="normal">96</span>
+<span class="normal">97</span>
+<span class="normal">98</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_transcript_consequence_df</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Dataframe of exploded transcript consequences.</span>
@@ -3872,11 +4047,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.get_transcript_conseque
 
 
 
-
-<h3 id="otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_annotation.VariantAnnotation.max_maf" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">max_maf</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
 
-<a href="#otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_annotation.VariantAnnotation.max_maf" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3908,11 +4082,8 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="doc doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_annotation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">34</span>
-<span class="normal">35</span>
-<span class="normal">36</span>
-<span class="normal">37</span>
+            <summary>Source code in <code>src/gentropy/dataset/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">37</span>
 <span class="normal">38</span>
 <span class="normal">39</span>
 <span class="normal">40</span>
@@ -3922,7 +4093,10 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="doc doc
 <span class="normal">44</span>
 <span class="normal">45</span>
 <span class="normal">46</span>
-<span class="normal">47</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">max_maf</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="normal">47</span>
+<span class="normal">48</span>
+<span class="normal">49</span>
+<span class="normal">50</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">max_maf</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Maximum minor allele frequency accross all populations.</span>
 
 <span class="sd">    Returns:</span>
@@ -3948,6 +4122,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="doc doc
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- variantId: string (nullable = false)
@@ -4007,7 +4182,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="doc doc
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -4074,7 +4249,7 @@ <h3 id="otg.dataset.variant_annotation.VariantAnnotation.max_maf" class="doc doc
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/dataset/variant_index/index.html b/python_api/datasets/variant_index/index.html
similarity index 84%
rename from python_api/dataset/variant_index/index.html
rename to python_api/datasets/variant_index/index.html
index 6ac736a86..74349514c 100644
--- a/python_api/dataset/variant_index/index.html
+++ b/python_api/datasets/variant_index/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Variant index - Open Targets Genetics</title>
+        <title>Variant index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.variant_index.VariantIndex" class="md-skip">
+        <a href="#gentropy.dataset.variant_index.VariantIndex" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
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+      
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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           <ul class="md-nav__list" data-md-scrollfix>
             
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         <li class="md-nav__item">
-  <a href="#otg.dataset.variant_index.VariantIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_index.VariantIndex" class="md-nav__link">
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       VariantIndex
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@@ -939,18 +1090,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_index.VariantIndex.from_variant_annotation" class="md-nav__link">
     <span class="md-ellipsis">
-      from_variant_annotation()
+      from_variant_annotation
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_index.VariantIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_index.VariantIndex.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -1024,32 +1175,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1069,12 +1220,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1085,14 +1236,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1105,7 +1256,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1143,12 +1315,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1159,14 +1331,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1179,7 +1351,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1217,12 +1410,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1233,14 +1426,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1253,7 +1446,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1274,7 +1467,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1312,12 +1505,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1328,14 +1521,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1348,7 +1541,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,7 +1562,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1390,7 +1583,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1411,7 +1604,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1449,12 +1642,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1465,14 +1658,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1485,7 +1678,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,7 +1699,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1527,7 +1720,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1548,7 +1741,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1586,12 +1779,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1602,14 +1795,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1622,7 +1815,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1643,7 +1836,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1665,80 +1858,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1763,32 +1882,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1799,11 +1918,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1820,11 +1939,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1841,11 +1960,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1862,11 +1981,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1883,11 +2002,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1904,11 +2023,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1934,12 +2053,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1950,14 +2069,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1970,7 +2089,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1991,7 +2110,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2012,7 +2131,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2033,7 +2152,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2079,32 +2198,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2115,11 +2234,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2136,11 +2255,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2157,11 +2276,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2178,11 +2297,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2199,11 +2318,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2220,11 +2339,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2241,11 +2360,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2262,11 +2381,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2283,11 +2402,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2304,11 +2423,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2325,11 +2444,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2346,11 +2465,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2367,11 +2486,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2388,11 +2507,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2442,7 +2624,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.variant_index.VariantIndex" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_index.VariantIndex" class="md-nav__link">
     <span class="md-ellipsis">
       VariantIndex
     </span>
@@ -2452,18 +2634,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_index.VariantIndex.from_variant_annotation" class="md-nav__link">
     <span class="md-ellipsis">
-      from_variant_annotation()
+      from_variant_annotation
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.variant_index.VariantIndex.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.variant_index.VariantIndex.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -2507,28 +2689,27 @@ <h1>Variant index</h1>
 
 
 
-
-<h2 id="otg.dataset.variant_index.VariantIndex" class="doc doc-heading">
-          <code>otg.dataset.variant_index.VariantIndex</code>
+<h2 id="gentropy.dataset.variant_index.VariantIndex" class="doc doc-heading">
+          <code>gentropy.dataset.variant_index.VariantIndex</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.variant_index.VariantIndex" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.variant_index.VariantIndex" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Variant index dataset.</p>
 <p>Variant index dataset is the result of intersecting the variant annotation dataset with the variants with V2D available information.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/variant_index.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/variant_index.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">20</span>
 <span class="normal">21</span>
 <span class="normal">22</span>
@@ -2666,15 +2847,14 @@ <h2 id="otg.dataset.variant_index.VariantIndex" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_index.VariantIndex.from_variant_annotation" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_variant_annotation</span><span class="p">(</span><span class="n">variant_annotation</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span> <span class="n">study_locus</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">VariantIndex</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_index.VariantIndex.from_variant_annotation" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2697,7 +2877,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="d
         <tr>
           <td><code>variant_annotation</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.variant_annotation.VariantAnnotation" href="../variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.variant_annotation.VariantAnnotation" href="../variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2711,7 +2891,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="d
         <tr>
           <td><code>study_locus</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2738,7 +2918,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="d
     <tbody>
         <tr>
 <td><code>VariantIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.variant_index.VariantIndex" href="#otg.dataset.variant_index.VariantIndex">VariantIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.variant_index.VariantIndex" href="#gentropy.dataset.variant_index.VariantIndex">VariantIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2750,7 +2930,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="d
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/variant_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">36</span>
 <span class="normal">37</span>
 <span class="normal">38</span>
@@ -2847,15 +3027,14 @@ <h3 id="otg.dataset.variant_index.VariantIndex.from_variant_annotation" class="d
 
 
 
-
-<h3 id="otg.dataset.variant_index.VariantIndex.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.variant_index.VariantIndex.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.variant_index.VariantIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.variant_index.VariantIndex.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2887,7 +3066,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.get_schema" class="doc doc-headin
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/variant_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/variant_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">27</span>
 <span class="normal">28</span>
 <span class="normal">29</span>
@@ -2915,6 +3094,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.get_schema" class="doc doc-headin
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- variantId: string (nullable = false)
@@ -2965,7 +3145,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.get_schema" class="doc doc-headin
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3032,7 +3212,7 @@ <h3 id="otg.dataset.variant_index.VariantIndex.get_schema" class="doc doc-headin
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/dataset/variant_to_gene/index.html b/python_api/datasets/variant_to_gene/index.html
similarity index 83%
rename from python_api/dataset/variant_to_gene/index.html
rename to python_api/datasets/variant_to_gene/index.html
index 29bbec5a3..89902b8a0 100644
--- a/python_api/dataset/variant_to_gene/index.html
+++ b/python_api/datasets/variant_to_gene/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../variant_index/">
       
       
-        <link rel="next" href="../../datasource/_datasource/">
+        <link rel="next" href="../../datasources/_datasources/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Variant-to-gene - Open Targets Genetics</title>
+        <title>Variant-to-gene - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.dataset.v2g.V2G" class="md-skip">
+        <a href="#gentropy.dataset.v2g.V2G" class="md-skip">
           Skip to content
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@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
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+  
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+        
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
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+    </li>
+  
+
+      
+        
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@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
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-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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@@ -414,6 +448,123 @@
         
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
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+    </li>
+  
+
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+                
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
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+  
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+        </nav>
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+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+    </li>
+  
+
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+      
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+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -578,32 +729,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_dataset/" class="md-nav__link ">
+            <a href="../_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -950,7 +1101,7 @@
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         <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G" class="md-nav__link">
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       V2G
     </span>
@@ -960,27 +1111,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G.extract_distance_tss_minimum" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G.extract_distance_tss_minimum" class="md-nav__link">
     <span class="md-ellipsis">
-      extract_distance_tss_minimum()
+      extract_distance_tss_minimum
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G.filter_by_genes" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G.filter_by_genes" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_by_genes()
+      filter_by_genes
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -1033,32 +1184,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
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-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
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-    Datasource
+    Datasources
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
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@@ -1078,12 +1229,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
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-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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@@ -1094,14 +1245,14 @@
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1114,7 +1265,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1152,12 +1324,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1168,14 +1340,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1188,7 +1360,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1226,12 +1419,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1242,14 +1435,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1262,7 +1455,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1283,7 +1476,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1321,12 +1514,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1337,14 +1530,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1357,7 +1550,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1378,7 +1571,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1399,7 +1592,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1420,7 +1613,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1458,12 +1651,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1474,14 +1667,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1494,7 +1687,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1515,7 +1708,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1536,7 +1729,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1557,7 +1750,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1595,12 +1788,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1611,14 +1804,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1631,7 +1824,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1652,7 +1845,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1674,80 +1867,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1772,32 +1891,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1808,11 +1927,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1829,11 +1948,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1850,11 +1969,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1871,11 +1990,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1892,11 +2011,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1913,11 +2032,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1943,12 +2062,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1959,14 +2078,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1979,7 +2098,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2000,7 +2119,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2021,7 +2140,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2042,7 +2161,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2088,32 +2207,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2124,11 +2243,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2145,11 +2264,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2166,11 +2285,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2187,11 +2306,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2208,11 +2327,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2229,11 +2348,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2250,11 +2369,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2271,11 +2390,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2292,11 +2411,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2313,11 +2432,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2334,11 +2453,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2355,11 +2474,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2376,11 +2495,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2397,11 +2516,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2451,7 +2633,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G" class="md-nav__link">
     <span class="md-ellipsis">
       V2G
     </span>
@@ -2461,27 +2643,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G.extract_distance_tss_minimum" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G.extract_distance_tss_minimum" class="md-nav__link">
     <span class="md-ellipsis">
-      extract_distance_tss_minimum()
+      extract_distance_tss_minimum
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G.filter_by_genes" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G.filter_by_genes" class="md-nav__link">
     <span class="md-ellipsis">
-      filter_by_genes()
+      filter_by_genes
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.dataset.v2g.V2G.get_schema" class="md-nav__link">
+  <a href="#gentropy.dataset.v2g.V2G.get_schema" class="md-nav__link">
     <span class="md-ellipsis">
-      get_schema()
+      get_schema
     </span>
   </a>
   
@@ -2525,28 +2707,27 @@ <h1>Variant-to-gene</h1>
 
 
 
-
-<h2 id="otg.dataset.v2g.V2G" class="doc doc-heading">
-          <code>otg.dataset.v2g.V2G</code>
+<h2 id="gentropy.dataset.v2g.V2G" class="doc doc-heading">
+          <code>gentropy.dataset.v2g.V2G</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.dataset.v2g.V2G" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.dataset.v2g.V2G" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.dataset.Dataset" href="../_dataset/#otg.dataset.dataset.Dataset">Dataset</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.dataset.Dataset" href="../_datasets/#gentropy.dataset.dataset.Dataset">Dataset</a></code></p>
 
   
       <p>Variant-to-gene (V2G) evidence dataset.</p>
 <p>A variant-to-gene (V2G) evidence is understood as any piece of evidence that supports the association of a variant with a likely causal gene. The evidence can sometimes be context-specific and refer to specific <code>biofeatures</code> (e.g. cell types)</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/dataset/v2g.py</code></summary>
+              <summary>Source code in <code>src/gentropy/dataset/v2g.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">18</span>
 <span class="normal">19</span>
 <span class="normal">20</span>
@@ -2634,11 +2815,10 @@ <h2 id="otg.dataset.v2g.V2G" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.v2g.V2G.extract_distance_tss_minimum" class="doc doc-heading">
+<h3 id="gentropy.dataset.v2g.V2G.extract_distance_tss_minimum" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">extract_distance_tss_minimum</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
 
-<a href="#otg.dataset.v2g.V2G.extract_distance_tss_minimum" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.v2g.V2G.extract_distance_tss_minimum" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2646,7 +2826,7 @@ <h3 id="otg.dataset.v2g.V2G.extract_distance_tss_minimum" class="doc doc-heading
       <p>Extract minimum distance to TSS.</p>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/v2g.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/v2g.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">46</span>
 <span class="normal">47</span>
 <span class="normal">48</span>
@@ -2669,11 +2849,10 @@ <h3 id="otg.dataset.v2g.V2G.extract_distance_tss_minimum" class="doc doc-heading
 
 
 
-
-<h3 id="otg.dataset.v2g.V2G.filter_by_genes" class="doc doc-heading">
+<h3 id="gentropy.dataset.v2g.V2G.filter_by_genes" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">filter_by_genes</span><span class="p">(</span><span class="n">genes</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">V2G</span></code>
 
-<a href="#otg.dataset.v2g.V2G.filter_by_genes" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.v2g.V2G.filter_by_genes" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2696,7 +2875,7 @@ <h3 id="otg.dataset.v2g.V2G.filter_by_genes" class="doc doc-heading">
         <tr>
           <td><code>genes</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2723,7 +2902,7 @@ <h3 id="otg.dataset.v2g.V2G.filter_by_genes" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>V2G</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2735,7 +2914,7 @@ <h3 id="otg.dataset.v2g.V2G.filter_by_genes" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/v2g.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/v2g.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">34</span>
 <span class="normal">35</span>
 <span class="normal">36</span>
@@ -2768,15 +2947,14 @@ <h3 id="otg.dataset.v2g.V2G.filter_by_genes" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.dataset.v2g.V2G.get_schema" class="doc doc-heading">
+<h3 id="gentropy.dataset.v2g.V2G.get_schema" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_schema</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StructType</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.dataset.v2g.V2G.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.dataset.v2g.V2G.get_schema" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2808,7 +2986,7 @@ <h3 id="otg.dataset.v2g.V2G.get_schema" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/dataset/v2g.py</code></summary>
+            <summary>Source code in <code>src/gentropy/dataset/v2g.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">25</span>
 <span class="normal">26</span>
 <span class="normal">27</span>
@@ -2836,6 +3014,7 @@ <h3 id="otg.dataset.v2g.V2G.get_schema" class="doc doc-heading">
 
   </div>
 
+
 </div><h2 id="schema">Schema<a class="headerlink" href="#schema" title="Permanent link">&para;</a></h2>
 <div class="highlight"><pre><span></span><code>root
  |-- geneId: string (nullable = false)
@@ -2873,7 +3052,7 @@ <h3 id="otg.dataset.v2g.V2G.get_schema" class="doc doc-heading">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2940,7 +3119,7 @@ <h3 id="otg.dataset.v2g.V2G.get_schema" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/ukbiobank/study_index/index.html b/python_api/datasource/ukbiobank/study_index/index.html
deleted file mode 100644
index f54c1403c..000000000
--- a/python_api/datasource/ukbiobank/study_index/index.html
+++ /dev/null
@@ -1,3075 +0,0 @@
-
-<!doctype html>
-<html lang="en" class="no-js">
-  <head>
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-      <meta charset="utf-8">
-      <meta name="viewport" content="width=device-width,initial-scale=1">
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
-    
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-      
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-  <h1>Study Index</h1>
-
-<div class="doc doc-object doc-class">
-
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-
-
-<h2 id="otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex" class="doc doc-heading">
-          <code>otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex</code>
-
-
-<a href="#otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex" class="headerlink" title="Permanent link">&para;</a></h2>
-
-
-  <div class="doc doc-contents first">
-
-  
-      <p>Study index dataset from UKBiobank.</p>
-<p>The following information is extracted:</p>
-<ul>
-<li>studyId</li>
-<li>pubmedId</li>
-<li>publicationDate</li>
-<li>publicationJournal</li>
-<li>publicationTitle</li>
-<li>publicationFirstAuthor</li>
-<li>traitFromSource</li>
-<li>ancestry_discoverySamples</li>
-<li>ancestry_replicationSamples</li>
-<li>initialSampleSize</li>
-<li>nCases</li>
-<li>replicationSamples</li>
-</ul>
-<p>Some fields are populated as constants, such as projectID, studyType, and initial sample size.</p>
-
-            <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/ukbiobank/study_index.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 14</span>
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-<span class="normal">110</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">UKBiobankStudyIndex</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Study index dataset from UKBiobank.</span>
-
-<span class="sd">    The following information is extracted:</span>
-
-<span class="sd">    - studyId</span>
-<span class="sd">    - pubmedId</span>
-<span class="sd">    - publicationDate</span>
-<span class="sd">    - publicationJournal</span>
-<span class="sd">    - publicationTitle</span>
-<span class="sd">    - publicationFirstAuthor</span>
-<span class="sd">    - traitFromSource</span>
-<span class="sd">    - ancestry_discoverySamples</span>
-<span class="sd">    - ancestry_replicationSamples</span>
-<span class="sd">    - initialSampleSize</span>
-<span class="sd">    - nCases</span>
-<span class="sd">    - replicationSamples</span>
-
-<span class="sd">    Some fields are populated as constants, such as projectID, studyType, and initial sample size.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="nd">@classmethod</span>
-    <span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
-        <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">UKBiobankStudyIndex</span><span class="p">],</span>
-        <span class="n">ukbiobank_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;This function ingests study level metadata from UKBiobank.</span>
-
-<span class="sd">        The University of Michigan SAIGE analysis (N=1281) utilized PheCode derived phenotypes and a novel method that ensures accurate P values, even with highly unbalanced case-control ratios (Zhou et al., 2018).</span>
-
-<span class="sd">        The Neale lab Round 2 study (N=2139) used GWAS with imputed genotypes from HRC to analyze all data fields in UK Biobank, excluding ICD-10 related traits to reduce overlap with the SAIGE results.</span>
-
-<span class="sd">        Args:</span>
-<span class="sd">            ukbiobank_studies (DataFrame): UKBiobank study manifest file loaded in spark session.</span>
-
-<span class="sd">        Returns:</span>
-<span class="sd">            StudyIndex: Annotated UKBiobank study table.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">StudyIndex</span><span class="p">(</span>
-            <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
-                <span class="n">ukbiobank_studies</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;UKBiobank&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;projectId&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;gwas&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;trait&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span>
-                    <span class="c1"># Make publication and ancestry schema columns.</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span> <span class="s2">&quot;30104761&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                        <span class="s2">&quot;pubmedId&quot;</span>
-                    <span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span>
-                        <span class="s2">&quot;Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies&quot;</span><span class="p">,</span>
-                    <span class="p">)</span>
-                    <span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span>
-                    <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationTitle&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span> <span class="s2">&quot;Wei Zhou&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                        <span class="s2">&quot;publicationFirstAuthor&quot;</span>
-                    <span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;NEALE2_&quot;</span><span class="p">),</span> <span class="s2">&quot;2018-08-01&quot;</span><span class="p">)</span>
-                    <span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="s2">&quot;2018-10-24&quot;</span><span class="p">)</span>
-                    <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationDate&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span> <span class="s2">&quot;Nature Genetics&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                        <span class="s2">&quot;publicationJournal&quot;</span>
-                    <span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_total&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;string&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;initialSampleSize&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_cases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_total&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;European=&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_total&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                                <span class="s2">&quot;ancestry&quot;</span>
-                            <span class="p">),</span>
-                        <span class="p">)</span>
-                    <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;in_path&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
-                <span class="p">)</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                    <span class="s2">&quot;traitFromSource&quot;</span><span class="p">,</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">contains</span><span class="p">(</span><span class="s2">&quot;:&quot;</span><span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">initcap</span><span class="p">(</span>
-                                <span class="n">f</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span> <span class="s2">&quot;: &quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-                            <span class="p">),</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot; | &quot;</span><span class="p">),</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">lower</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span> <span class="s2">&quot;: &quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">0</span><span class="p">)),</span>
-                        <span class="p">),</span>
-                    <span class="p">)</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">)),</span>
-                <span class="p">)</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                    <span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">,</span>
-                    <span class="n">StudyIndex</span><span class="o">.</span><span class="n">aggregate_and_map_ancestries</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">)),</span>
-                <span class="p">)</span>
-            <span class="p">),</span>
-            <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndex</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
-        <span class="p">)</span>
-</code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
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-
-<div class="doc doc-object doc-function">
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-<h3 id="otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex.from_source" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">ukbiobank_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span></code>
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
-  </span>
-
-<a href="#otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
-
-
-  <div class="doc doc-contents ">
-  
-      <p>This function ingests study level metadata from UKBiobank.</p>
-<p>The University of Michigan SAIGE analysis (N=1281) utilized PheCode derived phenotypes and a novel method that ensures accurate P values, even with highly unbalanced case-control ratios (Zhou et al., 2018).</p>
-<p>The Neale lab Round 2 study (N=2139) used GWAS with imputed genotypes from HRC to analyze all data fields in UK Biobank, excluding ICD-10 related traits to reduce overlap with the SAIGE results.</p>
-
-
-
-  <p><strong>Parameters:</strong></p>
-  <table>
-    <thead>
-      <tr>
-        <th>Name</th>
-        <th>Type</th>
-        <th>Description</th>
-        <th>Default</th>
-      </tr>
-    </thead>
-    <tbody>
-        <tr>
-          <td><code>ukbiobank_studies</code></td>
-          <td>
-                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>UKBiobank study manifest file loaded in spark session.</p>
-            </div>
-          </td>
-          <td>
-              <em>required</em>
-          </td>
-        </tr>
-    </tbody>
-  </table>
-
-
-
-  <p><strong>Returns:</strong></p>
-  <table>
-    <thead>
-      <tr>
-<th>Name</th>        <th>Type</th>
-        <th>Description</th>
-      </tr>
-    </thead>
-    <tbody>
-        <tr>
-<td><code>StudyIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../../../dataset/study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Annotated UKBiobank study table.</p>
-            </div>
-          </td>
-        </tr>
-    </tbody>
-  </table>
-
-          <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/ukbiobank/study_index.py</code></summary>
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-<span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
-    <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">UKBiobankStudyIndex</span><span class="p">],</span>
-    <span class="n">ukbiobank_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
-<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;This function ingests study level metadata from UKBiobank.</span>
-
-<span class="sd">    The University of Michigan SAIGE analysis (N=1281) utilized PheCode derived phenotypes and a novel method that ensures accurate P values, even with highly unbalanced case-control ratios (Zhou et al., 2018).</span>
-
-<span class="sd">    The Neale lab Round 2 study (N=2139) used GWAS with imputed genotypes from HRC to analyze all data fields in UK Biobank, excluding ICD-10 related traits to reduce overlap with the SAIGE results.</span>
-
-<span class="sd">    Args:</span>
-<span class="sd">        ukbiobank_studies (DataFrame): UKBiobank study manifest file loaded in spark session.</span>
-
-<span class="sd">    Returns:</span>
-<span class="sd">        StudyIndex: Annotated UKBiobank study table.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">StudyIndex</span><span class="p">(</span>
-        <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
-            <span class="n">ukbiobank_studies</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;UKBiobank&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;projectId&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;gwas&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;trait&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span>
-                <span class="c1"># Make publication and ancestry schema columns.</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span> <span class="s2">&quot;30104761&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                    <span class="s2">&quot;pubmedId&quot;</span>
-                <span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span>
-                    <span class="s2">&quot;Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies&quot;</span><span class="p">,</span>
-                <span class="p">)</span>
-                <span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span>
-                <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationTitle&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span> <span class="s2">&quot;Wei Zhou&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                    <span class="s2">&quot;publicationFirstAuthor&quot;</span>
-                <span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;NEALE2_&quot;</span><span class="p">),</span> <span class="s2">&quot;2018-08-01&quot;</span><span class="p">)</span>
-                <span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="s2">&quot;2018-10-24&quot;</span><span class="p">)</span>
-                <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationDate&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;code&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;SAIGE_&quot;</span><span class="p">),</span> <span class="s2">&quot;Nature Genetics&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                    <span class="s2">&quot;publicationJournal&quot;</span>
-                <span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_total&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;string&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;initialSampleSize&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_cases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_total&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;European=&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;n_total&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                            <span class="s2">&quot;ancestry&quot;</span>
-                        <span class="p">),</span>
-                    <span class="p">)</span>
-                <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;in_path&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
-            <span class="p">)</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="s2">&quot;traitFromSource&quot;</span><span class="p">,</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">contains</span><span class="p">(</span><span class="s2">&quot;:&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">initcap</span><span class="p">(</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span> <span class="s2">&quot;: &quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
-                        <span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot; | &quot;</span><span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">lower</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span> <span class="s2">&quot;: &quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">0</span><span class="p">)),</span>
-                    <span class="p">),</span>
-                <span class="p">)</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">)),</span>
-            <span class="p">)</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">,</span>
-                <span class="n">StudyIndex</span><span class="o">.</span><span class="n">aggregate_and_map_ancestries</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">)),</span>
-            <span class="p">)</span>
-        <span class="p">),</span>
-        <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndex</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
-    <span class="p">)</span>
-</code></pre></div></td></tr></table></div>
-          </details>
-  </div>
-
-</div>
-
-
-
-  </div>
-
-  </div>
-
-</div>
-<hr />
-<div class="md-source-file">
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
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-          <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 2A10 10 0 0 0 2 12c0 4.42 2.87 8.17 6.84 9.5.5.08.66-.23.66-.5v-1.69c-2.77.6-3.36-1.34-3.36-1.34-.46-1.16-1.11-1.47-1.11-1.47-.91-.62.07-.6.07-.6 1 .07 1.53 1.03 1.53 1.03.87 1.52 2.34 1.07 2.91.83.09-.65.35-1.09.63-1.34-2.22-.25-4.55-1.11-4.55-4.92 0-1.11.38-2 1.03-2.71-.1-.25-.45-1.29.1-2.64 0 0 .84-.27 2.75 1.02.79-.22 1.65-.33 2.5-.33.85 0 1.71.11 2.5.33 1.91-1.29 2.75-1.02 2.75-1.02.55 1.35.2 2.39.1 2.64.65.71 1.03 1.6 1.03 2.71 0 3.82-2.34 4.66-4.57 4.91.36.31.69.92.69 1.85V21c0 .27.16.59.67.5C19.14 20.16 22 16.42 22 12A10 10 0 0 0 12 2Z"/></svg>
-        </span>
-        <span class="label"> Contributors </span>
-      </li>
-      <li class="contributors-holder">
-        <ul class="contributors" data-bi-name="contributors"><li>
-            <a
-              href="https://github.com/d0choa"
-              title="d0choa"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
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-          </li></ul>
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-  
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\ No newline at end of file
diff --git a/python_api/datasource/_datasource/index.html b/python_api/datasources/_datasources/index.html
similarity index 76%
rename from python_api/datasource/_datasource/index.html
rename to python_api/datasources/_datasources/index.html
index 0abdcd241..c17c116e7 100644
--- a/python_api/datasource/_datasource/index.html
+++ b/python_api/datasources/_datasources/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../dataset/variant_to_gene/">
+        <link rel="prev" href="../../datasets/variant_to_gene/">
       
       
-        <link rel="next" href="../eqtl_catalogue/study_index/">
+        <link rel="next" href="../eqtl_catalogue/_eqtl_catalogue/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Data Source - Open Targets Genetics</title>
+        <title>Data Sources - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#data-source" class="md-skip">
+        <a href="#data-sources" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Data Source
+              Data Sources
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
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+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,7 +1097,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
@@ -955,23 +1106,23 @@
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1234,7 +1427,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1250,14 +1443,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1371,7 +1564,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1387,14 +1580,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1508,7 +1701,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1524,14 +1717,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1587,80 +1780,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,32 +1804,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1742,11 +1861,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1763,11 +1882,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1903,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1924,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1826,11 +1945,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1856,12 +1975,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1872,14 +1991,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1892,7 +2011,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1913,7 +2032,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1934,7 +2053,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1955,7 +2074,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2121,11 +2240,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2142,11 +2261,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2163,11 +2282,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2184,11 +2303,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2205,11 +2324,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2226,11 +2345,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2247,11 +2366,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2268,11 +2387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2289,11 +2408,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2310,11 +2429,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2359,6 +2541,77 @@
     
   
   
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gwas-study-sources" class="md-nav__link">
+    <span class="md-ellipsis">
+      GWAS study sources
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#molecular-qtls" class="md-nav__link">
+    <span class="md-ellipsis">
+      Molecular QTLs
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#interaction-interval-based-experiments" class="md-nav__link">
+    <span class="md-ellipsis">
+      Interaction / Interval-based Experiments
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#variant-annotationvalidation" class="md-nav__link">
+    <span class="md-ellipsis">
+      Variant annotation/validation
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#linkage-desiquilibrium" class="md-nav__link">
+    <span class="md-ellipsis">
+      Linkage desiquilibrium
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#locus-to-gene-gold-standard" class="md-nav__link">
+    <span class="md-ellipsis">
+      Locus-to-gene gold standard
+    </span>
+  </a>
+  
+</li>
+      
+        <li class="md-nav__item">
+  <a href="#gene-annotation" class="md-nav__link">
+    <span class="md-ellipsis">
+      Gene annotation
+    </span>
+  </a>
+  
+</li>
+      
+    </ul>
+  
 </nav>
                   </div>
                 </div>
@@ -2375,8 +2628,38 @@
   
 
 
-<h1 id="data-source">Data Source<a class="headerlink" href="#data-source" title="Permanent link">&para;</a></h1>
-<p>TBC</p>
+<h1 id="data-sources">Data Sources<a class="headerlink" href="#data-sources" title="Permanent link">&para;</a></h1>
+<p>This section contains information about the data source harmonisation tools available in Open Targets Gentropy.</p>
+<h2 id="gwas-study-sources">GWAS study sources<a class="headerlink" href="#gwas-study-sources" title="Permanent link">&para;</a></h2>
+<ol>
+<li><a href="../gwas_catalog/_gwas_catalog/">GWAS Catalog</a> (with or without full summary statistics)</li>
+<li><a href="../finngen/_finngen/">FinnGen</a></li>
+</ol>
+<h2 id="molecular-qtls">Molecular QTLs<a class="headerlink" href="#molecular-qtls" title="Permanent link">&para;</a></h2>
+<ol>
+<li><a href="../eqtl_catalogue/_eqtl_catalogue/">GTEx (eQTL catalogue)</a></li>
+</ol>
+<h2 id="interaction-interval-based-experiments">Interaction / Interval-based Experiments<a class="headerlink" href="#interaction-interval-based-experiments" title="Permanent link">&para;</a></h2>
+<ol>
+<li><a href="../intervals/_intervals/">Intervals</a>-based datasets, informing about the relationships between genetic elements and their functional implications.</li>
+</ol>
+<h2 id="variant-annotationvalidation">Variant annotation/validation<a class="headerlink" href="#variant-annotationvalidation" title="Permanent link">&para;</a></h2>
+<ol>
+<li><a href="../gnomad/_gnomad/">GnomAD</a> v4.0</li>
+<li>GWAS catalog harmonisation pipeline <a href="https://www.ebi.ac.uk/gwas/docs/methods/summary-statistics#_harmonised_summary_statistics_data">more info</a></li>
+</ol>
+<h2 id="linkage-desiquilibrium">Linkage desiquilibrium<a class="headerlink" href="#linkage-desiquilibrium" title="Permanent link">&para;</a></h2>
+<ol>
+<li><a href="../gnomad/_gnomad/">GnomAD</a> v2.1.1 LD matrixes (7 ancestries)</li>
+</ol>
+<h2 id="locus-to-gene-gold-standard">Locus-to-gene gold standard<a class="headerlink" href="#locus-to-gene-gold-standard" title="Permanent link">&para;</a></h2>
+<ol>
+<li><a href="../open_targets/l2g_gold_standard/">Open Targets training set</a></li>
+</ol>
+<h2 id="gene-annotation">Gene annotation<a class="headerlink" href="#gene-annotation" title="Permanent link">&para;</a></h2>
+<ol>
+<li><a href="../open_targets/target/">Open Targets Platform Target Dataset</a> (derived from Ensembl)</li>
+</ol>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2392,14 +2675,14 @@ <h1 id="data-source">Data Source<a class="headerlink" href="#data-source" title=
         <span class="icon twemoji">
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-16T08:22:37+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-16</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
        
       <li>
         <span class="icon twemoji">
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2466,7 +2749,7 @@ <h1 id="data-source">Data Source<a class="headerlink" href="#data-source" title=
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/ukbiobank/_ukbiobank/index.html b/python_api/datasources/eqtl_catalogue/_eqtl_catalogue/index.html
similarity index 81%
rename from python_api/datasource/ukbiobank/_ukbiobank/index.html
rename to python_api/datasources/eqtl_catalogue/_eqtl_catalogue/index.html
index eef0c302c..25d30b1c9 100644
--- a/python_api/datasource/ukbiobank/_ukbiobank/index.html
+++ b/python_api/datasources/eqtl_catalogue/_eqtl_catalogue/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../open_targets/target/">
+        <link rel="prev" href="../../_datasources/">
       
       
         <link rel="next" href="../study_index/">
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>UK Biobank - Open Targets Genetics</title>
+        <title>eQTL Catalogue - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,13 +102,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              UK Biobank
+              eQTL Catalogue
             
           </span>
         </div>
@@ -187,13 +187,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -228,7 +245,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -244,6 +261,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -304,22 +338,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
     </div>
@@ -333,11 +367,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -353,11 +387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -390,11 +424,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -409,6 +443,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -526,7 +677,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -571,32 +722,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
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-            Dataset
+            Datasets
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           <ul class="md-nav__list" data-md-scrollfix>
             
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     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -628,7 +779,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -649,7 +800,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -670,7 +821,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -691,7 +842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -712,7 +863,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -733,7 +884,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -754,7 +905,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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@@ -775,7 +926,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -796,7 +947,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -817,7 +968,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -838,7 +989,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -859,7 +1010,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -880,7 +1031,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -901,7 +1052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -941,32 +1092,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -974,6 +1125,8 @@
                 
   
   
+    
+  
   
   
     
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-    <li class="md-nav__item md-nav__item--nested">
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
       
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="./" class="md-nav__link md-nav__link--active">
               
   
   <span class="md-ellipsis">
@@ -1002,14 +1155,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1022,7 +1175,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1060,7 +1234,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1110,6 +1284,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1134,7 +1329,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1519,14 +1714,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1582,82 +1777,6 @@
 
               
             
-              
-                
-  
-  
-    
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" checked>
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="./" class="md-nav__link md-nav__link--active">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1682,32 +1801,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1718,11 +1837,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1739,11 +1858,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1760,11 +1879,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1781,11 +1900,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1802,11 +1921,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1823,11 +1942,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1853,12 +1972,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1869,14 +1988,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1889,7 +2008,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1910,7 +2029,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1931,7 +2050,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1952,7 +2071,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1998,32 +2117,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,11 +2153,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2055,11 +2174,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2076,11 +2195,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2307,11 +2426,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2370,28 +2552,14 @@
   
 
 
-  <h1>Ukbiobank</h1>
-
-<p align="center">
-  <img width="400" height="200" src="../../../../assets/imgs/UK_biobank_logo.png">
-</p>
-<style>
-  .md-typeset h1,
-  .md-content__button {
-    display: none;
-  }
-</style>
+  <h1>Eqtl catalogue</h1>
 
-<p>The UK Biobank is a large-scale biomedical database and research resource that contains a diverse range of in-depth information from 500,000 volunteers in the United Kingdom. Its genomic data comprises whole-genome sequencing for a subset of participants, along with genotyping arrays for the entire cohort. The data has been a cornerstone for numerous genome-wide association studies (GWAS) and other genetic analyses, advancing our understanding of human health and disease.</p>
-<p>Recent efforts to rapidly and systematically apply established GWAS methods to all available data fields in UK Biobank have made available large repositories of summary statistics. To leverage these data disease locus discovery, we used full summary statistics from:
-The Neale lab Round 2 (N=2139).</p>
-<ul>
-<li>These analyses applied GWAS (implemented in Hail) to all data fields using imputed genotypes from HRC as released by UK Biobank in May 2017, consisting of 337,199 individuals post-QC. Full details of the Neale lab GWAS implementation are available here. We have remove all ICD-10 related traits from the Neale data to reduce overlap with the SAIGE results.</li>
-<li>http://www.nealelab.is/uk-biobank/
-  The University of Michigan SAIGE analysis (N=1281).</li>
-<li>The SAIGE analysis uses PheCode derived phenotypes and applies a new method that "provides accurate P values even when case-control ratios are extremely unbalanced". See Zhou et al. (2018) for further details.</li>
-<li>https://pubmed.ncbi.nlm.nih.gov/30104761/</li>
-</ul>
+<p>The <a href="https://www.ebi.ac.uk/eqtl/">eQTL Catalogue</a> aims to provide uniformly processed gene expression and splicing Quantitative Trait Loci (QTLs) from all available public studies on humans.</p>
+<p>It serves as the ultimate resource of eQTLs that we use for colocalization and target prioritization.</p>
+<p>We utilize data from the following study within the eQTL Catalogue:</p>
+<ol>
+<li><strong>GTEx v8</strong>, 49 tissues</li>
+</ol>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2407,14 +2575,14 @@ <h1>Ukbiobank</h1>
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         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-16T08:22:37+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-16</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-20T09:55:14+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-20</span> </span>
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         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2433,22 +2601,6 @@ <h1>Ukbiobank</h1>
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/apps/pre-commit-ci"
-              title="pre-commit-ci[bot]"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/in/68672?v=4" alt="pre-commit-ci[bot]"
-            /></a>
-          </li><li>
-            <a
-              href="https://github.com/hlnicholls"
-              title="hlnicholls"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/53306752?v=4" alt="hlnicholls"
-            /></a>
           </li></ul>
       </li>
     </ul>
@@ -2497,7 +2649,7 @@ <h1>Ukbiobank</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/eqtl_catalogue/study_index/index.html b/python_api/datasources/eqtl_catalogue/study_index/index.html
similarity index 61%
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rename to python_api/datasources/eqtl_catalogue/study_index/index.html
index a634a7571..02f5f832b 100644
--- a/python_api/datasource/eqtl_catalogue/study_index/index.html
+++ b/python_api/datasources/eqtl_catalogue/study_index/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../_datasource/">
+        <link rel="prev" href="../_eqtl_catalogue/">
       
       
         <link rel="next" href="../summary_stats/">
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Study Index - Open Targets Genetics</title>
+        <title>Study Index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="md-skip">
+        <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
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-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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 </a>
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@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
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-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
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+  
+  
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+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
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+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
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+                <span class="md-nav__icon md-icon"></span>
+              </label>
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -946,32 +1097,32 @@
         
         
         
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
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-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
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+    Datasources
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+            <a href="../_eqtl_catalogue/" class="md-nav__link ">
               
   
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+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,105 @@
                 
   
   
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="md-nav__link">
+    <span class="md-ellipsis">
+      EqtlCatalogueStudyIndex
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="EqtlCatalogueStudyIndex">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_to_study_id" class="md-nav__link">
+    <span class="md-ellipsis">
+      add_gene_to_study_id
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source" class="md-nav__link">
+    <span class="md-ellipsis">
+      from_source
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.get_study_attribute" class="md-nav__link">
+    <span class="md-ellipsis">
+      get_study_attribute
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
   
   
     <li class="md-nav__item">
@@ -1067,7 +1317,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1083,14 +1333,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1117,6 +1367,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1141,7 +1412,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1157,14 +1428,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1236,7 +1507,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1252,14 +1523,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1373,7 +1644,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1389,14 +1660,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1510,7 +1781,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1526,14 +1797,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1589,84 +1860,10 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
+          </ul>
+        </nav>
+      
+    </li>
   
 
               
@@ -1687,32 +1884,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1723,11 +1920,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1744,11 +1941,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1765,11 +1962,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1786,11 +1983,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1807,11 +2004,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1828,11 +2025,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1858,12 +2055,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1874,14 +2071,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1894,7 +2091,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1915,7 +2112,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1936,7 +2133,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1957,7 +2154,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2003,32 +2200,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2039,11 +2236,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2060,11 +2257,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2081,11 +2278,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2102,11 +2299,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2123,11 +2320,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2144,11 +2341,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2165,11 +2362,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2186,11 +2383,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2207,11 +2404,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2228,11 +2425,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2249,11 +2446,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2270,11 +2467,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2291,11 +2488,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2312,11 +2509,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2366,7 +2626,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="md-nav__link">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="md-nav__link">
     <span class="md-ellipsis">
       EqtlCatalogueStudyIndex
     </span>
@@ -2376,18 +2636,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_id_column" class="md-nav__link">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_to_study_id" class="md-nav__link">
+    <span class="md-ellipsis">
+      add_gene_to_study_id
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      add_gene_id_column()
+      from_source
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.get_study_attribute" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      get_study_attribute
     </span>
   </a>
   
@@ -2416,18 +2685,17 @@
   
 
 
-  <h1>Eqtl catalogue</h1>
+  <h1>Study Index</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
-
-<h2 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="doc doc-heading">
-          <code>otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex</code>
+<h2 id="gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="doc doc-heading">
+          <code>gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex</code>
 
 
-<a href="#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2436,7 +2704,7 @@ <h2 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class
       <p>Study index dataset from eQTL Catalogue.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/eqtl_catalogue/study_index.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 15</span>
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@@ -2573,25 +2841,112 @@ <h2 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class
 <span class="normal">148</span>
 <span class="normal">149</span>
 <span class="normal">150</span>
-<span class="normal">151</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">EqtlCatalogueStudyIndex</span><span class="p">:</span>
+<span class="normal">151</span>
+<span class="normal">152</span>
+<span class="normal">153</span>
+<span class="normal">154</span>
+<span class="normal">155</span>
+<span class="normal">156</span>
+<span class="normal">157</span>
+<span class="normal">158</span>
+<span class="normal">159</span>
+<span class="normal">160</span>
+<span class="normal">161</span>
+<span class="normal">162</span>
+<span class="normal">163</span>
+<span class="normal">164</span>
+<span class="normal">165</span>
+<span class="normal">166</span>
+<span class="normal">167</span>
+<span class="normal">168</span>
+<span class="normal">169</span>
+<span class="normal">170</span>
+<span class="normal">171</span>
+<span class="normal">172</span>
+<span class="normal">173</span>
+<span class="normal">174</span>
+<span class="normal">175</span>
+<span class="normal">176</span>
+<span class="normal">177</span>
+<span class="normal">178</span>
+<span class="normal">179</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">EqtlCatalogueStudyIndex</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study index dataset from eQTL Catalogue.&quot;&quot;&quot;</span>
 
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">_all_attributes</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">List</span><span class="p">[</span><span class="n">Column</span><span class="p">]:</span>
+    <span class="n">study_config</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s2">&quot;GTEx_V8&quot;</span><span class="p">:</span> <span class="p">{</span>
+            <span class="s2">&quot;nSamples&quot;</span><span class="p">:</span> <span class="mi">838</span><span class="p">,</span>
+            <span class="s2">&quot;initialSampleSize&quot;</span><span class="p">:</span> <span class="s2">&quot;838 (281 females and 557 males)&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;discoverySamples&quot;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="p">{</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">:</span> <span class="mi">715</span><span class="p">,</span> <span class="s2">&quot;ancestry&quot;</span><span class="p">:</span> <span class="s2">&quot;European American&quot;</span><span class="p">},</span>
+                <span class="p">{</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">:</span> <span class="mi">103</span><span class="p">,</span> <span class="s2">&quot;ancestry&quot;</span><span class="p">:</span> <span class="s2">&quot;African American&quot;</span><span class="p">},</span>
+                <span class="p">{</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">:</span> <span class="mi">12</span><span class="p">,</span> <span class="s2">&quot;ancestry&quot;</span><span class="p">:</span> <span class="s2">&quot;Asian American&quot;</span><span class="p">},</span>
+                <span class="p">{</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">:</span> <span class="mi">16</span><span class="p">,</span> <span class="s2">&quot;ancestry&quot;</span><span class="p">:</span> <span class="s2">&quot;Hispanic or Latino&quot;</span><span class="p">},</span>
+            <span class="p">],</span>
+            <span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">:</span> <span class="p">[</span>
+                <span class="p">{</span><span class="s2">&quot;ldPopulation&quot;</span><span class="p">:</span> <span class="s2">&quot;nfe&quot;</span><span class="p">,</span> <span class="s2">&quot;relativeSampleSize&quot;</span><span class="p">:</span> <span class="mf">0.85</span><span class="p">},</span>
+                <span class="p">{</span><span class="s2">&quot;ldPopulation&quot;</span><span class="p">:</span> <span class="s2">&quot;afr&quot;</span><span class="p">,</span> <span class="s2">&quot;relativeSampleSize&quot;</span><span class="p">:</span> <span class="mf">0.12</span><span class="p">},</span>
+                <span class="p">{</span><span class="s2">&quot;ldPopulation&quot;</span><span class="p">:</span> <span class="s2">&quot;eas&quot;</span><span class="p">,</span> <span class="s2">&quot;relativeSampleSize&quot;</span><span class="p">:</span> <span class="mf">0.01</span><span class="p">},</span>
+                <span class="p">{</span><span class="s2">&quot;ldPopulation&quot;</span><span class="p">:</span> <span class="s2">&quot;amr&quot;</span><span class="p">,</span> <span class="s2">&quot;relativeSampleSize&quot;</span><span class="p">:</span> <span class="mf">0.02</span><span class="p">},</span>
+            <span class="p">],</span>
+            <span class="s2">&quot;pubmedId&quot;</span><span class="p">:</span> <span class="s2">&quot;32913098&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;publicationTitle&quot;</span><span class="p">:</span> <span class="s2">&quot;The GTEx Consortium atlas of genetic regulatory effects across human tissues&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;publicationFirstAuthor&quot;</span><span class="p">:</span> <span class="s2">&quot;GTEx Consortium&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;publicationDate&quot;</span><span class="p">:</span> <span class="s2">&quot;2020-09-11&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;publicationJournal&quot;</span><span class="p">:</span> <span class="s2">&quot;Science&quot;</span><span class="p">,</span>
+        <span class="p">},</span>
+    <span class="p">}</span>
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">get_study_attribute</span><span class="p">(</span>
+        <span class="bp">cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">],</span> <span class="n">attribute_key</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Returns a Column expression that dynamically assigns the attribute based on the study.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            attribute_key (str): The attribute key to assign.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: The dynamically assigned attribute.</span>
+
+<span class="sd">        Raises:</span>
+<span class="sd">            ValueError: If the attribute key is not known for the study.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">study_column</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;study&quot;</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">study</span><span class="p">,</span> <span class="n">config</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">study_config</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+            <span class="n">attribute_value</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">attribute_key</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">attribute_value</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                    <span class="sa">f</span><span class="s2">&quot;Unknown attribute key </span><span class="si">{</span><span class="n">attribute_key</span><span class="si">}</span><span class="s2"> for study </span><span class="si">{</span><span class="n">study</span><span class="si">}</span><span class="s2">&quot;</span>
+                <span class="p">)</span>
+            <span class="c1"># Convert list of dicts to array of structs</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">attribute_value</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span>
+                <span class="n">attribute_value</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">dict</span>
+            <span class="p">):</span>
+                <span class="n">struct_fields</span> <span class="o">=</span> <span class="p">[</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">value</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">items</span><span class="p">()])</span>
+                    <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">attribute_value</span>
+                <span class="p">]</span>
+                <span class="n">attribute_value</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">struct_fields</span><span class="p">)</span>
+            <span class="c1"># Convert dict to struct</span>
+            <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">attribute_value</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+                <span class="n">attribute_value</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
+                    <span class="o">*</span><span class="p">[</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">value</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">attribute_value</span><span class="o">.</span><span class="n">items</span><span class="p">()]</span>
+                <span class="p">)</span>
+        <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">study_column</span> <span class="o">==</span> <span class="n">study</span><span class="p">,</span> <span class="n">attribute_value</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">attribute_key</span><span class="p">)</span>
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">_all_attributes</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">Column</span><span class="p">]:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;A helper function to return all study index attribute expressions.</span>
 
 <span class="sd">        Returns:</span>
-<span class="sd">            List[Column]: all study index attribute expressions.</span>
+<span class="sd">            list[Column]: A list of all study index attribute expressions.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">study_attributes</span> <span class="o">=</span> <span class="p">[</span>
-            <span class="c1"># Project ID, example: &quot;GTEx_V8&quot;.</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;study&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;projectId&quot;</span><span class="p">),</span>
-            <span class="c1"># Partial study ID, example: &quot;GTEx_V8_Adipose_Subcutaneous&quot;. This ID will be converted to final only when</span>
-            <span class="c1"># summary statistics are parsed, because it must also include a gene ID.</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;study&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qtl_group&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
-            <span class="c1"># Summary stats location.</span>
+        <span class="n">study_column</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;study&quot;</span><span class="p">)</span>
+
+        <span class="n">static_study_attributes</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="n">study_column</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;projectId&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span><span class="n">study_column</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;_&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qtl_group&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ftp_path&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">),</span>
-            <span class="c1"># Constant value fields.</span>
             <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;eqtl&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">),</span>
         <span class="p">]</span>
@@ -2611,72 +2966,26 @@ <h2 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class
                 <span class="p">)</span>
             <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;traitFromSourceMappedIds&quot;</span><span class="p">),</span>
         <span class="p">]</span>
-        <span class="n">sample_attributes</span> <span class="o">=</span> <span class="p">[</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">838</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;838 (281 females and 557 males)&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;initialSampleSize&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">715</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;European American&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
-                <span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">103</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;African American&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
-                <span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">12</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;Asian American&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
-                <span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">16</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;Hispanic or Latino&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
-                <span class="p">),</span>
-            <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">),</span>
+        <span class="n">dynamic_study_attributes</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;initialSampleSize&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;pubmedId&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;publicationTitle&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;publicationFirstAuthor&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;publicationDate&quot;</span><span class="p">),</span>
+            <span class="bp">cls</span><span class="o">.</span><span class="n">get_study_attribute</span><span class="p">(</span><span class="s2">&quot;publicationJournal&quot;</span><span class="p">),</span>
         <span class="p">]</span>
-        <span class="n">publication_attributes</span> <span class="o">=</span> <span class="p">[</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;32913098&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;pubmedId&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span>
-                <span class="s2">&quot;The GTEx Consortium atlas of genetic regulatory effects across human tissues&quot;</span>
-            <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationTitle&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;GTEx Consortium&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationFirstAuthor&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;2020-09-11&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationDate&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;Science&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;publicationJournal&quot;</span><span class="p">),</span>
-        <span class="p">]</span>
-        <span class="k">return</span> <span class="p">(</span>
-            <span class="n">study_attributes</span>
-            <span class="o">+</span> <span class="n">tissue_attributes</span>
-            <span class="o">+</span> <span class="n">sample_attributes</span>
-            <span class="o">+</span> <span class="n">publication_attributes</span>
-        <span class="p">)</span>
+        <span class="k">return</span> <span class="n">static_study_attributes</span> <span class="o">+</span> <span class="n">tissue_attributes</span> <span class="o">+</span> <span class="n">dynamic_study_attributes</span>
 
     <span class="nd">@classmethod</span>
-    <span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
-        <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">],</span>
-        <span class="n">eqtl_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Ingest study level metadata from eQTL Catalogue.</span>
-
-<span class="sd">        Args:</span>
-<span class="sd">            eqtl_studies (DataFrame): ingested but unprocessed eQTL Catalogue studies.</span>
-
-<span class="sd">        Returns:</span>
-<span class="sd">            StudyIndex: preliminary processed study index for eQTL Catalogue studies.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">StudyIndex</span><span class="p">(</span>
-            <span class="n">_df</span><span class="o">=</span><span class="n">eqtl_studies</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">_all_attributes</span><span class="p">())</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">,</span>
-                <span class="n">StudyIndex</span><span class="o">.</span><span class="n">aggregate_and_map_ancestries</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">)),</span>
-            <span class="p">),</span>
-            <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndex</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
-        <span class="p">)</span>
-
-    <span class="nd">@classmethod</span>
-    <span class="k">def</span> <span class="nf">add_gene_id_column</span><span class="p">(</span>
+    <span class="k">def</span> <span class="nf">add_gene_to_study_id</span><span class="p">(</span>
         <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">],</span>
         <span class="n">study_index_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
         <span class="n">summary_stats_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Add a geneId column to the study index and explode.</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Update the studyId to include gene information from summary statistics. A geneId column is also added.</span>
 
 <span class="sd">        While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for</span>
 <span class="sd">        an expression of a _particular gene_ in a particular study.  At this stage we have a study index with partial</span>
@@ -2690,26 +2999,41 @@ <h2 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class
 <span class="sd">        Returns:</span>
 <span class="sd">            StudyIndex: final study index for eQTL Catalogue studies.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">partial_to_full_study_id</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="n">summary_stats_df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">))</span>
-            <span class="o">.</span><span class="n">distinct</span><span class="p">()</span>
-            <span class="o">.</span><span class="n">select</span><span class="p">(</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP_GENEID</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;(.*)_[\_]+&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                    <span class="s2">&quot;studyId&quot;</span>
-                <span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP</span>
-            <span class="p">)</span>
-            <span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">agg</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;fullStudyIdList&quot;</span><span class="p">))</span>
-        <span class="p">)</span>
+        <span class="n">partial_to_full_study_id</span> <span class="o">=</span> <span class="n">summary_stats_df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP_GENEID</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;^(.*)_ENSG\d+&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+                <span class="s2">&quot;studyId&quot;</span>
+            <span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">distinct</span><span class="p">()</span>
         <span class="n">study_index_df</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="n">study_index_df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">partial_to_full_study_id</span><span class="p">,</span> <span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;inner&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">explode</span><span class="p">(</span><span class="s2">&quot;fullStudyIdList&quot;</span><span class="p">))</span>
-            <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;fullStudyIdList&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;.*_([\_]+)&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
-            <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">)</span>
+            <span class="n">partial_to_full_study_id</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">broadcast</span><span class="p">(</span><span class="n">study_index_df</span><span class="p">),</span> <span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;inner&quot;</span>
+            <span class="p">)</span>
+            <span class="c1"># Change studyId to fullStudyId</span>
+            <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">,</span> <span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
+            <span class="c1"># Add geneId column</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;([^_]+)$&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
         <span class="p">)</span>
         <span class="k">return</span> <span class="n">StudyIndex</span><span class="p">(</span><span class="n">_df</span><span class="o">=</span><span class="n">study_index_df</span><span class="p">,</span> <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndex</span><span class="o">.</span><span class="n">get_schema</span><span class="p">())</span>
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
+        <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">],</span>
+        <span class="n">eqtl_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Ingest study level metadata from eQTL Catalogue.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            eqtl_studies (DataFrame): ingested but unprocessed eQTL Catalogue studies.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            StudyIndex: preliminary processed study index for eQTL Catalogue studies.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">StudyIndex</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">eqtl_studies</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">_all_attributes</span><span class="p">()),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndex</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
             </details>
 
@@ -2730,20 +3054,19 @@ <h2 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex" class
 
 
 
-
-<h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_id_column" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">add_gene_id_column</span><span class="p">(</span><span class="n">study_index_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">summary_stats_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span></code>
+<h3 id="gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_to_study_id" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">add_gene_to_study_id</span><span class="p">(</span><span class="n">study_index_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">summary_stats_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_id_column" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_to_study_id" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
   
-      <p>Add a geneId column to the study index and explode.</p>
+      <p>Update the studyId to include gene information from summary statistics. A geneId column is also added.</p>
 <p>While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for
 an expression of a <em>particular gene</em> in a particular study.  At this stage we have a study index with partial
 study IDs like "PROJECT_QTLGROUP", and a summary statistics object with full study IDs like
@@ -2806,7 +3129,7 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_ge
     <tbody>
         <tr>
 <td><code>StudyIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../../../dataset/study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../../../datasets/study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2818,21 +3141,8 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_ge
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/eqtl_catalogue/study_index.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">112</span>
-<span class="normal">113</span>
-<span class="normal">114</span>
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+            <summary>Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">125</span>
 <span class="normal">126</span>
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@@ -2858,13 +3168,23 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_ge
 <span class="normal">148</span>
 <span class="normal">149</span>
 <span class="normal">150</span>
-<span class="normal">151</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
-<span class="k">def</span> <span class="nf">add_gene_id_column</span><span class="p">(</span>
+<span class="normal">151</span>
+<span class="normal">152</span>
+<span class="normal">153</span>
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+<span class="normal">159</span>
+<span class="normal">160</span>
+<span class="normal">161</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="k">def</span> <span class="nf">add_gene_to_study_id</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">],</span>
     <span class="n">study_index_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
     <span class="n">summary_stats_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Add a geneId column to the study index and explode.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Update the studyId to include gene information from summary statistics. A geneId column is also added.</span>
 
 <span class="sd">    While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for</span>
 <span class="sd">    an expression of a _particular gene_ in a particular study.  At this stage we have a study index with partial</span>
@@ -2878,24 +3198,21 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_ge
 <span class="sd">    Returns:</span>
 <span class="sd">        StudyIndex: final study index for eQTL Catalogue studies.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">partial_to_full_study_id</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="n">summary_stats_df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">))</span>
-        <span class="o">.</span><span class="n">distinct</span><span class="p">()</span>
-        <span class="o">.</span><span class="n">select</span><span class="p">(</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP_GENEID</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;(.*)_[\_]+&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                <span class="s2">&quot;studyId&quot;</span>
-            <span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP</span>
-        <span class="p">)</span>
-        <span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
-        <span class="o">.</span><span class="n">agg</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;fullStudyIdList&quot;</span><span class="p">))</span>
-    <span class="p">)</span>
+    <span class="n">partial_to_full_study_id</span> <span class="o">=</span> <span class="n">summary_stats_df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP_GENEID</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;^(.*)_ENSG\d+&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+            <span class="s2">&quot;studyId&quot;</span>
+        <span class="p">),</span>  <span class="c1"># PROJECT_QTLGROUP</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">distinct</span><span class="p">()</span>
     <span class="n">study_index_df</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="n">study_index_df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">partial_to_full_study_id</span><span class="p">,</span> <span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;inner&quot;</span><span class="p">)</span>
-        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">explode</span><span class="p">(</span><span class="s2">&quot;fullStudyIdList&quot;</span><span class="p">))</span>
-        <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;fullStudyIdList&quot;</span><span class="p">)</span>
-        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;.*_([\_]+)&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
-        <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">)</span>
+        <span class="n">partial_to_full_study_id</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">broadcast</span><span class="p">(</span><span class="n">study_index_df</span><span class="p">),</span> <span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;inner&quot;</span>
+        <span class="p">)</span>
+        <span class="c1"># Change studyId to fullStudyId</span>
+        <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span><span class="s2">&quot;fullStudyId&quot;</span><span class="p">,</span> <span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
+        <span class="c1"># Add geneId column</span>
+        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;([^_]+)$&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">))</span>
     <span class="p">)</span>
     <span class="k">return</span> <span class="n">StudyIndex</span><span class="p">(</span><span class="n">_df</span><span class="o">=</span><span class="n">study_index_df</span><span class="p">,</span> <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndex</span><span class="o">.</span><span class="n">get_schema</span><span class="p">())</span>
 </code></pre></div></td></tr></table></div>
@@ -2909,15 +3226,14 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_ge
 
 
 
-
-<h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source" class="doc doc-heading">
+<h3 id="gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">eqtl_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2967,7 +3283,7 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_s
     <tbody>
         <tr>
 <td><code>StudyIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../../../dataset/study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../../../datasets/study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2979,27 +3295,24 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_s
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/eqtl_catalogue/study_index.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 91</span>
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-<span class="normal">109</span>
-<span class="normal">110</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+            <summary>Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">163</span>
+<span class="normal">164</span>
+<span class="normal">165</span>
+<span class="normal">166</span>
+<span class="normal">167</span>
+<span class="normal">168</span>
+<span class="normal">169</span>
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+<span class="normal">171</span>
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+<span class="normal">174</span>
+<span class="normal">175</span>
+<span class="normal">176</span>
+<span class="normal">177</span>
+<span class="normal">178</span>
+<span class="normal">179</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">],</span>
     <span class="n">eqtl_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
@@ -3013,10 +3326,7 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_s
 <span class="sd">        StudyIndex: preliminary processed study index for eQTL Catalogue studies.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="n">StudyIndex</span><span class="p">(</span>
-        <span class="n">_df</span><span class="o">=</span><span class="n">eqtl_studies</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">_all_attributes</span><span class="p">())</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-            <span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">,</span>
-            <span class="n">StudyIndex</span><span class="o">.</span><span class="n">aggregate_and_map_ancestries</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">)),</span>
-        <span class="p">),</span>
+        <span class="n">_df</span><span class="o">=</span><span class="n">eqtl_studies</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">*</span><span class="bp">cls</span><span class="o">.</span><span class="n">_all_attributes</span><span class="p">()),</span>
         <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndex</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
     <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
@@ -3026,11 +3336,190 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_s
 </div>
 
 
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.get_study_attribute" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">get_study_attribute</span><span class="p">(</span><span class="n">attribute_key</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
+  </span>
+
+<a href="#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.get_study_attribute" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Returns a Column expression that dynamically assigns the attribute based on the study.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>attribute_key</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>The attribute key to assign.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>Column</code></td>          <td>
+                <code><span title="pyspark.sql.column.Column">Column</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>The dynamically assigned attribute.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Raises:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td>
+                <code>ValueError</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>If the attribute key is not known for the study.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">42</span>
+<span class="normal">43</span>
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+<span class="normal">78</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="k">def</span> <span class="nf">get_study_attribute</span><span class="p">(</span>
+    <span class="bp">cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">EqtlCatalogueStudyIndex</span><span class="p">],</span> <span class="n">attribute_key</span><span class="p">:</span> <span class="nb">str</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Returns a Column expression that dynamically assigns the attribute based on the study.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        attribute_key (str): The attribute key to assign.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        Column: The dynamically assigned attribute.</span>
+
+<span class="sd">    Raises:</span>
+<span class="sd">        ValueError: If the attribute key is not known for the study.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">study_column</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;study&quot;</span><span class="p">)</span>
+    <span class="k">for</span> <span class="n">study</span><span class="p">,</span> <span class="n">config</span> <span class="ow">in</span> <span class="bp">cls</span><span class="o">.</span><span class="n">study_config</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+        <span class="n">attribute_value</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="n">attribute_key</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">attribute_value</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s2">&quot;Unknown attribute key </span><span class="si">{</span><span class="n">attribute_key</span><span class="si">}</span><span class="s2"> for study </span><span class="si">{</span><span class="n">study</span><span class="si">}</span><span class="s2">&quot;</span>
+            <span class="p">)</span>
+        <span class="c1"># Convert list of dicts to array of structs</span>
+        <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">attribute_value</span><span class="p">,</span> <span class="nb">list</span><span class="p">)</span> <span class="ow">and</span> <span class="nb">isinstance</span><span class="p">(</span>
+            <span class="n">attribute_value</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="nb">dict</span>
+        <span class="p">):</span>
+            <span class="n">struct_fields</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span><span class="o">*</span><span class="p">[</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">value</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">item</span><span class="o">.</span><span class="n">items</span><span class="p">()])</span>
+                <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">attribute_value</span>
+            <span class="p">]</span>
+            <span class="n">attribute_value</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">struct_fields</span><span class="p">)</span>
+        <span class="c1"># Convert dict to struct</span>
+        <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">attribute_value</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+            <span class="n">attribute_value</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
+                <span class="o">*</span><span class="p">[</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">value</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">key</span><span class="p">)</span> <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">attribute_value</span><span class="o">.</span><span class="n">items</span><span class="p">()]</span>
+            <span class="p">)</span>
+    <span class="k">return</span> <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span><span class="n">study_column</span> <span class="o">==</span> <span class="n">study</span><span class="p">,</span> <span class="n">attribute_value</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">attribute_key</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
 
   </div>
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3054,7 +3543,7 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_s
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3073,14 +3562,6 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_s
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/tskir"
-              title="tskir"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/10669118?v=4" alt="tskir"
-            /></a>
           </li></ul>
       </li>
     </ul>
@@ -3129,7 +3610,7 @@ <h3 id="otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_s
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/datasource/eqtl_catalogue/summary_stats/index.html b/python_api/datasources/eqtl_catalogue/summary_stats/index.html
similarity index 85%
rename from python_api/datasource/eqtl_catalogue/summary_stats/index.html
rename to python_api/datasources/eqtl_catalogue/summary_stats/index.html
index 19470c9b3..f3dcf6ce6 100644
--- a/python_api/datasource/eqtl_catalogue/summary_stats/index.html
+++ b/python_api/datasources/eqtl_catalogue/summary_stats/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Summary Stats - Open Targets Genetics</title>
+        <title>Summary Stats - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="md-skip">
+        <a href="#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
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-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -993,12 +1144,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../study_index/" class="md-nav__link ">
+            <a href="../_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1009,14 +1160,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
                 
   
   
+  
+  
+    <li class="md-nav__item">
+      <a href="../study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
     
   
   
@@ -1071,7 +1243,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="md-nav__link">
+  <a href="#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="md-nav__link">
     <span class="md-ellipsis">
       EqtlCatalogueSummaryStats
     </span>
@@ -1081,9 +1253,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
@@ -1127,7 +1299,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1143,14 +1315,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1177,6 +1349,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1201,7 +1394,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1217,14 +1410,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1296,7 +1489,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1312,14 +1505,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1433,7 +1626,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1449,14 +1642,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1570,7 +1763,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1586,14 +1779,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1649,80 +1842,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1747,32 +1866,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1783,11 +1902,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1804,11 +1923,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1825,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1846,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1867,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1888,11 +2007,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1918,12 +2037,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1934,14 +2053,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1954,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1975,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1996,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2017,7 +2136,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2063,32 +2182,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2099,11 +2218,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2120,11 +2239,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2141,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2162,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2183,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2204,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2225,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2246,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2267,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2288,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2309,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2330,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2351,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2372,11 +2491,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2426,7 +2608,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="md-nav__link">
+  <a href="#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="md-nav__link">
     <span class="md-ellipsis">
       EqtlCatalogueSummaryStats
     </span>
@@ -2436,9 +2618,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
@@ -2473,16 +2655,15 @@ <h1>Summary Stats</h1>
 
 
 
-
-<h2 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="doc doc-heading">
-          <code>otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats</code>
+<h2 id="gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="doc doc-heading">
+          <code>gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2491,7 +2672,7 @@ <h2 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" c
       <p>Summary statistics dataset for eQTL Catalogue.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/eqtl_catalogue/summary_stats.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/eqtl_catalogue/summary_stats.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">19</span>
 <span class="normal">20</span>
 <span class="normal">21</span>
@@ -2661,15 +2842,14 @@ <h2 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats" c
 
 
 
-
-<h3 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="doc doc-heading">
+<h3 id="gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">summary_stats_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">SummaryStatistics</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2719,7 +2899,7 @@ <h3 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.fr
     <tbody>
         <tr>
 <td><code>SummaryStatistics</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="../../../dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.summary_statistics.SummaryStatistics" href="../../../datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2731,7 +2911,7 @@ <h3 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.fr
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/eqtl_catalogue/summary_stats.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/eqtl_catalogue/summary_stats.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">48</span>
 <span class="normal">49</span>
 <span class="normal">50</span>
@@ -2835,6 +3015,7 @@ <h3 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.fr
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2858,7 +3039,7 @@ <h3 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.fr
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2877,14 +3058,6 @@ <h3 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.fr
               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/tskir"
-              title="tskir"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/10669118?v=4" alt="tskir"
-            /></a>
           </li></ul>
       </li>
     </ul>
@@ -2933,7 +3106,7 @@ <h3 id="otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.fr
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/datasource/finngen/_finngen/index.html b/python_api/datasources/finngen/_finngen/index.html
similarity index 80%
rename from python_api/datasource/finngen/_finngen/index.html
rename to python_api/datasources/finngen/_finngen/index.html
index 2cbd34a84..9888c010a 100644
--- a/python_api/datasource/finngen/_finngen/index.html
+++ b/python_api/datasources/finngen/_finngen/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>FinnGen - Open Targets Genetics</title>
+        <title>FinnGen - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,7 +102,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -187,13 +187,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -228,7 +245,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -244,6 +261,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -304,22 +338,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -333,11 +367,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -353,11 +387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -390,11 +424,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -409,6 +443,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -526,7 +677,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -542,14 +693,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -571,32 +722,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -607,7 +758,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -628,7 +779,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -649,7 +800,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -670,7 +821,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -691,7 +842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -712,7 +863,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -733,7 +884,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -754,7 +905,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -775,7 +926,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -796,7 +947,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -817,7 +968,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -838,7 +989,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -859,7 +1010,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -880,7 +1031,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -901,7 +1052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -941,32 +1092,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -986,12 +1137,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1002,14 +1153,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1021,6 +1172,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1062,7 +1234,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" checked>
         
           
           
@@ -1078,14 +1250,14 @@
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1112,6 +1284,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1136,7 +1329,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1152,14 +1345,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1231,7 +1424,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1247,14 +1440,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1368,7 +1561,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1384,14 +1577,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1505,7 +1698,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1521,14 +1714,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1584,80 +1777,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1682,32 +1801,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1718,11 +1837,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1739,11 +1858,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1760,11 +1879,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1781,11 +1900,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1802,11 +1921,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1823,11 +1942,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1853,12 +1972,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1869,14 +1988,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1889,7 +2008,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1910,7 +2029,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1931,7 +2050,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1952,7 +2071,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1998,32 +2117,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,11 +2153,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2055,11 +2174,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2076,11 +2195,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2307,11 +2426,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2382,7 +2564,8 @@ <h1>Finngen</h1>
   }
 </style>
 
-<p>FinnGen is a research project in genomics and personalized medicine. It is large public-private partnership that has collected and analysed genome and health data from 500,000 Finnish biobank donors to understand the genetic basis of diseases. FinnGen is a now expanding into understanding the progression and biological mechanisms of diseases. FinnGen provides a world-class resource for further breakthroughs in disease prevention, diagnosis, and treatment and a outlook into our genetic make-up.</p>
+<p><a href="https://www.finngen.fi/en">FinnGen</a> is a research project in genomics and personalized medicine, representing a large public-private partnership. The project has collected and analyzed genome and health data from 500,000 Finnish biobank donors to understand the genetic basis of diseases. FinnGen is now expanding its focus to comprehend the progression and biological mechanisms of diseases. This initiative provides a world-class resource for further breakthroughs in disease prevention, diagnosis, and treatment, offering insights into our genetic makeup.</p>
+<p>For a comprehensive understanding of the dataset and methods, refer to <a href="https://www.nature.com/articles/s41586-022-05473-8">Kurki et al., 2023</a>.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2405,7 +2588,7 @@ <h1>Finngen</h1>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-14T15:17:33+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-14</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2417,14 +2600,6 @@ <h1>Finngen</h1>
       </li>
       <li class="contributors-holder">
         <ul class="contributors" data-bi-name="contributors"><li>
-            <a
-              href="https://github.com/addramir"
-              title="addramir"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/22906976?v=4" alt="addramir"
-            /></a>
-          </li><li>
             <a
               href="https://github.com/d0choa"
               title="d0choa"
@@ -2480,7 +2655,7 @@ <h1>Finngen</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/datasource/finngen/study_index/index.html b/python_api/datasources/finngen/study_index/index.html
similarity index 83%
rename from python_api/datasource/finngen/study_index/index.html
rename to python_api/datasources/finngen/study_index/index.html
index c08246c31..9929b75a3 100644
--- a/python_api/datasource/finngen/study_index/index.html
+++ b/python_api/datasources/finngen/study_index/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../_finngen/">
       
       
-        <link rel="next" href="../../gnomad/_gnomad/">
+        <link rel="next" href="../summary_stats/">
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Study Index - Open Targets Genetics</title>
+        <title>Study Index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.finngen.study_index.FinnGenStudyIndex" class="md-skip">
+        <a href="#gentropy.datasource.finngen.study_index.FinnGenStudyIndex" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
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+  
+
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+            
+              
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
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+      <a href="../../../../roadmap/" class="md-nav__link">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
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+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
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+              
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+  
+  
+  
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       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
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+  <a href="#gentropy.datasource.finngen.study_index.FinnGenStudyIndex" class="md-nav__link">
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+  <a href="#gentropy.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
@@ -1177,6 +1349,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
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             Gnomad
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
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             Gwas catalog
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             Intervals
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-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
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@@ -1649,80 +1842,6 @@
 
               
             
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-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
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-
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-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1747,32 +1866,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1783,11 +1902,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1804,11 +1923,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1825,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1846,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1867,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1888,11 +2007,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1918,12 +2037,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1934,14 +2053,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1954,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1975,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1996,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2017,7 +2136,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2063,32 +2182,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2099,11 +2218,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2120,11 +2239,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2141,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2162,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2183,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2204,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2225,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2246,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2267,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2288,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2309,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2330,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2351,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2372,11 +2491,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2426,7 +2608,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.finngen.study_index.FinnGenStudyIndex" class="md-nav__link">
+  <a href="#gentropy.datasource.finngen.study_index.FinnGenStudyIndex" class="md-nav__link">
     <span class="md-ellipsis">
       FinnGenStudyIndex
     </span>
@@ -2436,9 +2618,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
@@ -2473,12 +2655,11 @@ <h1>Study Index</h1>
 
 
 
-
-<h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-heading">
-          <code>otg.datasource.finngen.study_index.FinnGenStudyIndex</code>
+<h2 id="gentropy.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-heading">
+          <code>gentropy.datasource.finngen.study_index.FinnGenStudyIndex</code>
 
 
-<a href="#otg.datasource.finngen.study_index.FinnGenStudyIndex" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.finngen.study_index.FinnGenStudyIndex" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2487,7 +2668,7 @@ <h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-hea
       <p>Study index dataset from FinnGen.</p>
 <p>The following information is aggregated/extracted:</p>
 <ul>
-<li>Study ID in the special format (FINNGEN_R9_*)</li>
+<li>Study ID in the special format (e.g. FINNGEN_R10_*)</li>
 <li>Trait name (for example, Amoebiasis)</li>
 <li>Number of cases and controls</li>
 <li>Link to the summary statistics location</li>
@@ -2495,7 +2676,7 @@ <h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-hea
 <p>Some fields are also populated as constants, such as study type and the initial sample size.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/finngen/study_index.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/finngen/study_index.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">12</span>
 <span class="normal">13</span>
 <span class="normal">14</span>
@@ -2565,12 +2746,14 @@ <h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-hea
 <span class="normal">78</span>
 <span class="normal">79</span>
 <span class="normal">80</span>
-<span class="normal">81</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">FinnGenStudyIndex</span><span class="p">:</span>
+<span class="normal">81</span>
+<span class="normal">82</span>
+<span class="normal">83</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">FinnGenStudyIndex</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study index dataset from FinnGen.</span>
 
 <span class="sd">    The following information is aggregated/extracted:</span>
 
-<span class="sd">    - Study ID in the special format (FINNGEN_R9_*)</span>
+<span class="sd">    - Study ID in the special format (e.g. FINNGEN_R10_*)</span>
 <span class="sd">    - Trait name (for example, Amoebiasis)</span>
 <span class="sd">    - Number of cases and controls</span>
 <span class="sd">    - Link to the summary statistics location</span>
@@ -2578,10 +2761,10 @@ <h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-hea
 <span class="sd">    Some fields are also populated as constants, such as study type and the initial sample size.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="n">finngen_phenotype_table_url</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;https://r9.finngen.fi/api/phenos&quot;</span>
-    <span class="n">finngen_release_prefix</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;FINNGEN_R9&quot;</span>
+    <span class="n">finngen_phenotype_table_url</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;https://r10.finngen.fi/api/phenos&quot;</span>
+    <span class="n">finngen_release_prefix</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;FINNGEN_R10&quot;</span>
     <span class="n">finngen_summary_stats_url_prefix</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="s2">&quot;gs://finngen-public-data-r9/summary_stats/finngen_R9_&quot;</span>
+        <span class="s2">&quot;gs://finngen-public-data-r10/summary_stats/finngen_R10_&quot;</span>
     <span class="p">)</span>
     <span class="n">finngen_summary_stats_url_suffix</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="s2">&quot;.gz&quot;</span>
 
@@ -2607,9 +2790,11 @@ <h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-hea
                     <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="n">finngen_release_prefix</span><span class="si">}</span><span class="s2">_&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;phenocode&quot;</span><span class="p">)</span>
                 <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;phenostring&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
-                <span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
+                <span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">))</span>
+                <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span>
+                <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">finngen_release_prefix</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;projectId&quot;</span><span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;gwas&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
@@ -2618,7 +2803,7 @@ <h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-hea
                 <span class="p">),</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
                     <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">377277</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">377277</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
                         <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;Finnish&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
                     <span class="p">)</span>
                 <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">),</span>
@@ -2655,15 +2840,14 @@ <h2 id="otg.datasource.finngen.study_index.FinnGenStudyIndex" class="doc doc-hea
 
 
 
-
-<h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class="doc doc-heading">
+<h3 id="gentropy.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndex</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2713,7 +2897,7 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
     <tbody>
         <tr>
 <td><code>StudyIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../../../dataset/study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../../../datasets/study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2725,7 +2909,7 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/finngen/study_index.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/finngen/study_index.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">32</span>
 <span class="normal">33</span>
 <span class="normal">34</span>
@@ -2775,7 +2959,9 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
 <span class="normal">78</span>
 <span class="normal">79</span>
 <span class="normal">80</span>
-<span class="normal">81</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">81</span>
+<span class="normal">82</span>
+<span class="normal">83</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">FinnGenStudyIndex</span><span class="p">],</span>
     <span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span>
@@ -2797,9 +2983,11 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
                 <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">cls</span><span class="o">.</span><span class="n">finngen_release_prefix</span><span class="si">}</span><span class="s2">_&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;phenocode&quot;</span><span class="p">)</span>
             <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;phenostring&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;traitFromSource&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
-            <span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
+            <span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_cases&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;num_controls&quot;</span><span class="p">))</span>
+            <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">finngen_release_prefix</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;projectId&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;gwas&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
@@ -2808,7 +2996,7 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
             <span class="p">),</span>
             <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">377277</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;long&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">377277</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
                     <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;Finnish&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
                 <span class="p">)</span>
             <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;discoverySamples&quot;</span><span class="p">),</span>
@@ -2837,6 +3025,7 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2860,7 +3049,7 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
         <span class="icon twemoji">
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2927,7 +3116,7 @@ <h3 id="otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source" class=
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasources/finngen/summary_stats/index.html b/python_api/datasources/finngen/summary_stats/index.html
new file mode 100644
index 000000000..c84b6e65c
--- /dev/null
+++ b/python_api/datasources/finngen/summary_stats/index.html
@@ -0,0 +1,3178 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
+  <head>
+    
+      <meta charset="utf-8">
+      <meta name="viewport" content="width=device-width,initial-scale=1">
+      
+      
+      
+      
+        <link rel="prev" href="../study_index/">
+      
+      
+        <link rel="next" href="../../gnomad/_gnomad/">
+      
+      
+      <link rel="icon" href="../../../../assets/imgs/favicon.png">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
+    
+    
+      
+        <title>Study Index - Open Targets Gentropy</title>
+      
+    
+    
+      <link rel="stylesheet" href="../../../../assets/stylesheets/main.50c56a3b.min.css">
+      
+        
+        <link rel="stylesheet" href="../../../../assets/stylesheets/palette.06af60db.min.css">
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+
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+      
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+        <link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
+        <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Roboto:300,300i,400,400i,700,700i%7CRoboto+Mono:400,400i,700,700i&display=fallback">
+        <style>:root{--md-text-font:"Roboto";--md-code-font:"Roboto Mono"}</style>
+      
+    
+    
+      <link rel="stylesheet" href="../../../../css/timeago.css">
+    
+      <link rel="stylesheet" href="../../../../assets/_mkdocstrings.css">
+    
+      <link rel="stylesheet" href="../../../../assets/stylesheets/extra.css">
+    
+    <script>__md_scope=new URL("../../../..",location),__md_hash=e=>[...e].reduce((e,_)=>(e<<5)-e+_.charCodeAt(0),0),__md_get=(e,_=localStorage,t=__md_scope)=>JSON.parse(_.getItem(t.pathname+"."+e)),__md_set=(e,_,t=localStorage,a=__md_scope)=>{try{t.setItem(a.pathname+"."+e,JSON.stringify(_))}catch(e){}}</script>
+    
+      
+
+    
+    
+    
+  </head>
+  
+  
+    
+    
+      
+    
+    
+    
+    
+    <body dir="ltr" data-md-color-scheme="default" data-md-color-primary="blue-grey" data-md-color-accent="light-blue">
+  
+    
+    <input class="md-toggle" data-md-toggle="drawer" type="checkbox" id="__drawer" autocomplete="off">
+    <input class="md-toggle" data-md-toggle="search" type="checkbox" id="__search" autocomplete="off">
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+  <span class="md-ellipsis">
+    L2G Feature Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Prediction
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus Overlap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant-to-gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../_datasources/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasources
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
+            <span class="md-nav__icon md-icon"></span>
+            Datasources
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Eqtl catalogue
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
+            <span class="md-nav__icon md-icon"></span>
+            Eqtl catalogue
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Stats
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../_finngen/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Finngen
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_2">
+            <span class="md-nav__icon md-icon"></span>
+            Finngen
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats" class="md-nav__link">
+    <span class="md-ellipsis">
+      FinnGenSummaryStats
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="FinnGenSummaryStats">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats.from_source" class="md-nav__link">
+    <span class="md-ellipsis">
+      from_source
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../gnomad/_gnomad/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gnomad
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../methods/carma/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../methods/coloc/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Coloc
+  </span>
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+    </li>
+  
+
+              
+            
+              
+                
+  
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
+        
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+  
+    <li class="md-nav__item">
+      <a href="../../../methods/pics/" class="md-nav__link">
+        
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+    PICS
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+  
+
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+  
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+    <li class="md-nav__item">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
+        
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+  </span>
+  
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+    </li>
+  
+
+              
+            
+              
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+  
+  
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+    <li class="md-nav__item">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
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+  </span>
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+    <li class="md-nav__item">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
+        
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+    colocalisation
+  </span>
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+
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+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
+        
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+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats" class="md-nav__link">
+    <span class="md-ellipsis">
+      FinnGenSummaryStats
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="FinnGenSummaryStats">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats.from_source" class="md-nav__link">
+    <span class="md-ellipsis">
+      from_source
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+  <h1>Study Index</h1>
+
+<div class="doc doc-object doc-class">
+
+
+
+<h2 id="gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats" class="doc doc-heading">
+          <code>gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats</code>
+
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
+  </span>
+
+<a href="#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
+
+  
+      <p>Summary statistics dataset for FinnGen.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/datasource/finngen/summary_stats.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
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+<span class="normal">34</span>
+<span class="normal">35</span>
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+<span class="normal">37</span>
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+<span class="normal">41</span>
+<span class="normal">42</span>
+<span class="normal">43</span>
+<span class="normal">44</span>
+<span class="normal">45</span>
+<span class="normal">46</span>
+<span class="normal">47</span>
+<span class="normal">48</span>
+<span class="normal">49</span>
+<span class="normal">50</span>
+<span class="normal">51</span>
+<span class="normal">52</span>
+<span class="normal">53</span>
+<span class="normal">54</span>
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+<span class="normal">56</span>
+<span class="normal">57</span>
+<span class="normal">58</span>
+<span class="normal">59</span>
+<span class="normal">60</span>
+<span class="normal">61</span>
+<span class="normal">62</span>
+<span class="normal">63</span>
+<span class="normal">64</span>
+<span class="normal">65</span>
+<span class="normal">66</span>
+<span class="normal">67</span>
+<span class="normal">68</span>
+<span class="normal">69</span>
+<span class="normal">70</span>
+<span class="normal">71</span>
+<span class="normal">72</span>
+<span class="normal">73</span>
+<span class="normal">74</span>
+<span class="normal">75</span>
+<span class="normal">76</span>
+<span class="normal">77</span>
+<span class="normal">78</span>
+<span class="normal">79</span>
+<span class="normal">80</span>
+<span class="normal">81</span>
+<span class="normal">82</span>
+<span class="normal">83</span>
+<span class="normal">84</span>
+<span class="normal">85</span>
+<span class="normal">86</span>
+<span class="normal">87</span>
+<span class="normal">88</span>
+<span class="normal">89</span>
+<span class="normal">90</span>
+<span class="normal">91</span>
+<span class="normal">92</span>
+<span class="normal">93</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="k">class</span> <span class="nc">FinnGenSummaryStats</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Summary statistics dataset for FinnGen.&quot;&quot;&quot;</span>
+
+    <span class="n">raw_schema</span><span class="p">:</span> <span class="n">t</span><span class="o">.</span><span class="n">StructType</span> <span class="o">=</span> <span class="n">StructType</span><span class="p">(</span>
+        <span class="p">[</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;#chrom&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;ref&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;alt&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;rsids&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;nearest_genes&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;pval&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;mlogp&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;beta&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;sebeta&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;af_alt&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;af_alt_cases&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+            <span class="n">StructField</span><span class="p">(</span><span class="s2">&quot;af_alt_controls&quot;</span><span class="p">,</span> <span class="n">StringType</span><span class="p">(),</span> <span class="kc">True</span><span class="p">),</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
+        <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">FinnGenSummaryStats</span><span class="p">],</span>
+        <span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span>
+        <span class="n">raw_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">SummaryStatistics</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Ingests all summary statst for all FinnGen studies.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            spark (SparkSession): Spark session object.</span>
+<span class="sd">            raw_file (str): Path to raw summary statistics .gz files.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            SummaryStatistics: Processed summary statistics dataset</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">study_id</span> <span class="o">=</span> <span class="n">raw_file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;/&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+        <span class="n">processed_summary_stats_df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">schema</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">raw_schema</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">csv</span><span class="p">(</span><span class="n">raw_file</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+            <span class="c1"># Drop rows which don&#39;t have proper position.</span>
+            <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">())</span>
+            <span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                <span class="c1"># From the full path, extracts just the filename, and converts to upper case to get the study ID.</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">study_id</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
+                <span class="c1"># Add variant information.</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">concat_ws</span><span class="p">(</span>
+                    <span class="s2">&quot;_&quot;</span><span class="p">,</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;#chrom&quot;</span><span class="p">),</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">),</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ref&quot;</span><span class="p">),</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;alt&quot;</span><span class="p">),</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;variantId&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;#chrom&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;position&quot;</span><span class="p">),</span>
+                <span class="c1"># Parse p-value into mantissa and exponent.</span>
+                <span class="o">*</span><span class="n">parse_pvalue</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pval&quot;</span><span class="p">)),</span>
+                <span class="c1"># Add beta, standard error, and allele frequency information.</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;beta&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;double&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sebeta&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;double&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;standardError&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;af_alt&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;float&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;effectAlleleFrequencyFromSource&quot;</span><span class="p">),</span>
+            <span class="p">)</span>
+            <span class="c1"># Calculating the confidence intervals.</span>
+            <span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">()</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;beta&quot;</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">)</span>
+            <span class="p">)</span>
+            <span class="c1"># Average ~20Mb partitions with 30 partitions per study</span>
+            <span class="o">.</span><span class="n">repartitionByRange</span><span class="p">(</span><span class="mi">30</span><span class="p">,</span> <span class="s2">&quot;chromosome&quot;</span><span class="p">,</span> <span class="s2">&quot;position&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">sortWithinPartitions</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">,</span> <span class="s2">&quot;position&quot;</span><span class="p">)</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Initializing summary statistics object:</span>
+        <span class="k">return</span> <span class="n">SummaryStatistics</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">processed_summary_stats_df</span><span class="p">,</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="n">SummaryStatistics</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats.from_source" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span> <span class="n">raw_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">SummaryStatistics</span></code>
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
+  </span>
+
+<a href="#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Ingests all summary statst for all FinnGen studies.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>spark</code></td>
+          <td>
+                <code><span title="pyspark.sql.SparkSession">SparkSession</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Spark session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>raw_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to raw summary statistics .gz files.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>SummaryStatistics</code></td>          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.summary_statistics.SummaryStatistics" href="../../../datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Processed summary statistics dataset</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/datasource/finngen/summary_stats.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">38</span>
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+<span class="normal">93</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
+    <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">FinnGenSummaryStats</span><span class="p">],</span>
+    <span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span>
+    <span class="n">raw_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">SummaryStatistics</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Ingests all summary statst for all FinnGen studies.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        spark (SparkSession): Spark session object.</span>
+<span class="sd">        raw_file (str): Path to raw summary statistics .gz files.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        SummaryStatistics: Processed summary statistics dataset</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">study_id</span> <span class="o">=</span> <span class="n">raw_file</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;/&quot;</span><span class="p">)[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;.&quot;</span><span class="p">)[</span><span class="mi">0</span><span class="p">]</span><span class="o">.</span><span class="n">upper</span><span class="p">()</span>
+    <span class="n">processed_summary_stats_df</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">schema</span><span class="p">(</span><span class="bp">cls</span><span class="o">.</span><span class="n">raw_schema</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">csv</span><span class="p">(</span><span class="n">raw_file</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="c1"># Drop rows which don&#39;t have proper position.</span>
+        <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">())</span>
+        <span class="o">.</span><span class="n">select</span><span class="p">(</span>
+            <span class="c1"># From the full path, extracts just the filename, and converts to upper case to get the study ID.</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">study_id</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
+            <span class="c1"># Add variant information.</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">concat_ws</span><span class="p">(</span>
+                <span class="s2">&quot;_&quot;</span><span class="p">,</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;#chrom&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ref&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;alt&quot;</span><span class="p">),</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;variantId&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;#chrom&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;position&quot;</span><span class="p">),</span>
+            <span class="c1"># Parse p-value into mantissa and exponent.</span>
+            <span class="o">*</span><span class="n">parse_pvalue</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pval&quot;</span><span class="p">)),</span>
+            <span class="c1"># Add beta, standard error, and allele frequency information.</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;beta&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;double&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sebeta&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;double&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;standardError&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;af_alt&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;float&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;effectAlleleFrequencyFromSource&quot;</span><span class="p">),</span>
+        <span class="p">)</span>
+        <span class="c1"># Calculating the confidence intervals.</span>
+        <span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;pos&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">()</span> <span class="o">&amp;</span> <span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;beta&quot;</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="c1"># Average ~20Mb partitions with 30 partitions per study</span>
+        <span class="o">.</span><span class="n">repartitionByRange</span><span class="p">(</span><span class="mi">30</span><span class="p">,</span> <span class="s2">&quot;chromosome&quot;</span><span class="p">,</span> <span class="s2">&quot;position&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">sortWithinPartitions</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">,</span> <span class="s2">&quot;position&quot;</span><span class="p">)</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Initializing summary statistics object:</span>
+    <span class="k">return</span> <span class="n">SummaryStatistics</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="n">processed_summary_stats_df</span><span class="p">,</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="n">SummaryStatistics</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
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+        </span>
+        <span class="label"> Contributors </span>
+      </li>
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diff --git a/python_api/datasource/gnomad/_gnomad/index.html b/python_api/datasources/gnomad/_gnomad/index.html
similarity index 80%
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--- a/python_api/datasource/gnomad/_gnomad/index.html
+++ b/python_api/datasources/gnomad/_gnomad/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../finngen/study_index/">
+        <link rel="prev" href="../../finngen/summary_stats/">
       
       
         <link rel="next" href="../gnomad_ld/">
       
       
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>GnomAD - Open Targets Genetics</title>
+        <title>GnomAD - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,7 +102,7 @@
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         <div class="md-header__topic">
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-            Open Targets Genetics
+            Open Targets Gentropy
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       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
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+      
+        
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-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
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+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
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+    </li>
+  
+
+      
+        
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+  
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 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
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-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
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-    Installation
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-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
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-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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+          <ul class="md-nav__list" data-md-scrollfix>
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+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
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+    </li>
+  
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+            
+              
+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
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+      
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
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+  
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+    </li>
+  
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+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
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+    Development
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+  
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+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
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+            
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+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
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+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -607,7 +758,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -628,7 +779,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -649,7 +800,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -670,7 +821,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -691,7 +842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -712,7 +863,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -733,7 +884,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -754,7 +905,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -775,7 +926,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -796,7 +947,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -817,7 +968,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -838,7 +989,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -859,7 +1010,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -880,7 +1031,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -901,7 +1052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -941,32 +1092,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -986,12 +1137,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1002,14 +1153,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1021,6 +1172,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1060,7 +1232,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1076,14 +1248,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1110,6 +1282,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1136,7 +1329,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" checked>
         
           
           
@@ -1152,14 +1345,14 @@
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1231,7 +1424,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1247,14 +1440,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1368,7 +1561,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1384,14 +1577,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1505,7 +1698,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1521,14 +1714,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1584,80 +1777,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1682,32 +1801,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1718,11 +1837,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1739,11 +1858,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1760,11 +1879,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1781,11 +1900,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1802,11 +1921,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1823,11 +1942,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1853,12 +1972,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1869,14 +1988,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1889,7 +2008,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1910,7 +2029,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1931,7 +2050,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1952,7 +2071,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1998,32 +2117,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,11 +2153,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2055,11 +2174,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2076,11 +2195,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2307,11 +2426,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2381,6 +2563,10 @@ <h1>Gnomad</h1>
     display: none;
   }
 </style>
+
+<p><a href="https://gnomad.broadinstitute.org/">GnomAD</a> (Genome Aggregation Database) is a comprehensive resource that provides aggregated genomic data from large-scale sequencing projects. It encompasses variants from diverse populations and is widely used for variant annotation and population genetics studies.</p>
+<p>We use <strong>GnomAD v4.0</strong> as a source for variant annotation, offering detailed information about the prevalence and distribution of genetic variants across different populations. This version of GnomAD provides valuable insights into the genomic landscape, aiding in the interpretation of genetic variants and their potential functional implications.</p>
+<p>Additionally, <a href="https://gnomad.broadinstitute.org/news/2018-10-gnomad-v2-1/"><strong>GnomAD v2.1.1</strong></a> is utilized as a source for linkage disequilibrium (LD) information.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2403,7 +2589,7 @@ <h1>Gnomad</h1>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2470,7 +2656,7 @@ <h1>Gnomad</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/gnomad/gnomad_ld/index.html b/python_api/datasources/gnomad/gnomad_ld/index.html
similarity index 91%
rename from python_api/datasource/gnomad/gnomad_ld/index.html
rename to python_api/datasources/gnomad/gnomad_ld/index.html
index a05e854ca..993415f54 100644
--- a/python_api/datasource/gnomad/gnomad_ld/index.html
+++ b/python_api/datasources/gnomad/gnomad_ld/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>LD Matrix - Open Targets Genetics</title>
+        <title>LD Matrix - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix" class="md-skip">
+        <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1141,7 +1334,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" checked>
         
           
           
@@ -1157,14 +1350,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1219,7 +1412,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix" class="md-nav__link">
     <span class="md-ellipsis">
       GnomADLDMatrix
     </span>
@@ -1229,27 +1422,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="md-nav__link">
     <span class="md-ellipsis">
-      as_ld_index()
+      as_ld_index
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="md-nav__link">
     <span class="md-ellipsis">
-      get_ld_matrix_slice()
+      get_ld_matrix_slice
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="md-nav__link">
     <span class="md-ellipsis">
-      get_ld_variants()
+      get_ld_variants
     </span>
   </a>
   
@@ -1314,7 +1507,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1330,14 +1523,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1451,7 +1644,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1467,14 +1660,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1588,7 +1781,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1604,14 +1797,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1667,80 +1860,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1765,32 +1884,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1801,11 +1920,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1822,11 +1941,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1843,11 +1962,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1864,11 +1983,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1885,11 +2004,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1906,11 +2025,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1936,12 +2055,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1952,14 +2071,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1972,7 +2091,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1993,7 +2112,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2014,7 +2133,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2035,7 +2154,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2081,32 +2200,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2117,11 +2236,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2138,11 +2257,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2159,11 +2278,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2180,11 +2299,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2201,11 +2320,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2222,11 +2341,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2243,11 +2362,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2264,11 +2383,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2285,11 +2404,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2306,11 +2425,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2327,11 +2446,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2348,11 +2467,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2369,11 +2488,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2390,11 +2509,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2444,7 +2626,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix" class="md-nav__link">
     <span class="md-ellipsis">
       GnomADLDMatrix
     </span>
@@ -2454,27 +2636,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="md-nav__link">
     <span class="md-ellipsis">
-      as_ld_index()
+      as_ld_index
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="md-nav__link">
     <span class="md-ellipsis">
-      get_ld_matrix_slice()
+      get_ld_matrix_slice
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="md-nav__link">
     <span class="md-ellipsis">
-      get_ld_variants()
+      get_ld_variants
     </span>
   </a>
   
@@ -2509,16 +2691,15 @@ <h1>LD Matrix</h1>
 
 
 
-
-<h2 id="otg.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
-          <code>otg.datasource.gnomad.ld.GnomADLDMatrix</code>
+<h2 id="gentropy.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
+          <code>gentropy.datasource.gnomad.ld.GnomADLDMatrix</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.gnomad.ld.GnomADLDMatrix" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2540,7 +2721,7 @@ <h2 id="otg.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
     </thead>
     <tbody>
         <tr>
-          <td><code>ld_matrix_template</code></td>
+          <td><code><span title="gentropy.datasource.gnomad.ld.GnomADLDMatrix.ld_matrix_template">ld_matrix_template</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2551,7 +2732,7 @@ <h2 id="otg.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>ld_index_raw_template</code></td>
+          <td><code><span title="gentropy.datasource.gnomad.ld.GnomADLDMatrix.ld_index_raw_template">ld_index_raw_template</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2562,7 +2743,7 @@ <h2 id="otg.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>grch37_to_grch38_chain_path</code></td>
+          <td><code><span title="gentropy.datasource.gnomad.ld.GnomADLDMatrix.grch37_to_grch38_chain_path">grch37_to_grch38_chain_path</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2573,7 +2754,7 @@ <h2 id="otg.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>ld_populations</code></td>
+          <td><code><span title="gentropy.datasource.gnomad.ld.GnomADLDMatrix.ld_populations">ld_populations</span></code></td>
           <td>
                 <code>list[str]</code>
           </td>
@@ -2587,7 +2768,7 @@ <h2 id="otg.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
   </table>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gnomad/ld.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/gnomad/ld.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 22</span>
 <span class="normal"> 23</span>
 <span class="normal"> 24</span>
@@ -3465,11 +3646,10 @@ <h2 id="otg.datasource.gnomad.ld.GnomADLDMatrix" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="doc doc-heading">
+<h3 id="gentropy.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">as_ld_index</span><span class="p">(</span><span class="n">min_r2</span><span class="p">:</span> <span class="nb">float</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">LDIndex</span></code>
 
-<a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3525,7 +3705,7 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="doc doc-head
     <tbody>
         <tr>
 <td><code>LDIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.ld_index.LDIndex" href="../../../dataset/ld_index/#otg.dataset.ld_index.LDIndex">LDIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.ld_index.LDIndex" href="../../../datasets/ld_index/#gentropy.dataset.ld_index.LDIndex">LDIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3537,7 +3717,7 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="doc doc-head
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gnomad/ld.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gnomad/ld.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">271</span>
 <span class="normal">272</span>
 <span class="normal">273</span>
@@ -3640,11 +3820,10 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index" class="doc doc-head
 
 
 
-
-<h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="doc doc-heading">
+<h3 id="gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_ld_matrix_slice</span><span class="p">(</span><span class="n">gnomad_ancestry</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">start_index</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">end_index</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
 
-<a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3738,7 +3917,7 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gnomad/ld.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gnomad/ld.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">414</span>
 <span class="normal">415</span>
 <span class="normal">416</span>
@@ -3823,11 +4002,10 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice" class="doc
 
 
 
-
-<h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="doc doc-heading">
+<h3 id="gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_ld_variants</span><span class="p">(</span><span class="n">gnomad_ancestry</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">chromosome</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">start</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">end</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span></code>
 
-<a href="#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3931,7 +4109,7 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="doc doc-
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gnomad/ld.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gnomad/ld.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">318</span>
 <span class="normal">319</span>
 <span class="normal">320</span>
@@ -4051,6 +4229,7 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="doc doc-
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -4074,7 +4253,7 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="doc doc-
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -4141,7 +4320,7 @@ <h3 id="otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants" class="doc doc-
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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similarity index 89%
rename from python_api/datasource/gnomad/gnomad_variants/index.html
rename to python_api/datasources/gnomad/gnomad_variants/index.html
index 26118da9e..14d0e0935 100644
--- a/python_api/datasource/gnomad/gnomad_variants/index.html
+++ b/python_api/datasources/gnomad/gnomad_variants/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Variants - Open Targets Genetics</title>
+        <title>Variants - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.gnomad.variants.GnomADVariants" class="md-skip">
+        <a href="#gentropy.datasource.gnomad.variants.GnomADVariants" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
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+            Open Targets Gentropy
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       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
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+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
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+  
+  
+  
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+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+    Run step using YAML config
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+    </li>
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+      
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+
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
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+  
+
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+    </li>
+  
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+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
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             Python API
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+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
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-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
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+    Datasources
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
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-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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             Eqtl catalogue
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@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1141,7 +1334,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" checked>
         
           
           
@@ -1157,14 +1350,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1240,7 +1433,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.variants.GnomADVariants" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.variants.GnomADVariants" class="md-nav__link">
     <span class="md-ellipsis">
       GnomADVariants
     </span>
@@ -1250,9 +1443,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="md-nav__link">
     <span class="md-ellipsis">
-      as_variant_annotation()
+      as_variant_annotation
     </span>
   </a>
   
@@ -1296,7 +1489,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1312,14 +1505,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1433,7 +1626,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1449,14 +1642,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1570,7 +1763,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1586,14 +1779,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1649,80 +1842,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1747,32 +1866,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1783,11 +1902,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1804,11 +1923,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1825,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1846,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1867,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1888,11 +2007,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1918,12 +2037,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1934,14 +2053,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1954,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1975,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1996,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2017,7 +2136,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2063,32 +2182,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2099,11 +2218,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2120,11 +2239,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2141,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2162,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2183,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2204,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2225,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2246,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2267,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2288,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2309,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2330,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2351,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2372,11 +2491,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2426,7 +2608,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.variants.GnomADVariants" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.variants.GnomADVariants" class="md-nav__link">
     <span class="md-ellipsis">
       GnomADVariants
     </span>
@@ -2436,9 +2618,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="md-nav__link">
+  <a href="#gentropy.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="md-nav__link">
     <span class="md-ellipsis">
-      as_variant_annotation()
+      as_variant_annotation
     </span>
   </a>
   
@@ -2473,16 +2655,15 @@ <h1>Variants</h1>
 
 
 
-
-<h2 id="otg.datasource.gnomad.variants.GnomADVariants" class="doc doc-heading">
-          <code>otg.datasource.gnomad.variants.GnomADVariants</code>
+<h2 id="gentropy.datasource.gnomad.variants.GnomADVariants" class="doc doc-heading">
+          <code>gentropy.datasource.gnomad.variants.GnomADVariants</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.gnomad.variants.GnomADVariants" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gnomad.variants.GnomADVariants" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2503,7 +2684,7 @@ <h2 id="otg.datasource.gnomad.variants.GnomADVariants" class="doc doc-heading">
     </thead>
     <tbody>
         <tr>
-          <td><code>gnomad_genomes</code></td>
+          <td><code><span title="gentropy.datasource.gnomad.variants.GnomADVariants.gnomad_genomes">gnomad_genomes</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2514,7 +2695,7 @@ <h2 id="otg.datasource.gnomad.variants.GnomADVariants" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>chain_hail_38_37</code></td>
+          <td><code><span title="gentropy.datasource.gnomad.variants.GnomADVariants.chain_hail_38_37">chain_hail_38_37</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2525,7 +2706,7 @@ <h2 id="otg.datasource.gnomad.variants.GnomADVariants" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>populations</code></td>
+          <td><code><span title="gentropy.datasource.gnomad.variants.GnomADVariants.populations">populations</span></code></td>
           <td>
                 <code>list[str]</code>
           </td>
@@ -2539,7 +2720,7 @@ <h2 id="otg.datasource.gnomad.variants.GnomADVariants" class="doc doc-heading">
   </table>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gnomad/variants.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/gnomad/variants.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 15</span>
 <span class="normal"> 16</span>
 <span class="normal"> 17</span>
@@ -2869,11 +3050,10 @@ <h2 id="otg.datasource.gnomad.variants.GnomADVariants" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="doc doc-heading">
+<h3 id="gentropy.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">as_variant_annotation</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">VariantAnnotation</span></code>
 
-<a href="#otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2899,7 +3079,7 @@ <h3 id="otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" cla
     <tbody>
         <tr>
 <td><code>VariantAnnotation</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.variant_annotation.VariantAnnotation" href="../../../dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.variant_annotation.VariantAnnotation" href="../../../datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2911,7 +3091,7 @@ <h3 id="otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" cla
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gnomad/variants.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gnomad/variants.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 65</span>
 <span class="normal"> 66</span>
 <span class="normal"> 67</span>
@@ -3133,6 +3313,7 @@ <h3 id="otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation" cla
 
   </div>
 
+
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
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-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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similarity index 80%
rename from python_api/datasource/gwas_catalog/_gwas_catalog/index.html
rename to python_api/datasources/gwas_catalog/_gwas_catalog/index.html
index 9bf2289e8..4f5844b6a 100644
--- a/python_api/datasource/gwas_catalog/_gwas_catalog/index.html
+++ b/python_api/datasources/gwas_catalog/_gwas_catalog/index.html
@@ -16,11 +16,11 @@
       
       
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>GWAS Catalog - Open Targets Genetics</title>
+        <title>GWAS Catalog - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,7 +102,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -187,13 +187,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -228,7 +245,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -244,6 +261,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -304,22 +338,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
     </div>
@@ -333,11 +367,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -353,11 +387,11 @@
   
   
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-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -390,11 +424,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
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+                
+  
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
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+  
+
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+            
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+        </nav>
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+  
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+      <a href="../../../../roadmap/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+  
+
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+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
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             Development
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
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             Python API
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@@ -607,7 +758,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -628,7 +779,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -649,7 +800,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -670,7 +821,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -691,7 +842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -712,7 +863,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -733,7 +884,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -754,7 +905,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -775,7 +926,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -796,7 +947,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -817,7 +968,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -838,7 +989,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -859,7 +1010,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -880,7 +1031,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -901,7 +1052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -941,32 +1092,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -986,12 +1137,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1002,14 +1153,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1021,6 +1172,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1060,7 +1232,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1076,14 +1248,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1110,6 +1282,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1134,7 +1327,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1150,14 +1343,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1231,7 +1424,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" checked>
         
           
           
@@ -1247,14 +1440,14 @@
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1368,7 +1561,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1384,14 +1577,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1505,7 +1698,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1521,14 +1714,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1584,80 +1777,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1682,32 +1801,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1718,11 +1837,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1739,11 +1858,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1760,11 +1879,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1781,11 +1900,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1802,11 +1921,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1823,11 +1942,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1853,12 +1972,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1869,14 +1988,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1889,7 +2008,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1910,7 +2029,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1931,7 +2050,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1952,7 +2071,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1998,32 +2117,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,11 +2153,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2055,11 +2174,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2076,11 +2195,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2307,11 +2426,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2374,6 +2556,20 @@
   <img width="100" height="100" src="../../../../assets/imgs/GWAS_Catalog_circle_178x178.png">
   <h1>GWAS Catalog</h1>
 </div>
+
+<p>The <a href="https://www.ebi.ac.uk/gwas/">GWAS Catalog</a> is a comprehensive resource that aims to provide a curated collection of Genome-Wide Association Studies (GWAS) (including harmonized full GWAS summary statistics) across various traits and diseases in humans.</p>
+<p>It serves as a valuable repository of genetic associations identified in diverse populations, offering insights into the genetic basis of complex traits and diseases.</p>
+<p>We rely on the GWAS Catalog for a rich source of genetic associations, utilizing the data for analysis and interpretation.</p>
+<p>For detailed information on specific genetic associations, their significance, and associated studies, refer to the <a href="https://www.ebi.ac.uk/gwas/">GWAS Catalog</a>.</p>
+<p>Within our analyses, we leverage two different types of studies from the GWAS Catalog:</p>
+<ol>
+<li>
+<p><strong>Studies with (full) GWAS summary stats</strong></p>
+</li>
+<li>
+<p><strong>Studies with top hits only - GWAS curated studies</strong></p>
+</li>
+</ol>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2396,7 +2592,7 @@ <h1>GWAS Catalog</h1>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2463,7 +2659,7 @@ <h1>GWAS Catalog</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/datasource/gwas_catalog/associations/index.html b/python_api/datasources/gwas_catalog/associations/index.html
similarity index 91%
rename from python_api/datasource/gwas_catalog/associations/index.html
rename to python_api/datasources/gwas_catalog/associations/index.html
index 0d046286a..cf9dedba0 100644
--- a/python_api/datasource/gwas_catalog/associations/index.html
+++ b/python_api/datasources/gwas_catalog/associations/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Associations - Open Targets Genetics</title>
+        <title>Associations - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="md-skip">
+        <a href="#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1236,7 +1429,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" checked>
         
           
           
@@ -1252,14 +1445,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1314,7 +1507,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogCuratedAssociationsParser
     </span>
@@ -1324,9 +1517,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
@@ -1338,7 +1531,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocusGWASCatalog
     </span>
@@ -1348,18 +1541,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.apply_inclusion_list" class="md-nav__link">
     <span class="md-ellipsis">
-      qc_ambiguous_study()
+      apply_inclusion_list
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="md-nav__link">
     <span class="md-ellipsis">
-      update_study_id()
+      qc_ambiguous_study
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="md-nav__link">
+    <span class="md-ellipsis">
+      update_study_id
     </span>
   </a>
   
@@ -1466,7 +1668,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1482,14 +1684,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1603,7 +1805,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1619,14 +1821,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1682,80 +1884,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1780,32 +1908,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1816,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1837,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1858,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1879,11 +2007,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1900,11 +2028,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1921,11 +2049,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1951,12 +2079,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1967,14 +2095,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1987,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2008,7 +2136,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2029,7 +2157,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2050,7 +2178,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2096,32 +2224,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2132,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2153,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2174,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2195,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2216,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2237,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2258,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2279,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2300,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2321,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2342,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2363,11 +2491,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2384,11 +2512,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2405,11 +2533,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2459,7 +2650,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogCuratedAssociationsParser
     </span>
@@ -2469,9 +2660,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
@@ -2483,7 +2674,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocusGWASCatalog
     </span>
@@ -2493,18 +2684,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.apply_inclusion_list" class="md-nav__link">
     <span class="md-ellipsis">
-      qc_ambiguous_study()
+      apply_inclusion_list
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="md-nav__link">
     <span class="md-ellipsis">
-      update_study_id()
+      qc_ambiguous_study
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="md-nav__link">
+    <span class="md-ellipsis">
+      update_study_id
     </span>
   </a>
   
@@ -2539,16 +2739,15 @@ <h1>Associations</h1>
 
 
 
-
-<h2 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="doc doc-heading">
-          <code>otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser</code>
+<h2 id="gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="doc doc-heading">
+          <code>gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2557,7 +2756,7 @@ <h2 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsP
       <p>GWAS Catalog curated associations parser.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">  30</span>
 <span class="normal">  31</span>
 <span class="normal">  32</span>
@@ -4653,15 +4852,14 @@ <h2 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsP
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">gwas_associations</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">variant_annotation</span><span class="p">:</span> <span class="n">VariantAnnotation</span><span class="p">,</span> <span class="n">pvalue_threshold</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">5e-08</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusGWASCatalog</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4700,7 +4898,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsP
         <tr>
           <td><code>variant_annotation</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.variant_annotation.VariantAnnotation" href="../../../dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.variant_annotation.VariantAnnotation" href="../../../datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation">VariantAnnotation</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4741,7 +4939,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsP
     <tbody>
         <tr>
 <td><code>StudyLocusGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4753,7 +4951,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsP
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 990</span>
 <span class="normal"> 991</span>
 <span class="normal"> 992</span>
@@ -4921,6 +5119,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsP
 
   </div>
 
+
 </div><hr />
 
 
@@ -4928,28 +5127,27 @@ <h3 id="otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsP
 
 
 
-
-<h2 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="doc doc-heading">
-          <code>otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog</code>
+<h2 id="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="doc doc-heading">
+          <code>gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code></p>
 
   
       <p>Study locus Dataset for GWAS Catalog curated associations.</p>
 <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">1070</span>
 <span class="normal">1071</span>
 <span class="normal">1072</span>
@@ -4998,7 +5196,23 @@ <h2 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="d
 <span class="normal">1115</span>
 <span class="normal">1116</span>
 <span class="normal">1117</span>
-<span class="normal">1118</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">1118</span>
+<span class="normal">1119</span>
+<span class="normal">1120</span>
+<span class="normal">1121</span>
+<span class="normal">1122</span>
+<span class="normal">1123</span>
+<span class="normal">1124</span>
+<span class="normal">1125</span>
+<span class="normal">1126</span>
+<span class="normal">1127</span>
+<span class="normal">1128</span>
+<span class="normal">1129</span>
+<span class="normal">1130</span>
+<span class="normal">1131</span>
+<span class="normal">1132</span>
+<span class="normal">1133</span>
+<span class="normal">1134</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">StudyLocusGWASCatalog</span><span class="p">(</span><span class="n">StudyLocus</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study locus Dataset for GWAS Catalog curated associations.</span>
 
@@ -5047,6 +5261,22 @@ <h2 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="d
             <span class="p">),</span>
         <span class="p">)</span>
         <span class="k">return</span> <span class="bp">self</span>
+
+    <span class="k">def</span> <span class="nf">apply_inclusion_list</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">,</span> <span class="n">inclusion_list</span><span class="p">:</span> <span class="n">DataFrame</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Restricting GWAS Catalog studies based on a list of accpected study ids.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            StudyLocusGWASCatalog: Filtered dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocusGWASCatalog</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
             </details>
 
@@ -5067,11 +5297,116 @@ <h2 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" class="d
 
 
 
+<h3 id="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.apply_inclusion_list" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">apply_inclusion_list</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusGWASCatalog</span></code>
+
+<a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.apply_inclusion_list" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Restricting GWAS Catalog studies based on a list of accpected study ids.</p>
+
+
 
-<h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="doc doc-heading">
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>inclusion_list</code></td>
+          <td>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of accepted GWAS Catalog study identifiers</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>StudyLocusGWASCatalog</code></td>          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Filtered dataset.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">1120</span>
+<span class="normal">1121</span>
+<span class="normal">1122</span>
+<span class="normal">1123</span>
+<span class="normal">1124</span>
+<span class="normal">1125</span>
+<span class="normal">1126</span>
+<span class="normal">1127</span>
+<span class="normal">1128</span>
+<span class="normal">1129</span>
+<span class="normal">1130</span>
+<span class="normal">1131</span>
+<span class="normal">1132</span>
+<span class="normal">1133</span>
+<span class="normal">1134</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">apply_inclusion_list</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">,</span> <span class="n">inclusion_list</span><span class="p">:</span> <span class="n">DataFrame</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Restricting GWAS Catalog studies based on a list of accpected study ids.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        StudyLocusGWASCatalog: Filtered dataset.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">),</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocusGWASCatalog</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">qc_ambiguous_study</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StudyLocusGWASCatalog</span></code>
 
-<a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -5091,7 +5426,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambigu
     <tbody>
         <tr>
 <td><code>StudyLocusGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -5103,7 +5438,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambigu
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">1100</span>
 <span class="normal">1101</span>
 <span class="normal">1102</span>
@@ -5152,11 +5487,10 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambigu
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">update_study_id</span><span class="p">(</span><span class="n">study_annotation</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocusGWASCatalog</span></code>
 
-<a href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -5206,7 +5540,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_st
     <tbody>
         <tr>
 <td><code>StudyLocusGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -5218,7 +5552,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_st
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">1077</span>
 <span class="normal">1078</span>
 <span class="normal">1079</span>
@@ -5274,6 +5608,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_st
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -5297,7 +5632,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_st
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-12T14:15:11+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-12</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -5364,7 +5699,7 @@ <h3 id="otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_st
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/datasource/gwas_catalog/study_index/index.html b/python_api/datasources/gwas_catalog/study_index/index.html
similarity index 67%
rename from python_api/datasource/gwas_catalog/study_index/index.html
rename to python_api/datasources/gwas_catalog/study_index/index.html
index 772c69a58..6fb230292 100644
--- a/python_api/datasource/gwas_catalog/study_index/index.html
+++ b/python_api/datasources/gwas_catalog/study_index/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Study Index - Open Targets Genetics</title>
+        <title>Study Index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="md-skip">
+        <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1236,7 +1429,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" checked>
         
           
           
@@ -1252,14 +1445,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1335,7 +1528,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="md-nav__link">
     <span class="md-ellipsis">
       StudyIndexGWASCatalogParser
     </span>
@@ -1345,18 +1538,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="md-nav__link">
     <span class="md-ellipsis">
-      parse_cohorts()
+      parse_cohorts
     </span>
   </a>
   
@@ -1368,7 +1561,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="md-nav__link">
     <span class="md-ellipsis">
       StudyIndexGWASCatalog
     </span>
@@ -1378,36 +1571,63 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="md-nav__link">
+    <span class="md-ellipsis">
+      annotate_ancestries
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="md-nav__link">
+    <span class="md-ellipsis">
+      annotate_discovery_sample_sizes
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_from_study_curation" class="md-nav__link">
+    <span class="md-ellipsis">
+      annotate_from_study_curation
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_ancestries()
+      annotate_sumstats_info
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.apply_inclusion_list" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_discovery_sample_sizes()
+      apply_inclusion_list
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.extract_studies_for_curation" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_sumstats_info()
+      extract_studies_for_curation
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="md-nav__link">
     <span class="md-ellipsis">
-      update_study_id()
+      update_study_id
     </span>
   </a>
   
@@ -1493,7 +1713,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1509,14 +1729,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1630,7 +1850,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1646,14 +1866,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1709,6 +1929,14 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
@@ -1725,32 +1953,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1761,11 +1989,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1775,17 +2003,22 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
   
 
-              
-            
-          </ul>
-        </nav>
-      
+      </a>
     </li>
   
 
@@ -1797,78 +2030,12 @@
   
   
   
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+    <li class="md-nav__item">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
-              
   
   <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Coloc
+    Coloc
   </span>
   
 
@@ -1885,7 +2052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1906,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1927,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1947,27 +2114,6 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     
     
     
@@ -1978,12 +2124,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1994,14 +2140,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2014,7 +2160,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2035,7 +2181,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2056,7 +2202,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2077,7 +2223,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2123,32 +2269,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2159,11 +2305,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2180,11 +2326,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2201,11 +2347,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2222,11 +2368,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2243,11 +2389,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2264,11 +2410,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2285,11 +2431,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2306,11 +2452,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2327,11 +2473,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2348,11 +2494,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2369,11 +2515,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2390,11 +2536,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2411,11 +2557,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2432,11 +2578,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2486,7 +2695,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="md-nav__link">
     <span class="md-ellipsis">
       StudyIndexGWASCatalogParser
     </span>
@@ -2496,18 +2705,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="md-nav__link">
     <span class="md-ellipsis">
-      from_source()
+      from_source
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="md-nav__link">
     <span class="md-ellipsis">
-      parse_cohorts()
+      parse_cohorts
     </span>
   </a>
   
@@ -2519,7 +2728,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="md-nav__link">
     <span class="md-ellipsis">
       StudyIndexGWASCatalog
     </span>
@@ -2529,36 +2738,63 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="md-nav__link">
+    <span class="md-ellipsis">
+      annotate_ancestries
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="md-nav__link">
+    <span class="md-ellipsis">
+      annotate_discovery_sample_sizes
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_from_study_curation" class="md-nav__link">
+    <span class="md-ellipsis">
+      annotate_from_study_curation
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_ancestries()
+      annotate_sumstats_info
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.apply_inclusion_list" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_discovery_sample_sizes()
+      apply_inclusion_list
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.extract_studies_for_curation" class="md-nav__link">
     <span class="md-ellipsis">
-      annotate_sumstats_info()
+      extract_studies_for_curation
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="md-nav__link">
     <span class="md-ellipsis">
-      update_study_id()
+      update_study_id
     </span>
   </a>
   
@@ -2593,16 +2829,15 @@ <h1>Study Index</h1>
 
 
 
-
-<h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="doc doc-heading">
-          <code>otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser</code>
+<h2 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="doc doc-heading">
+          <code>gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2621,54 +2856,8 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" cla
 </ul>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 18</span>
-<span class="normal"> 19</span>
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-<span class="normal"> 61</span>
-<span class="normal"> 62</span>
-<span class="normal"> 63</span>
-<span class="normal"> 64</span>
+              <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 64</span>
 <span class="normal"> 65</span>
 <span class="normal"> 66</span>
 <span class="normal"> 67</span>
@@ -2893,7 +3082,53 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" cla
 <span class="normal">286</span>
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 <span class="normal">288</span>
-<span class="normal">289</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">289</span>
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+<span class="normal">335</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">StudyIndexGWASCatalogParser</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;GWAS Catalog study index parser.</span>
 
@@ -2948,7 +3183,7 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" cla
 <span class="sd">            +--------------------------------------------+</span>
 <span class="sd">            &lt;BLANKLINE&gt;</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="c1"># To initialize return objects for aggregate functions, schema has to be definied:</span>
+        <span class="c1"># To initialize return objects for aggregate functions, schema has to be defined:</span>
         <span class="n">schema</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">ArrayType</span><span class="p">(</span>
             <span class="n">t</span><span class="o">.</span><span class="n">StructType</span><span class="p">(</span>
                 <span class="p">[</span>
@@ -2974,7 +3209,7 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" cla
             <span class="p">),</span>
             <span class="k">lambda</span> <span class="n">ancestry</span><span class="p">:</span> <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
                 <span class="n">ancestry</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">LongType</span><span class="p">())</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">0</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
             <span class="p">),</span>
         <span class="p">)</span>
 
@@ -3033,7 +3268,7 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" cla
                 <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
                     <span class="n">a</span><span class="o">.</span><span class="n">ancestry</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
                     <span class="p">(</span><span class="n">a</span><span class="o">.</span><span class="n">sampleSize</span> <span class="o">+</span> <span class="n">ancestry</span><span class="o">.</span><span class="n">sampleSize</span><span class="p">)</span>
-                    <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">LongType</span><span class="p">())</span>
+                    <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span>
                     <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
                 <span class="p">),</span>
             <span class="p">)</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">a</span><span class="p">),</span>
@@ -3185,15 +3420,14 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser" cla
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_source</span><span class="p">(</span><span class="n">catalog_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">ancestry_file</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">sumstats_lut</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3271,7 +3505,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from
     <tbody>
         <tr>
 <td><code>StudyIndexGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3283,31 +3517,31 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">266</span>
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-<span class="normal">289</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">312</span>
+<span class="normal">313</span>
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+<span class="normal">315</span>
+<span class="normal">316</span>
+<span class="normal">317</span>
+<span class="normal">318</span>
+<span class="normal">319</span>
+<span class="normal">320</span>
+<span class="normal">321</span>
+<span class="normal">322</span>
+<span class="normal">323</span>
+<span class="normal">324</span>
+<span class="normal">325</span>
+<span class="normal">326</span>
+<span class="normal">327</span>
+<span class="normal">328</span>
+<span class="normal">329</span>
+<span class="normal">330</span>
+<span class="normal">331</span>
+<span class="normal">332</span>
+<span class="normal">333</span>
+<span class="normal">334</span>
+<span class="normal">335</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">from_source</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">StudyIndexGWASCatalogParser</span><span class="p">],</span>
     <span class="n">catalog_studies</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
@@ -3342,15 +3576,14 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">parse_cohorts</span><span class="p">(</span><span class="n">raw_cohort</span><span class="p">:</span> <span class="n">Column</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3428,32 +3661,32 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.pars
 </blockquote>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">204</span>
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-<span class="normal">228</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">250</span>
+<span class="normal">251</span>
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+<span class="normal">271</span>
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+<span class="normal">273</span>
+<span class="normal">274</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
 <span class="k">def</span> <span class="nf">parse_cohorts</span><span class="p">(</span><span class="n">raw_cohort</span><span class="p">:</span> <span class="n">Column</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Return a list of unique cohort labels from pipe separated list if provided.</span>
 
@@ -3490,6 +3723,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.pars
 
   </div>
 
+
 </div><hr />
 
 
@@ -3497,75 +3731,28 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.pars
 
 
 
-
-<h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="doc doc-heading">
-          <code>otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog</code>
+<h2 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="doc doc-heading">
+          <code>gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../../../dataset/study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../../../datasets/study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code></p>
 
   
       <p>Study index dataset from GWAS Catalog.</p>
 <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">292</span>
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+              <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">338</span>
 <span class="normal">339</span>
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@@ -3779,7 +3966,229 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
 <span class="normal">549</span>
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+<span class="normal">552</span>
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+<span class="normal">657</span>
+<span class="normal">658</span>
+<span class="normal">659</span>
+<span class="normal">660</span>
+<span class="normal">661</span>
+<span class="normal">662</span>
+<span class="normal">663</span>
+<span class="normal">664</span>
+<span class="normal">665</span>
+<span class="normal">666</span>
+<span class="normal">667</span>
+<span class="normal">668</span>
+<span class="normal">669</span>
+<span class="normal">670</span>
+<span class="normal">671</span>
+<span class="normal">672</span>
+<span class="normal">673</span>
+<span class="normal">674</span>
+<span class="normal">675</span>
+<span class="normal">676</span>
+<span class="normal">677</span>
+<span class="normal">678</span>
+<span class="normal">679</span>
+<span class="normal">680</span>
+<span class="normal">681</span>
+<span class="normal">682</span>
+<span class="normal">683</span>
+<span class="normal">684</span>
+<span class="normal">685</span>
+<span class="normal">686</span>
+<span class="normal">687</span>
+<span class="normal">688</span>
+<span class="normal">689</span>
+<span class="normal">690</span>
+<span class="normal">691</span>
+<span class="normal">692</span>
+<span class="normal">693</span>
+<span class="normal">694</span>
+<span class="normal">695</span>
+<span class="normal">696</span>
+<span class="normal">697</span>
+<span class="normal">698</span>
+<span class="normal">699</span>
+<span class="normal">700</span>
+<span class="normal">701</span>
+<span class="normal">702</span>
+<span class="normal">703</span>
+<span class="normal">704</span>
+<span class="normal">705</span>
+<span class="normal">706</span>
+<span class="normal">707</span>
+<span class="normal">708</span>
+<span class="normal">709</span>
+<span class="normal">710</span>
+<span class="normal">711</span>
+<span class="normal">712</span>
+<span class="normal">713</span>
+<span class="normal">714</span>
+<span class="normal">715</span>
+<span class="normal">716</span>
+<span class="normal">717</span>
+<span class="normal">718</span>
+<span class="normal">719</span>
+<span class="normal">720</span>
+<span class="normal">721</span>
+<span class="normal">722</span>
+<span class="normal">723</span>
+<span class="normal">724</span>
+<span class="normal">725</span>
+<span class="normal">726</span>
+<span class="normal">727</span>
+<span class="normal">728</span>
+<span class="normal">729</span>
+<span class="normal">730</span>
+<span class="normal">731</span>
+<span class="normal">732</span>
+<span class="normal">733</span>
+<span class="normal">734</span>
+<span class="normal">735</span>
+<span class="normal">736</span>
+<span class="normal">737</span>
+<span class="normal">738</span>
+<span class="normal">739</span>
+<span class="normal">740</span>
+<span class="normal">741</span>
+<span class="normal">742</span>
+<span class="normal">743</span>
+<span class="normal">744</span>
+<span class="normal">745</span>
+<span class="normal">746</span>
+<span class="normal">747</span>
+<span class="normal">748</span>
+<span class="normal">749</span>
+<span class="normal">750</span>
+<span class="normal">751</span>
+<span class="normal">752</span>
+<span class="normal">753</span>
+<span class="normal">754</span>
+<span class="normal">755</span>
+<span class="normal">756</span>
+<span class="normal">757</span>
+<span class="normal">758</span>
+<span class="normal">759</span>
+<span class="normal">760</span>
+<span class="normal">761</span>
+<span class="normal">762</span>
+<span class="normal">763</span>
+<span class="normal">764</span>
+<span class="normal">765</span>
+<span class="normal">766</span>
+<span class="normal">767</span>
+<span class="normal">768</span>
+<span class="normal">769</span>
+<span class="normal">770</span>
+<span class="normal">771</span>
+<span class="normal">772</span>
+<span class="normal">773</span>
+<span class="normal">774</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">StudyIndexGWASCatalog</span><span class="p">(</span><span class="n">StudyIndex</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Study index dataset from GWAS Catalog.</span>
 
@@ -3830,6 +4239,138 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
 
         <span class="k">return</span> <span class="bp">self</span>
 
+    <span class="k">def</span> <span class="nf">annotate_from_study_curation</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">curation_table</span><span class="p">:</span> <span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Annotating study index with curation.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            curation_table (DataFrame | None): Curated GWAS Catalog studies with summary statistics</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            StudyIndexGWASCatalog: Updated study index</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Providing curation table is optional. However once this method is called, the quality and studyFlag columns are added.</span>
+        <span class="k">if</span> <span class="n">curation_table</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="bp">self</span>
+
+        <span class="n">columns</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span>
+
+        <span class="c1"># Adding prefix to columns in the curation table:</span>
+        <span class="n">curation_table</span> <span class="o">=</span> <span class="n">curation_table</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+            <span class="o">*</span><span class="p">[</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;curation_</span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">column</span> <span class="o">!=</span> <span class="s2">&quot;studyId&quot;</span>
+                <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">curation_table</span><span class="o">.</span><span class="n">columns</span>
+            <span class="p">]</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Create expression how to update/create quality controls dataset:</span>
+        <span class="n">qualityControls_expression</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="s2">&quot;qualityControls&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">columns</span>
+            <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">(),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">array_union</span><span class="p">(</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">))</span>
+                <span class="p">),</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">))</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Create expression how to update/create analysis flag:</span>
+        <span class="n">analysis_expression</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="s2">&quot;analysisFlags&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">columns</span>
+            <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">(),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">array_union</span><span class="p">(</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;analysisFlags&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">))</span>
+                <span class="p">),</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;analysisFlags&quot;</span><span class="p">))</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Updating columns list. We might or might not list columns twice, but that doesn&#39;t matter, unique set will generated:</span>
+        <span class="n">columns</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">columns</span> <span class="o">+</span> <span class="p">[</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span> <span class="s2">&quot;analysisFlags&quot;</span><span class="p">]))</span>
+
+        <span class="c1"># Based on the curation table, columns needs to be updated:</span>
+        <span class="n">curated_df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">curation_table</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
+            <span class="c1"># Updating study type:</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                <span class="s2">&quot;studyType&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_studyType&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">))</span>
+            <span class="p">)</span>
+            <span class="c1"># Updating quality controls:</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span> <span class="n">qualityControls_expression</span><span class="p">)</span>
+            <span class="c1"># Updating study annotation flags:</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;analysisFlags&quot;</span><span class="p">,</span> <span class="n">analysis_expression</span><span class="p">)</span>
+            <span class="c1"># Dropping columns coming from the curation table:</span>
+            <span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">*</span><span class="n">columns</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">return</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">curated_df</span><span class="p">,</span> <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndexGWASCatalog</span><span class="o">.</span><span class="n">get_schema</span><span class="p">()</span>
+        <span class="p">)</span>
+
+    <span class="k">def</span> <span class="nf">extract_studies_for_curation</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">curation</span><span class="p">:</span> <span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Extract studies for curation.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            curation (DataFrame | None): Dataframe with curation.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            DataFrame: Updated curation table. New studies are have the `isCurated` False.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># If no curation table provided, assume all studies needs curation:</span>
+        <span class="k">if</span> <span class="n">curation</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">df</span>
+                <span class="c1"># Curation only applyed on studies with summary statistics:</span>
+                <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">))</span>
+                <span class="c1"># Adding columns expected in the curation table - array columns aready flattened:</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;analysisFlag&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;qualityControl&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;isCurated&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+            <span class="p">)</span>
+
+        <span class="c1"># Adding prefix to columns in the curation table:</span>
+        <span class="n">curation</span> <span class="o">=</span> <span class="n">curation</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+            <span class="o">*</span><span class="p">[</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;curation_</span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+                <span class="k">if</span> <span class="n">column</span> <span class="o">!=</span> <span class="s2">&quot;studyId&quot;</span>
+                <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span>
+                <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">curation</span><span class="o">.</span><span class="n">columns</span>
+            <span class="p">]</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span>
+            <span class="c1"># Curation only applyed on studies with summary statistics:</span>
+            <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">))</span>
+            <span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">curation</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                <span class="s2">&quot;studyId&quot;</span><span class="p">,</span>
+                <span class="c1"># Propagate existing curation - array columns are being flattened:</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_studyType&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">array_join</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">),</span> <span class="s2">&quot;|&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+                    <span class="s2">&quot;analysisFlag&quot;</span>
+                <span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">array_join</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">),</span> <span class="s2">&quot;|&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+                    <span class="s2">&quot;qualityControl&quot;</span>
+                <span class="p">),</span>
+                <span class="c1"># This boolean flag needs to be casted to string, because saving to tsv would fail otherwise:</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_isCurated&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">))</span>
+                <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">())</span>
+                <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;isCurated&quot;</span><span class="p">),</span>
+                <span class="c1"># The following columns are propagated to make curation easier:</span>
+                <span class="s2">&quot;pubmedId&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;publicationTitle&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;traitFromSource&quot;</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+
     <span class="k">def</span> <span class="nf">annotate_ancestries</span><span class="p">(</span>
         <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">ancestry_lut</span><span class="p">:</span> <span class="n">DataFrame</span>
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
@@ -3844,7 +4385,7 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
 <span class="sd">        Returns:</span>
 <span class="sd">            StudyIndexGWASCatalog: Slimmed and cleaned version of the ancestry annotation.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="kn">from</span> <span class="nn">otg.datasource.gwas_catalog.study_index</span> <span class="kn">import</span> <span class="p">(</span>
+        <span class="kn">from</span> <span class="nn">gentropy.datasource.gwas_catalog.study_index</span> <span class="kn">import</span> <span class="p">(</span>
             <span class="n">StudyIndexGWASCatalogParser</span> <span class="k">as</span> <span class="n">GWASCatalogStudyIndexParser</span><span class="p">,</span>
         <span class="p">)</span>
 
@@ -3877,7 +4418,7 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
                     <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
                         <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;broadAncestralCategory&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
                         <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;numberOfIndividuals&quot;</span><span class="p">)</span>
-                        <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">LongType</span><span class="p">())</span>
+                        <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span>
                         <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
                     <span class="p">)</span>
                 <span class="p">)</span>
@@ -3953,8 +4494,9 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
 
         <span class="n">parsed_ancestry_lut</span> <span class="o">=</span> <span class="n">ancestry_stages</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
             <span class="n">europeans_deconvoluted</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;outer&quot;</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+            <span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;discoverySamples&quot;</span><span class="p">,</span> <span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">,</span> <span class="s2">&quot;replicationSamples&quot;</span>
         <span class="p">)</span>
-
         <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">parsed_ancestry_lut</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
             <span class="n">cohorts</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span>
         <span class="p">)</span>
@@ -3970,11 +4512,19 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
 
 <span class="sd">        Returns:</span>
 <span class="sd">            StudyIndexGWASCatalog: including `summarystatsLocation` and `hasSumstats` columns</span>
+
+<span class="sd">        Raises:</span>
+<span class="sd">            ValueError: if the sumstats_lut table doesn&#39;t have the right columns</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">gwas_sumstats_base_uri</span> <span class="o">=</span> <span class="p">(</span>
             <span class="s2">&quot;ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/&quot;</span>
         <span class="p">)</span>
 
+        <span class="k">if</span> <span class="s2">&quot;_c0&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">sumstats_lut</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s1">&#39;Sumstats look-up table needs to have `_c0` column. However it has: </span><span class="si">{</span><span class="s2">&quot;,&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sumstats_lut</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span>
+            <span class="p">)</span>
+
         <span class="n">parsed_sumstats_lut</span> <span class="o">=</span> <span class="n">sumstats_lut</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
             <span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">,</span>
             <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
@@ -3982,13 +4532,10 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
                 <span class="n">f</span><span class="o">.</span><span class="n">regexp_replace</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;_c0&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;^\.\/&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">),</span>
             <span class="p">),</span>
         <span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;\/(GCST\d+)\/&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                <span class="s2">&quot;studyId&quot;</span>
-            <span class="p">),</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">_parse_gwas_catalog_study_id</span><span class="p">(</span><span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
             <span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">,</span>
             <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
         <span class="p">)</span>
-
         <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
             <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">)</span>
             <span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">parsed_sumstats_lut</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
@@ -4033,13 +4580,51 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
             <span class="c1"># Aggregating sample sizes for all ancestries:</span>
             <span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span>  <span class="c1"># studyId has not been split yet</span>
             <span class="o">.</span><span class="n">agg</span><span class="p">(</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
             <span class="p">)</span>
         <span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sample_size_lut</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
         <span class="k">return</span> <span class="bp">self</span>
+
+    <span class="k">def</span> <span class="nf">apply_inclusion_list</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">inclusion_list</span><span class="p">:</span> <span class="n">DataFrame</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Restricting GWAS Catalog studies based on a list of accepted study identifiers.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            StudyIndexGWASCatalog: Filtered dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndexGWASCatalog</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_parse_gwas_catalog_study_id</span><span class="p">(</span><span class="n">sumstats_path_column</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Extract GWAS Catalog study accession from the summary statistics path.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            sumstats_path_column (str): column *name* for the summary statistics path</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: GWAS Catalog study accession.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">            &gt;&gt;&gt; data = [</span>
+<span class="sd">            ... (&#39;./GCST90086001-GCST90087000/GCST90086758/harmonised/35078996-GCST90086758-EFO_0007937.h.tsv.gz&#39;,),</span>
+<span class="sd">            ...    (&#39;gs://open-targets-gwas-summary-stats/harmonised/GCST000568.parquet/&#39;,),</span>
+<span class="sd">            ...    (None,)</span>
+<span class="sd">            ... ]</span>
+<span class="sd">            &gt;&gt;&gt; spark.createDataFrame(data, [&#39;testColumn&#39;]).select(StudyIndexGWASCatalog._parse_gwas_catalog_study_id(&#39;testColumn&#39;).alias(&#39;accessions&#39;)).collect()</span>
+<span class="sd">            [Row(accessions=&#39;GCST90086758&#39;), Row(accessions=&#39;GCST000568&#39;), Row(accessions=None)]</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">accesions</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">expr</span><span class="p">(</span><span class="sa">rf</span><span class="s2">&quot;regexp_extract_all(</span><span class="si">{</span><span class="n">sumstats_path_column</span><span class="si">}</span><span class="s2">, &#39;(GCST</span><span class="se">\\</span><span class="s2">d+)&#39;)&quot;</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">accesions</span><span class="p">[</span><span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">accesions</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">]</span>
 </code></pre></div></td></tr></table></div>
             </details>
 
@@ -4060,11 +4645,10 @@ <h2 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" class="do
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">annotate_ancestries</span><span class="p">(</span><span class="n">ancestry_lut</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
 
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4116,7 +4700,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_a
     <tbody>
         <tr>
 <td><code>StudyIndexGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4128,136 +4712,137 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_a
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
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-<span class="normal">471</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_ancestries</span><span class="p">(</span>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">521</span>
+<span class="normal">522</span>
+<span class="normal">523</span>
+<span class="normal">524</span>
+<span class="normal">525</span>
+<span class="normal">526</span>
+<span class="normal">527</span>
+<span class="normal">528</span>
+<span class="normal">529</span>
+<span class="normal">530</span>
+<span class="normal">531</span>
+<span class="normal">532</span>
+<span class="normal">533</span>
+<span class="normal">534</span>
+<span class="normal">535</span>
+<span class="normal">536</span>
+<span class="normal">537</span>
+<span class="normal">538</span>
+<span class="normal">539</span>
+<span class="normal">540</span>
+<span class="normal">541</span>
+<span class="normal">542</span>
+<span class="normal">543</span>
+<span class="normal">544</span>
+<span class="normal">545</span>
+<span class="normal">546</span>
+<span class="normal">547</span>
+<span class="normal">548</span>
+<span class="normal">549</span>
+<span class="normal">550</span>
+<span class="normal">551</span>
+<span class="normal">552</span>
+<span class="normal">553</span>
+<span class="normal">554</span>
+<span class="normal">555</span>
+<span class="normal">556</span>
+<span class="normal">557</span>
+<span class="normal">558</span>
+<span class="normal">559</span>
+<span class="normal">560</span>
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+<span class="normal">590</span>
+<span class="normal">591</span>
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+<span class="normal">594</span>
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+<span class="normal">596</span>
+<span class="normal">597</span>
+<span class="normal">598</span>
+<span class="normal">599</span>
+<span class="normal">600</span>
+<span class="normal">601</span>
+<span class="normal">602</span>
+<span class="normal">603</span>
+<span class="normal">604</span>
+<span class="normal">605</span>
+<span class="normal">606</span>
+<span class="normal">607</span>
+<span class="normal">608</span>
+<span class="normal">609</span>
+<span class="normal">610</span>
+<span class="normal">611</span>
+<span class="normal">612</span>
+<span class="normal">613</span>
+<span class="normal">614</span>
+<span class="normal">615</span>
+<span class="normal">616</span>
+<span class="normal">617</span>
+<span class="normal">618</span>
+<span class="normal">619</span>
+<span class="normal">620</span>
+<span class="normal">621</span>
+<span class="normal">622</span>
+<span class="normal">623</span>
+<span class="normal">624</span>
+<span class="normal">625</span>
+<span class="normal">626</span>
+<span class="normal">627</span>
+<span class="normal">628</span>
+<span class="normal">629</span>
+<span class="normal">630</span>
+<span class="normal">631</span>
+<span class="normal">632</span>
+<span class="normal">633</span>
+<span class="normal">634</span>
+<span class="normal">635</span>
+<span class="normal">636</span>
+<span class="normal">637</span>
+<span class="normal">638</span>
+<span class="normal">639</span>
+<span class="normal">640</span>
+<span class="normal">641</span>
+<span class="normal">642</span>
+<span class="normal">643</span>
+<span class="normal">644</span>
+<span class="normal">645</span>
+<span class="normal">646</span>
+<span class="normal">647</span>
+<span class="normal">648</span>
+<span class="normal">649</span>
+<span class="normal">650</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_ancestries</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">ancestry_lut</span><span class="p">:</span> <span class="n">DataFrame</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Extracting sample sizes and ancestry information.</span>
@@ -4271,7 +4856,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_a
 <span class="sd">    Returns:</span>
 <span class="sd">        StudyIndexGWASCatalog: Slimmed and cleaned version of the ancestry annotation.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="kn">from</span> <span class="nn">otg.datasource.gwas_catalog.study_index</span> <span class="kn">import</span> <span class="p">(</span>
+    <span class="kn">from</span> <span class="nn">gentropy.datasource.gwas_catalog.study_index</span> <span class="kn">import</span> <span class="p">(</span>
         <span class="n">StudyIndexGWASCatalogParser</span> <span class="k">as</span> <span class="n">GWASCatalogStudyIndexParser</span><span class="p">,</span>
     <span class="p">)</span>
 
@@ -4304,7 +4889,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_a
                 <span class="n">f</span><span class="o">.</span><span class="n">struct</span><span class="p">(</span>
                     <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;broadAncestralCategory&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;ancestry&quot;</span><span class="p">),</span>
                     <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;numberOfIndividuals&quot;</span><span class="p">)</span>
-                    <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">LongType</span><span class="p">())</span>
+                    <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">IntegerType</span><span class="p">())</span>
                     <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">),</span>
                 <span class="p">)</span>
             <span class="p">)</span>
@@ -4380,8 +4965,9 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_a
 
     <span class="n">parsed_ancestry_lut</span> <span class="o">=</span> <span class="n">ancestry_stages</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
         <span class="n">europeans_deconvoluted</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;outer&quot;</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+        <span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;discoverySamples&quot;</span><span class="p">,</span> <span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">,</span> <span class="s2">&quot;replicationSamples&quot;</span>
     <span class="p">)</span>
-
     <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">parsed_ancestry_lut</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
         <span class="n">cohorts</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span>
     <span class="p">)</span>
@@ -4397,11 +4983,10 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_a
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">annotate_discovery_sample_sizes</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
 
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4422,7 +5007,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_d
     <tbody>
         <tr>
 <td><code>StudyIndexGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4434,51 +5019,51 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_d
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">509</span>
-<span class="normal">510</span>
-<span class="normal">511</span>
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-<span class="normal">524</span>
-<span class="normal">525</span>
-<span class="normal">526</span>
-<span class="normal">527</span>
-<span class="normal">528</span>
-<span class="normal">529</span>
-<span class="normal">530</span>
-<span class="normal">531</span>
-<span class="normal">532</span>
-<span class="normal">533</span>
-<span class="normal">534</span>
-<span class="normal">535</span>
-<span class="normal">536</span>
-<span class="normal">537</span>
-<span class="normal">538</span>
-<span class="normal">539</span>
-<span class="normal">540</span>
-<span class="normal">541</span>
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-<span class="normal">543</span>
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-<span class="normal">547</span>
-<span class="normal">548</span>
-<span class="normal">549</span>
-<span class="normal">550</span>
-<span class="normal">551</span>
-<span class="normal">552</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_discovery_sample_sizes</span><span class="p">(</span>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">693</span>
+<span class="normal">694</span>
+<span class="normal">695</span>
+<span class="normal">696</span>
+<span class="normal">697</span>
+<span class="normal">698</span>
+<span class="normal">699</span>
+<span class="normal">700</span>
+<span class="normal">701</span>
+<span class="normal">702</span>
+<span class="normal">703</span>
+<span class="normal">704</span>
+<span class="normal">705</span>
+<span class="normal">706</span>
+<span class="normal">707</span>
+<span class="normal">708</span>
+<span class="normal">709</span>
+<span class="normal">710</span>
+<span class="normal">711</span>
+<span class="normal">712</span>
+<span class="normal">713</span>
+<span class="normal">714</span>
+<span class="normal">715</span>
+<span class="normal">716</span>
+<span class="normal">717</span>
+<span class="normal">718</span>
+<span class="normal">719</span>
+<span class="normal">720</span>
+<span class="normal">721</span>
+<span class="normal">722</span>
+<span class="normal">723</span>
+<span class="normal">724</span>
+<span class="normal">725</span>
+<span class="normal">726</span>
+<span class="normal">727</span>
+<span class="normal">728</span>
+<span class="normal">729</span>
+<span class="normal">730</span>
+<span class="normal">731</span>
+<span class="normal">732</span>
+<span class="normal">733</span>
+<span class="normal">734</span>
+<span class="normal">735</span>
+<span class="normal">736</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_discovery_sample_sizes</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Extract the sample size of the discovery stage of the study as annotated in the GWAS Catalog.</span>
@@ -4515,9 +5100,9 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_d
         <span class="c1"># Aggregating sample sizes for all ancestries:</span>
         <span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span>  <span class="c1"># studyId has not been split yet</span>
         <span class="o">.</span><span class="n">agg</span><span class="p">(</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nCases&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nControls&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="s2">&quot;sampleSize&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;integer&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;nSamples&quot;</span><span class="p">),</span>
         <span class="p">)</span>
     <span class="p">)</span>
     <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sample_size_lut</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
@@ -4533,16 +5118,15 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_d
 
 
 
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_from_study_curation" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">annotate_from_study_curation</span><span class="p">(</span><span class="n">curation_table</span><span class="p">:</span> <span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
 
-<h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">annotate_sumstats_info</span><span class="p">(</span><span class="n">sumstats_lut</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
-
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_from_study_curation" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
   
-      <p>Annotate summary stat locations.</p>
+      <p>Annotating study index with curation.</p>
 
 
 
@@ -4558,13 +5142,13 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_s
     </thead>
     <tbody>
         <tr>
-          <td><code>sumstats_lut</code></td>
+          <td><code>curation_table</code></td>
           <td>
-                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span> | None</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>listing GWAS Catalog summary stats paths</p>
+              <p>Curated GWAS Catalog studies with summary statistics</p>
             </div>
           </td>
           <td>
@@ -4587,11 +5171,11 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_s
     <tbody>
         <tr>
 <td><code>StudyIndexGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>including <code>summarystatsLocation</code> and <code>hasSumstats</code> columns</p>
+              <p>Updated study index</p>
             </div>
           </td>
         </tr>
@@ -4599,76 +5183,148 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_s
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">473</span>
-<span class="normal">474</span>
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-<span class="normal">507</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_sumstats_info</span><span class="p">(</span>
-    <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">sumstats_lut</span><span class="p">:</span> <span class="n">DataFrame</span>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">389</span>
+<span class="normal">390</span>
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+<span class="normal">458</span>
+<span class="normal">459</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_from_study_curation</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">curation_table</span><span class="p">:</span> <span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Annotate summary stat locations.</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Annotating study index with curation.</span>
 
 <span class="sd">    Args:</span>
-<span class="sd">        sumstats_lut (DataFrame): listing GWAS Catalog summary stats paths</span>
+<span class="sd">        curation_table (DataFrame | None): Curated GWAS Catalog studies with summary statistics</span>
 
 <span class="sd">    Returns:</span>
-<span class="sd">        StudyIndexGWASCatalog: including `summarystatsLocation` and `hasSumstats` columns</span>
+<span class="sd">        StudyIndexGWASCatalog: Updated study index</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="n">gwas_sumstats_base_uri</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="s2">&quot;ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/&quot;</span>
+    <span class="c1"># Providing curation table is optional. However once this method is called, the quality and studyFlag columns are added.</span>
+    <span class="k">if</span> <span class="n">curation_table</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">return</span> <span class="bp">self</span>
+
+    <span class="n">columns</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">columns</span>
+
+    <span class="c1"># Adding prefix to columns in the curation table:</span>
+    <span class="n">curation_table</span> <span class="o">=</span> <span class="n">curation_table</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+        <span class="o">*</span><span class="p">[</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;curation_</span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">column</span> <span class="o">!=</span> <span class="s2">&quot;studyId&quot;</span>
+            <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">curation_table</span><span class="o">.</span><span class="n">columns</span>
+        <span class="p">]</span>
     <span class="p">)</span>
 
-    <span class="n">parsed_sumstats_lut</span> <span class="o">=</span> <span class="n">sumstats_lut</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-        <span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">,</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">gwas_sumstats_base_uri</span><span class="p">),</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">regexp_replace</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;_c0&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;^\.\/&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">),</span>
-        <span class="p">),</span>
-    <span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">regexp_extract</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;\/(GCST\d+)\/&quot;</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-            <span class="s2">&quot;studyId&quot;</span>
-        <span class="p">),</span>
-        <span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">,</span>
-        <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
+    <span class="c1"># Create expression how to update/create quality controls dataset:</span>
+    <span class="n">qualityControls_expression</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="s2">&quot;qualityControls&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">columns</span>
+        <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">(),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">array_union</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">))</span>
+            <span class="p">),</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">))</span>
     <span class="p">)</span>
 
-    <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">)</span>
-        <span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">parsed_sumstats_lut</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
-        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">)))</span>
+    <span class="c1"># Create expression how to update/create analysis flag:</span>
+    <span class="n">analysis_expression</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="s2">&quot;analysisFlags&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">columns</span>
+        <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">(),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">array_union</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;analysisFlags&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">))</span>
+            <span class="p">),</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;analysisFlags&quot;</span><span class="p">))</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Updating columns list. We might or might not list columns twice, but that doesn&#39;t matter, unique set will generated:</span>
+    <span class="n">columns</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">columns</span> <span class="o">+</span> <span class="p">[</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span> <span class="s2">&quot;analysisFlags&quot;</span><span class="p">]))</span>
+
+    <span class="c1"># Based on the curation table, columns needs to be updated:</span>
+    <span class="n">curated_df</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">curation_table</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
+        <span class="c1"># Updating study type:</span>
+        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+            <span class="s2">&quot;studyType&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_studyType&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">))</span>
+        <span class="p">)</span>
+        <span class="c1"># Updating quality controls:</span>
+        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span> <span class="n">qualityControls_expression</span><span class="p">)</span>
+        <span class="c1"># Updating study annotation flags:</span>
+        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;analysisFlags&quot;</span><span class="p">,</span> <span class="n">analysis_expression</span><span class="p">)</span>
+        <span class="c1"># Dropping columns coming from the curation table:</span>
+        <span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="o">*</span><span class="n">columns</span><span class="p">)</span>
+    <span class="p">)</span>
+    <span class="k">return</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="n">curated_df</span><span class="p">,</span> <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndexGWASCatalog</span><span class="o">.</span><span class="n">get_schema</span><span class="p">()</span>
     <span class="p">)</span>
-    <span class="k">return</span> <span class="bp">self</span>
 </code></pre></div></td></tr></table></div>
           </details>
   </div>
@@ -4680,16 +5336,15 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_s
 
 
 
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">annotate_sumstats_info</span><span class="p">(</span><span class="n">sumstats_lut</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
 
-<h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">update_study_id</span><span class="p">(</span><span class="n">study_annotation</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
-
-<a href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
   
-      <p>Update studyId with a dataframe containing study.</p>
+      <p>Annotate summary stat locations.</p>
 
 
 
@@ -4705,13 +5360,13 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_stu
     </thead>
     <tbody>
         <tr>
-          <td><code>study_annotation</code></td>
+          <td><code>sumstats_lut</code></td>
           <td>
                 <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Dataframe containing <code>updatedStudyId</code>, <code>traitFromSource</code>, <code>traitFromSourceMappedIds</code> and key column <code>studyId</code>.</p>
+              <p>listing GWAS Catalog summary stats paths</p>
             </div>
           </td>
           <td>
@@ -4734,11 +5389,35 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_stu
     <tbody>
         <tr>
 <td><code>StudyIndexGWASCatalog</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Updated study table.</p>
+              <p>including <code>summarystatsLocation</code> and <code>hasSumstats</code> columns</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Raises:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td>
+                <code>ValueError</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>if the sumstats_lut table doesn't have the right columns</p>
             </div>
           </td>
         </tr>
@@ -4746,50 +5425,506 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_stu
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">299</span>
-<span class="normal">300</span>
-<span class="normal">301</span>
-<span class="normal">302</span>
-<span class="normal">303</span>
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-<span class="normal">305</span>
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-<span class="normal">307</span>
-<span class="normal">308</span>
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-<span class="normal">339</span>
-<span class="normal">340</span>
-<span class="normal">341</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">update_study_id</span><span class="p">(</span>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">652</span>
+<span class="normal">653</span>
+<span class="normal">654</span>
+<span class="normal">655</span>
+<span class="normal">656</span>
+<span class="normal">657</span>
+<span class="normal">658</span>
+<span class="normal">659</span>
+<span class="normal">660</span>
+<span class="normal">661</span>
+<span class="normal">662</span>
+<span class="normal">663</span>
+<span class="normal">664</span>
+<span class="normal">665</span>
+<span class="normal">666</span>
+<span class="normal">667</span>
+<span class="normal">668</span>
+<span class="normal">669</span>
+<span class="normal">670</span>
+<span class="normal">671</span>
+<span class="normal">672</span>
+<span class="normal">673</span>
+<span class="normal">674</span>
+<span class="normal">675</span>
+<span class="normal">676</span>
+<span class="normal">677</span>
+<span class="normal">678</span>
+<span class="normal">679</span>
+<span class="normal">680</span>
+<span class="normal">681</span>
+<span class="normal">682</span>
+<span class="normal">683</span>
+<span class="normal">684</span>
+<span class="normal">685</span>
+<span class="normal">686</span>
+<span class="normal">687</span>
+<span class="normal">688</span>
+<span class="normal">689</span>
+<span class="normal">690</span>
+<span class="normal">691</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">annotate_sumstats_info</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">sumstats_lut</span><span class="p">:</span> <span class="n">DataFrame</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Annotate summary stat locations.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        sumstats_lut (DataFrame): listing GWAS Catalog summary stats paths</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        StudyIndexGWASCatalog: including `summarystatsLocation` and `hasSumstats` columns</span>
+
+<span class="sd">    Raises:</span>
+<span class="sd">        ValueError: if the sumstats_lut table doesn&#39;t have the right columns</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">gwas_sumstats_base_uri</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="s2">&quot;ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/&quot;</span>
+    <span class="p">)</span>
+
+    <span class="k">if</span> <span class="s2">&quot;_c0&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">sumstats_lut</span><span class="o">.</span><span class="n">columns</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="sa">f</span><span class="s1">&#39;Sumstats look-up table needs to have `_c0` column. However it has: </span><span class="si">{</span><span class="s2">&quot;,&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">sumstats_lut</span><span class="o">.</span><span class="n">columns</span><span class="p">)</span><span class="si">}</span><span class="s1">&#39;</span>
+        <span class="p">)</span>
+
+    <span class="n">parsed_sumstats_lut</span> <span class="o">=</span> <span class="n">sumstats_lut</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+        <span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">,</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">concat</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">gwas_sumstats_base_uri</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">regexp_replace</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;_c0&quot;</span><span class="p">),</span> <span class="sa">r</span><span class="s2">&quot;^\.\/&quot;</span><span class="p">,</span> <span class="s2">&quot;&quot;</span><span class="p">),</span>
+        <span class="p">),</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">_parse_gwas_catalog_study_id</span><span class="p">(</span><span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">),</span>
+        <span class="s2">&quot;summarystatsLocation&quot;</span><span class="p">,</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span>
+    <span class="p">)</span>
+    <span class="bp">self</span><span class="o">.</span><span class="n">df</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">parsed_sumstats_lut</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">)))</span>
+    <span class="p">)</span>
+    <span class="k">return</span> <span class="bp">self</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.apply_inclusion_list" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">apply_inclusion_list</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
+
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.apply_inclusion_list" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Restricting GWAS Catalog studies based on a list of accepted study identifiers.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>inclusion_list</code></td>
+          <td>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of accepted GWAS Catalog study identifiers</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>StudyIndexGWASCatalog</code></td>          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Filtered dataset.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">738</span>
+<span class="normal">739</span>
+<span class="normal">740</span>
+<span class="normal">741</span>
+<span class="normal">742</span>
+<span class="normal">743</span>
+<span class="normal">744</span>
+<span class="normal">745</span>
+<span class="normal">746</span>
+<span class="normal">747</span>
+<span class="normal">748</span>
+<span class="normal">749</span>
+<span class="normal">750</span>
+<span class="normal">751</span>
+<span class="normal">752</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">apply_inclusion_list</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">inclusion_list</span><span class="p">:</span> <span class="n">DataFrame</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Restricting GWAS Catalog studies based on a list of accepted study identifiers.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        StudyIndexGWASCatalog: Filtered dataset.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">),</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="n">StudyIndexGWASCatalog</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.extract_studies_for_curation" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">extract_studies_for_curation</span><span class="p">(</span><span class="n">curation</span><span class="p">:</span> <span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
+
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.extract_studies_for_curation" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Extract studies for curation.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>curation</code></td>
+          <td>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span> | None</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Dataframe with curation.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>DataFrame</code></td>          <td>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Updated curation table. New studies are have the <code>isCurated</code> False.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">461</span>
+<span class="normal">462</span>
+<span class="normal">463</span>
+<span class="normal">464</span>
+<span class="normal">465</span>
+<span class="normal">466</span>
+<span class="normal">467</span>
+<span class="normal">468</span>
+<span class="normal">469</span>
+<span class="normal">470</span>
+<span class="normal">471</span>
+<span class="normal">472</span>
+<span class="normal">473</span>
+<span class="normal">474</span>
+<span class="normal">475</span>
+<span class="normal">476</span>
+<span class="normal">477</span>
+<span class="normal">478</span>
+<span class="normal">479</span>
+<span class="normal">480</span>
+<span class="normal">481</span>
+<span class="normal">482</span>
+<span class="normal">483</span>
+<span class="normal">484</span>
+<span class="normal">485</span>
+<span class="normal">486</span>
+<span class="normal">487</span>
+<span class="normal">488</span>
+<span class="normal">489</span>
+<span class="normal">490</span>
+<span class="normal">491</span>
+<span class="normal">492</span>
+<span class="normal">493</span>
+<span class="normal">494</span>
+<span class="normal">495</span>
+<span class="normal">496</span>
+<span class="normal">497</span>
+<span class="normal">498</span>
+<span class="normal">499</span>
+<span class="normal">500</span>
+<span class="normal">501</span>
+<span class="normal">502</span>
+<span class="normal">503</span>
+<span class="normal">504</span>
+<span class="normal">505</span>
+<span class="normal">506</span>
+<span class="normal">507</span>
+<span class="normal">508</span>
+<span class="normal">509</span>
+<span class="normal">510</span>
+<span class="normal">511</span>
+<span class="normal">512</span>
+<span class="normal">513</span>
+<span class="normal">514</span>
+<span class="normal">515</span>
+<span class="normal">516</span>
+<span class="normal">517</span>
+<span class="normal">518</span>
+<span class="normal">519</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">extract_studies_for_curation</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">curation</span><span class="p">:</span> <span class="n">DataFrame</span> <span class="o">|</span> <span class="kc">None</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Extract studies for curation.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        curation (DataFrame | None): Dataframe with curation.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        DataFrame: Updated curation table. New studies are have the `isCurated` False.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># If no curation table provided, assume all studies needs curation:</span>
+    <span class="k">if</span> <span class="n">curation</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">df</span>
+            <span class="c1"># Curation only applyed on studies with summary statistics:</span>
+            <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">))</span>
+            <span class="c1"># Adding columns expected in the curation table - array columns aready flattened:</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;analysisFlag&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;qualityControl&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">None</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;isCurated&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">()))</span>
+        <span class="p">)</span>
+
+    <span class="c1"># Adding prefix to columns in the curation table:</span>
+    <span class="n">curation</span> <span class="o">=</span> <span class="n">curation</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+        <span class="o">*</span><span class="p">[</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;curation_</span><span class="si">{</span><span class="n">column</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">column</span> <span class="o">!=</span> <span class="s2">&quot;studyId&quot;</span>
+            <span class="k">else</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">column</span><span class="p">)</span>
+            <span class="k">for</span> <span class="n">column</span> <span class="ow">in</span> <span class="n">curation</span><span class="o">.</span><span class="n">columns</span>
+        <span class="p">]</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="p">(</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">df</span>
+        <span class="c1"># Curation only applyed on studies with summary statistics:</span>
+        <span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;hasSumstats&quot;</span><span class="p">))</span>
+        <span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">curation</span><span class="p">,</span> <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="n">how</span><span class="o">=</span><span class="s2">&quot;left&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">select</span><span class="p">(</span>
+            <span class="s2">&quot;studyId&quot;</span><span class="p">,</span>
+            <span class="c1"># Propagate existing curation - array columns are being flattened:</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_studyType&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyType&quot;</span><span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">array_join</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_analysisFlags&quot;</span><span class="p">),</span> <span class="s2">&quot;|&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+                <span class="s2">&quot;analysisFlag&quot;</span>
+            <span class="p">),</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">array_join</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_qualityControls&quot;</span><span class="p">),</span> <span class="s2">&quot;|&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+                <span class="s2">&quot;qualityControl&quot;</span>
+            <span class="p">),</span>
+            <span class="c1"># This boolean flag needs to be casted to string, because saving to tsv would fail otherwise:</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;curation_isCurated&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">))</span>
+            <span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="n">t</span><span class="o">.</span><span class="n">StringType</span><span class="p">())</span>
+            <span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;isCurated&quot;</span><span class="p">),</span>
+            <span class="c1"># The following columns are propagated to make curation easier:</span>
+            <span class="s2">&quot;pubmedId&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;publicationTitle&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;traitFromSource&quot;</span><span class="p">,</span>
+        <span class="p">)</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">update_study_id</span><span class="p">(</span><span class="n">study_annotation</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
+
+<a href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Update studyId with a dataframe containing study.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>study_annotation</code></td>
+          <td>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Dataframe containing <code>updatedStudyId</code>, <code>traitFromSource</code>, <code>traitFromSourceMappedIds</code> and key column <code>studyId</code>.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>StudyIndexGWASCatalog</code></td>          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Updated study table.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">345</span>
+<span class="normal">346</span>
+<span class="normal">347</span>
+<span class="normal">348</span>
+<span class="normal">349</span>
+<span class="normal">350</span>
+<span class="normal">351</span>
+<span class="normal">352</span>
+<span class="normal">353</span>
+<span class="normal">354</span>
+<span class="normal">355</span>
+<span class="normal">356</span>
+<span class="normal">357</span>
+<span class="normal">358</span>
+<span class="normal">359</span>
+<span class="normal">360</span>
+<span class="normal">361</span>
+<span class="normal">362</span>
+<span class="normal">363</span>
+<span class="normal">364</span>
+<span class="normal">365</span>
+<span class="normal">366</span>
+<span class="normal">367</span>
+<span class="normal">368</span>
+<span class="normal">369</span>
+<span class="normal">370</span>
+<span class="normal">371</span>
+<span class="normal">372</span>
+<span class="normal">373</span>
+<span class="normal">374</span>
+<span class="normal">375</span>
+<span class="normal">376</span>
+<span class="normal">377</span>
+<span class="normal">378</span>
+<span class="normal">379</span>
+<span class="normal">380</span>
+<span class="normal">381</span>
+<span class="normal">382</span>
+<span class="normal">383</span>
+<span class="normal">384</span>
+<span class="normal">385</span>
+<span class="normal">386</span>
+<span class="normal">387</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">update_study_id</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">study_annotation</span><span class="p">:</span> <span class="n">DataFrame</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Update studyId with a dataframe containing study.</span>
@@ -4844,6 +5979,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_stu
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -4867,7 +6003,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_stu
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-12T14:15:11+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-12</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -4934,7 +6070,7 @@ <h3 id="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_stu
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/datasource/gwas_catalog/study_splitter/index.html b/python_api/datasources/gwas_catalog/study_splitter/index.html
similarity index 86%
rename from python_api/datasource/gwas_catalog/study_splitter/index.html
rename to python_api/datasources/gwas_catalog/study_splitter/index.html
index ffe0e0533..5bce0266f 100644
--- a/python_api/datasource/gwas_catalog/study_splitter/index.html
+++ b/python_api/datasources/gwas_catalog/study_splitter/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Study Splitter - Open Targets Genetics</title>
+        <title>Study Splitter - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="md-skip">
+        <a href="#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
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+  
+
+      </a>
+    </li>
+  
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+              
+            
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+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
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+          
+          <div class="md-nav__link md-nav__container">
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+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
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             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
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+            Datasets
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     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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@@ -1007,14 +1158,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" checked>
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
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         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogStudySplitter
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@@ -1366,9 +1559,9 @@
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           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="md-nav__link">
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-      split()
+      split
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   </a>
   
@@ -1433,7 +1626,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1449,14 +1642,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1570,7 +1763,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
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@@ -1649,80 +1842,6 @@
 
               
             
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-  
-  
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-      
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-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
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-  
-
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-            
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-                <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_7">
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-            Ukbiobank
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-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1747,32 +1866,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1783,11 +1902,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1804,11 +1923,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1825,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1846,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1867,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1888,11 +2007,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1918,12 +2037,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1934,14 +2053,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1954,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1975,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1996,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2017,7 +2136,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2063,32 +2182,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2099,11 +2218,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2120,11 +2239,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2141,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2162,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2183,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2204,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2225,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2246,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2267,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2288,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2309,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2330,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2351,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2372,11 +2491,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2426,7 +2608,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogStudySplitter
     </span>
@@ -2436,9 +2618,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="md-nav__link">
     <span class="md-ellipsis">
-      split()
+      split
     </span>
   </a>
   
@@ -2473,12 +2655,11 @@ <h1>Study Splitter</h1>
 
 
 
-
-<h2 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="doc doc-heading">
-          <code>otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter</code>
+<h2 id="gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="doc doc-heading">
+          <code>gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter</code>
 
 
-<a href="#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2487,7 +2668,7 @@ <h2 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" cla
       <p>Splitting multi-trait GWAS Catalog studies.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_splitter.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_splitter.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 17</span>
 <span class="normal"> 18</span>
 <span class="normal"> 19</span>
@@ -2747,15 +2928,14 @@ <h2 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter" cla
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">split</span><span class="p">(</span><span class="n">studies</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Tuple</span><span class="p">[</span><span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">StudyLocusGWASCatalog</span><span class="p">]</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2780,7 +2960,7 @@ <h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.spli
         <tr>
           <td><code>studies</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="../study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="../study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2794,7 +2974,7 @@ <h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.spli
         <tr>
           <td><code>associations</code></td>
           <td>
-                <code><span title="otg.datasource.gwas_catalog.study_locus_dataset.StudyLocusGWASCatalog">StudyLocusGWASCatalog</span></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="../associations/#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2821,7 +3001,7 @@ <h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.spli
     <tbody>
         <tr>
           <td>
-                <code><span title="typing.Tuple">Tuple</span>[<a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="../study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a>, <span title="otg.datasource.gwas_catalog.study_locus_dataset.StudyLocusGWASCatalog">StudyLocusGWASCatalog</span>]</code>
+                <code><span title="typing.Tuple">Tuple</span>[<a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="../study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a>, <a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog" href="../associations/#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog">StudyLocusGWASCatalog</a>]</code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2833,7 +3013,7 @@ <h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.spli
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/study_splitter.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/study_splitter.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 82</span>
 <span class="normal"> 83</span>
 <span class="normal"> 84</span>
@@ -2955,6 +3135,7 @@ <h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.spli
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2978,7 +3159,7 @@ <h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.spli
         <span class="icon twemoji">
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3045,7 +3226,7 @@ <h3 id="otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.spli
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/gwas_catalog/summary_statistics/index.html b/python_api/datasources/gwas_catalog/summary_statistics/index.html
similarity index 88%
rename from python_api/datasource/gwas_catalog/summary_statistics/index.html
rename to python_api/datasources/gwas_catalog/summary_statistics/index.html
index 40a8ff981..85d11929c 100644
--- a/python_api/datasource/gwas_catalog/summary_statistics/index.html
+++ b/python_api/datasources/gwas_catalog/summary_statistics/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Summary statistics - Open Targets Genetics</title>
+        <title>Summary statistics - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="md-skip">
+        <a href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+    
+    
+    
+    
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+      
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
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+            Datasets
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     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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@@ -1007,14 +1158,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1236,7 +1429,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" checked>
         
           
           
@@ -1252,14 +1445,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1377,7 +1570,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogSummaryStatistics
     </span>
@@ -1387,9 +1580,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="md-nav__link">
     <span class="md-ellipsis">
-      from_gwas_harmonized_summary_stats()
+      from_gwas_harmonized_summary_stats
     </span>
   </a>
   
@@ -1433,7 +1626,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1449,14 +1642,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1570,7 +1763,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1586,14 +1779,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1649,80 +1842,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1747,32 +1866,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1783,11 +1902,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1804,11 +1923,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1825,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1846,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1867,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1888,11 +2007,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1918,12 +2037,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1934,14 +2053,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1954,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1975,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1996,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2017,7 +2136,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2063,32 +2182,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2099,11 +2218,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2120,11 +2239,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2141,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2162,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2183,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2204,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2225,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2246,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2267,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2288,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2309,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2330,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2351,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2372,11 +2491,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2426,7 +2608,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogSummaryStatistics
     </span>
@@ -2436,9 +2618,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="md-nav__link">
+  <a href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="md-nav__link">
     <span class="md-ellipsis">
-      from_gwas_harmonized_summary_stats()
+      from_gwas_harmonized_summary_stats
     </span>
   </a>
   
@@ -2473,27 +2655,26 @@ <h1>Summary statistics</h1>
 
 
 
-
-<h2 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="doc doc-heading">
-          <code>otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics</code>
+<h2 id="gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="doc doc-heading">
+          <code>gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="../../../dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.summary_statistics.SummaryStatistics" href="../../../datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code></p>
 
   
       <p>GWAS Catalog Summary Statistics reader.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/gwas_catalog/summary_statistics.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/summary_statistics.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 53</span>
 <span class="normal"> 54</span>
 <span class="normal"> 55</span>
@@ -2797,15 +2978,14 @@ <h2 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatist
 
 
 
-
-<h3 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="doc doc-heading">
+<h3 id="gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">from_gwas_harmonized_summary_stats</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span> <span class="n">sumstats_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GWASCatalogSummaryStatistics</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2871,7 +3051,7 @@ <h3 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatist
     <tbody>
         <tr>
 <td><code>GWASCatalogSummaryStatistics</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" href="#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics">GWASCatalogSummaryStatistics</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics" href="#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics">GWASCatalogSummaryStatistics</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2883,7 +3063,7 @@ <h3 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatist
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/gwas_catalog/summary_statistics.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/gwas_catalog/summary_statistics.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 57</span>
 <span class="normal"> 58</span>
 <span class="normal"> 59</span>
@@ -3171,6 +3351,7 @@ <h3 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatist
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3194,7 +3375,7 @@ <h3 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatist
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3261,7 +3442,7 @@ <h3 id="otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatist
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/intervals/_intervals/index.html b/python_api/datasources/intervals/_intervals/index.html
similarity index 77%
rename from python_api/datasource/intervals/_intervals/index.html
rename to python_api/datasources/intervals/_intervals/index.html
index 538050f20..a243badfb 100644
--- a/python_api/datasource/intervals/_intervals/index.html
+++ b/python_api/datasources/intervals/_intervals/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Chromatin intevals - Open Targets Genetics</title>
+        <title>Interaction and Interval-based Studies - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#chromatin-intervals" class="md-skip">
+        <a href="#list-of-interaction-and-interval-based-studies" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Chromatin intevals
+              Interaction and Interval-based Studies
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1234,7 +1427,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1250,14 +1443,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1373,7 +1566,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" checked>
         
           
           
@@ -1389,14 +1582,14 @@
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1510,7 +1703,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1526,14 +1719,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1589,80 +1782,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1687,32 +1806,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1723,11 +1842,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1744,11 +1863,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1765,11 +1884,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1786,11 +1905,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1807,11 +1926,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1828,11 +1947,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1858,12 +1977,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1874,14 +1993,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1894,7 +2013,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1915,7 +2034,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1936,7 +2055,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1957,7 +2076,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2003,32 +2122,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2039,11 +2158,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2060,11 +2179,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2081,11 +2200,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2102,11 +2221,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2123,11 +2242,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2144,11 +2263,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2165,11 +2284,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2186,11 +2305,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2207,11 +2326,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2228,11 +2347,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2249,11 +2368,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2270,11 +2389,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2291,11 +2410,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2312,11 +2431,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2377,8 +2559,31 @@
   
 
 
-<h1 id="chromatin-intervals">Chromatin intervals<a class="headerlink" href="#chromatin-intervals" title="Permanent link">&para;</a></h1>
-<p>TBC</p>
+<h1 id="list-of-interaction-and-interval-based-studies">List of Interaction and Interval-based Studies<a class="headerlink" href="#list-of-interaction-and-interval-based-studies" title="Permanent link">&para;</a></h1>
+<p>In this section, we provide a list of studies that focus on interaction and interval-based investigations, shedding light on the intricate relationships between genetic elements and their functional implications.</p>
+<ol>
+<li>
+<p><strong>Promoter Capture Hi-C (Javierre et al., 2016):</strong>
+   <em>Title:</em> "Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters".
+   This study presents evidence linking genetic variation to genes through the application of Promoter Capture Hi-C across each of the 17 human primary hematopoietic cell types. The method captures interactions between promoters and distal regulatory elements, providing valuable insights into the three-dimensional chromatin architecture. DOI: 10.1016/j.cell.2016.09.037</p>
+</li>
+<li>
+<p><strong>Enhancer-TSS Correlation (Andersson et al., 2014):</strong>
+   <em>Title:</em> "An Atlas of Active Enhancers across Human Cell Types and Tissues".
+   This study explores genetic variation's impact on genes by examining the correlation between the transcriptional activity of enhancers and transcription start sites. The findings are documented in the FANTOM5 CAGE expression atlas, offering a comprehensive view of the regulatory landscape. DOI: 10.1038/nature12787</p>
+</li>
+<li>
+<p><strong>DHS-Promoter Correlation (Thurman et al., 2012):</strong>
+   <em>Title:</em> "The accessible chromatin landscape of the human genome".
+   Investigating genetic variation's connection to genes, this study employs the correlation of DNase I hypersensitive sites (DHS) and gene promoters. The analysis spans 125 cell and tissue types from the ENCODE project, providing a broad understanding of the regulatory interactions across diverse biological contexts. DOI: 10.1038/nature11232</p>
+</li>
+<li>
+<p><strong>Promoter Capture Hi-C (Jung et al., 2019):</strong>
+   <em>Title:</em> "A compendium of promoter-centered long-range chromatin interactions in the human genome".
+   This study compiles a compendium of promoter-centered long-range chromatin interactions in the human genome. By focusing on the three-dimensional organization of chromatin, the research contributes to our understanding of the spatial arrangement of genetic elements and their implications in gene regulation. DOI: 10.1038/s41588-019-0494-8</p>
+</li>
+</ol>
+<p>For in-depth details on each study, you may refer to the respective publications.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2401,7 +2606,7 @@ <h1 id="chromatin-intervals">Chromatin intervals<a class="headerlink" href="#chr
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2468,7 +2673,7 @@ <h1 id="chromatin-intervals">Chromatin intervals<a class="headerlink" href="#chr
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/datasource/intervals/andersson/index.html b/python_api/datasources/intervals/andersson/index.html
similarity index 89%
rename from python_api/datasource/intervals/andersson/index.html
rename to python_api/datasources/intervals/andersson/index.html
index 5836a67d0..82a4a997a 100644
--- a/python_api/datasource/intervals/andersson/index.html
+++ b/python_api/datasources/intervals/andersson/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Andersson et al. - Open Targets Genetics</title>
+        <title>Andersson et al. - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.intervals.andersson.IntervalsAndersson" class="md-skip">
+        <a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
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+      <a href="../../../../roadmap/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
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+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1234,7 +1427,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1250,14 +1443,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1373,7 +1566,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" checked>
         
           
           
@@ -1389,14 +1582,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1451,7 +1644,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.andersson.IntervalsAndersson" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson" class="md-nav__link">
     <span class="md-ellipsis">
       IntervalsAndersson
     </span>
@@ -1461,18 +1654,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson.parse" class="md-nav__link">
     <span class="md-ellipsis">
-      parse()
+      parse
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.andersson.IntervalsAndersson.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -1579,7 +1772,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1595,14 +1788,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1658,80 +1851,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1756,32 +1875,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1792,11 +1911,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1813,11 +1932,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1834,11 +1953,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1855,11 +1974,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1876,11 +1995,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1897,11 +2016,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1927,12 +2046,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
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@@ -1943,14 +2062,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
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+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
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     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1984,7 +2103,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2005,7 +2124,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2026,7 +2145,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2072,32 +2191,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
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-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
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+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
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@@ -2108,11 +2227,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2129,11 +2248,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2150,11 +2269,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2171,11 +2290,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
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@@ -2192,11 +2311,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2213,11 +2332,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2234,11 +2353,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2255,11 +2374,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2276,11 +2395,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2297,11 +2416,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2318,11 +2437,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2339,11 +2458,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2360,11 +2479,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2381,11 +2500,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2435,7 +2617,7 @@
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         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.andersson.IntervalsAndersson" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson" class="md-nav__link">
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       IntervalsAndersson
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@@ -2445,18 +2627,18 @@
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           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson.parse" class="md-nav__link">
     <span class="md-ellipsis">
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     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.andersson.IntervalsAndersson.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -2491,12 +2673,11 @@ <h1>Andersson et al.</h1>
 
 
 
-
-<h2 id="otg.datasource.intervals.andersson.IntervalsAndersson" class="doc doc-heading">
-          <code>otg.datasource.intervals.andersson.IntervalsAndersson</code>
+<h2 id="gentropy.datasource.intervals.andersson.IntervalsAndersson" class="doc doc-heading">
+          <code>gentropy.datasource.intervals.andersson.IntervalsAndersson</code>
 
 
-<a href="#otg.datasource.intervals.andersson.IntervalsAndersson" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2505,7 +2686,7 @@ <h2 id="otg.datasource.intervals.andersson.IntervalsAndersson" class="doc doc-he
       <p>Interval dataset from Andersson et al. 2014.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/intervals/andersson.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/intervals/andersson.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 21</span>
 <span class="normal"> 22</span>
 <span class="normal"> 23</span>
@@ -2765,15 +2946,14 @@ <h2 id="otg.datasource.intervals.andersson.IntervalsAndersson" class="doc doc-he
 
 
 
-
-<h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.andersson.IntervalsAndersson.parse" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">parse</span><span class="p">(</span><span class="n">raw_anderson_df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span> <span class="n">lift</span><span class="p">:</span> <span class="n">LiftOverSpark</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Intervals</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson.parse" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2810,7 +2990,7 @@ <h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="doc
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../../../dataset/gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../../../datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2824,7 +3004,7 @@ <h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="doc
         <tr>
           <td><code>lift</code></td>
           <td>
-                <code><span title="otg.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
+                <code><span title="gentropy.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2851,7 +3031,7 @@ <h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="doc
     <tbody>
         <tr>
 <td><code>Intervals</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.intervals.Intervals" href="../../../dataset/intervals/#otg.dataset.intervals.Intervals">Intervals</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.intervals.Intervals" href="../../../datasets/intervals/#gentropy.dataset.intervals.Intervals">Intervals</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2863,7 +3043,7 @@ <h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/andersson.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/andersson.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 48</span>
 <span class="normal"> 49</span>
 <span class="normal"> 50</span>
@@ -3060,15 +3240,14 @@ <h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.parse" class="doc
 
 
 
-
-<h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.read" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.andersson.IntervalsAndersson.read" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">read</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.andersson.IntervalsAndersson.read" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.andersson.IntervalsAndersson.read" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3144,7 +3323,7 @@ <h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.read" class="doc d
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/andersson.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/andersson.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">24</span>
 <span class="normal">25</span>
 <span class="normal">26</span>
@@ -3202,6 +3381,7 @@ <h3 id="otg.datasource.intervals.andersson.IntervalsAndersson.read" class="doc d
 
   </div>
 
+
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 <hr />
 <div class="md-source-file">
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diff --git a/python_api/datasource/intervals/javierre/index.html b/python_api/datasources/intervals/javierre/index.html
similarity index 90%
rename from python_api/datasource/intervals/javierre/index.html
rename to python_api/datasources/intervals/javierre/index.html
index d24a6b3dd..6881467e0 100644
--- a/python_api/datasource/intervals/javierre/index.html
+++ b/python_api/datasources/intervals/javierre/index.html
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+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
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+        <title>Javierre et al. - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.intervals.javierre.IntervalsJavierre" class="md-skip">
+        <a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre" class="md-skip">
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@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
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-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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@@ -107,7 +107,7 @@
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-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
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 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
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+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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+    Open Targets Gentropy
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-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
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+      <a href="../../../../installation/" class="md-nav__link">
         
   
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+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1373,7 +1566,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" checked>
         
           
           
@@ -1389,14 +1582,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1472,7 +1665,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.javierre.IntervalsJavierre" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre" class="md-nav__link">
     <span class="md-ellipsis">
       IntervalsJavierre
     </span>
@@ -1482,18 +1675,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre.parse" class="md-nav__link">
     <span class="md-ellipsis">
-      parse()
+      parse
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.javierre.IntervalsJavierre.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -1579,7 +1772,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1595,14 +1788,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1658,80 +1851,6 @@
 
               
             
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-  
-  
-  
-  
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-      
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-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
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-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
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-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1756,32 +1875,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
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               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1792,11 +1911,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1813,11 +1932,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1834,11 +1953,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1855,11 +1974,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1876,11 +1995,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1897,11 +2016,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1927,12 +2046,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1943,14 +2062,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1963,7 +2082,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1984,7 +2103,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2005,7 +2124,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2026,7 +2145,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2072,32 +2191,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2108,11 +2227,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2129,11 +2248,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2150,11 +2269,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2171,11 +2290,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2192,11 +2311,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2213,11 +2332,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2234,11 +2353,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2255,11 +2374,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2276,11 +2395,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2297,11 +2416,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2318,11 +2437,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2339,11 +2458,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2360,11 +2479,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2381,11 +2500,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2435,7 +2617,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.javierre.IntervalsJavierre" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre" class="md-nav__link">
     <span class="md-ellipsis">
       IntervalsJavierre
     </span>
@@ -2445,18 +2627,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre.parse" class="md-nav__link">
     <span class="md-ellipsis">
-      parse()
+      parse
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.javierre.IntervalsJavierre.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -2491,12 +2673,11 @@ <h1>Javierre et al.</h1>
 
 
 
-
-<h2 id="otg.datasource.intervals.javierre.IntervalsJavierre" class="doc doc-heading">
-          <code>otg.datasource.intervals.javierre.IntervalsJavierre</code>
+<h2 id="gentropy.datasource.intervals.javierre.IntervalsJavierre" class="doc doc-heading">
+          <code>gentropy.datasource.intervals.javierre.IntervalsJavierre</code>
 
 
-<a href="#otg.datasource.intervals.javierre.IntervalsJavierre" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2505,7 +2686,7 @@ <h2 id="otg.datasource.intervals.javierre.IntervalsJavierre" class="doc doc-head
       <p>Interval dataset from Javierre et al. 2016.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/intervals/javierre.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/intervals/javierre.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 18</span>
 <span class="normal"> 19</span>
 <span class="normal"> 20</span>
@@ -2833,15 +3014,14 @@ <h2 id="otg.datasource.intervals.javierre.IntervalsJavierre" class="doc doc-head
 
 
 
-
-<h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.javierre.IntervalsJavierre.parse" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">parse</span><span class="p">(</span><span class="n">javierre_raw</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span> <span class="n">lift</span><span class="p">:</span> <span class="n">LiftOverSpark</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Intervals</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre.parse" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2878,7 +3058,7 @@ <h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="doc do
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../../../dataset/gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../../../datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2892,7 +3072,7 @@ <h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="doc do
         <tr>
           <td><code>lift</code></td>
           <td>
-                <code><span title="otg.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
+                <code><span title="gentropy.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2919,7 +3099,7 @@ <h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="doc do
     <tbody>
         <tr>
 <td><code>Intervals</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.intervals.Intervals" href="../../../dataset/intervals/#otg.dataset.intervals.Intervals">Intervals</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.intervals.Intervals" href="../../../datasets/intervals/#gentropy.dataset.intervals.Intervals">Intervals</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2931,7 +3111,7 @@ <h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="doc do
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/javierre.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/javierre.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 34</span>
 <span class="normal"> 35</span>
 <span class="normal"> 36</span>
@@ -3218,15 +3398,14 @@ <h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.parse" class="doc do
 
 
 
-
-<h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.read" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.javierre.IntervalsJavierre.read" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">read</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.javierre.IntervalsJavierre.read" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.javierre.IntervalsJavierre.read" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3302,7 +3481,7 @@ <h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.read" class="doc doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/javierre.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/javierre.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">21</span>
 <span class="normal">22</span>
 <span class="normal">23</span>
@@ -3338,6 +3517,7 @@ <h3 id="otg.datasource.intervals.javierre.IntervalsJavierre.read" class="doc doc
 
   </div>
 
+
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
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diff --git a/python_api/datasource/intervals/jung/index.html b/python_api/datasources/intervals/jung/index.html
similarity index 87%
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rename to python_api/datasources/intervals/jung/index.html
index f0591e980..0ef07419e 100644
--- a/python_api/datasource/intervals/jung/index.html
+++ b/python_api/datasources/intervals/jung/index.html
@@ -16,11 +16,11 @@
       
       
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Jung et al. - Open Targets Genetics</title>
+        <title>Jung et al. - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.intervals.jung.IntervalsJung" class="md-skip">
+        <a href="#gentropy.datasource.intervals.jung.IntervalsJung" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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@@ -107,7 +107,7 @@
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+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
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-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
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+    </li>
+  
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       <a href="../../../../installation/" class="md-tabs__link">
         
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+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
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+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
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       <a href="../../../../development/_development/" class="md-tabs__link">
         
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 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
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-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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-    Development
+    How-to
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
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+
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+  
+  
+  
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+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+    Run step using YAML config
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+      <a href="../../../../roadmap/" class="md-nav__link">
+        
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+    Roadmap
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+
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
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             Python API
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1234,7 +1427,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1250,14 +1443,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1373,7 +1566,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" checked>
         
           
           
@@ -1389,14 +1582,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1493,7 +1686,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.jung.IntervalsJung" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.jung.IntervalsJung" class="md-nav__link">
     <span class="md-ellipsis">
       IntervalsJung
     </span>
@@ -1503,18 +1696,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.jung.IntervalsJung.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.jung.IntervalsJung.parse" class="md-nav__link">
     <span class="md-ellipsis">
-      parse()
+      parse
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.jung.IntervalsJung.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.jung.IntervalsJung.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -1579,7 +1772,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1595,14 +1788,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1658,80 +1851,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1756,32 +1875,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1792,11 +1911,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1813,11 +1932,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1834,11 +1953,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1855,11 +1974,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1876,11 +1995,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1897,11 +2016,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1927,12 +2046,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1943,14 +2062,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1963,7 +2082,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1984,7 +2103,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2005,7 +2124,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2026,7 +2145,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2072,32 +2191,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2108,11 +2227,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2129,11 +2248,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2150,11 +2269,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2171,11 +2290,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2192,11 +2311,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2213,11 +2332,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2234,11 +2353,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2255,11 +2374,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2276,11 +2395,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2297,11 +2416,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2318,11 +2437,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2339,11 +2458,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2360,11 +2479,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2381,11 +2500,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2435,7 +2617,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.jung.IntervalsJung" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.jung.IntervalsJung" class="md-nav__link">
     <span class="md-ellipsis">
       IntervalsJung
     </span>
@@ -2445,18 +2627,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.jung.IntervalsJung.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.jung.IntervalsJung.parse" class="md-nav__link">
     <span class="md-ellipsis">
-      parse()
+      parse
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.jung.IntervalsJung.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.jung.IntervalsJung.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -2491,12 +2673,11 @@ <h1>Jung et al.</h1>
 
 
 
-
-<h2 id="otg.datasource.intervals.jung.IntervalsJung" class="doc doc-heading">
-          <code>otg.datasource.intervals.jung.IntervalsJung</code>
+<h2 id="gentropy.datasource.intervals.jung.IntervalsJung" class="doc doc-heading">
+          <code>gentropy.datasource.intervals.jung.IntervalsJung</code>
 
 
-<a href="#otg.datasource.intervals.jung.IntervalsJung" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.intervals.jung.IntervalsJung" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2505,7 +2686,7 @@ <h2 id="otg.datasource.intervals.jung.IntervalsJung" class="doc doc-heading">
       <p>Interval dataset from Jung et al. 2019.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/intervals/jung.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/intervals/jung.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 18</span>
 <span class="normal"> 19</span>
 <span class="normal"> 20</span>
@@ -2697,15 +2878,14 @@ <h2 id="otg.datasource.intervals.jung.IntervalsJung" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.datasource.intervals.jung.IntervalsJung.parse" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.jung.IntervalsJung.parse" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">parse</span><span class="p">(</span><span class="n">jung_raw</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span> <span class="n">lift</span><span class="p">:</span> <span class="n">LiftOverSpark</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Intervals</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.jung.IntervalsJung.parse" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.jung.IntervalsJung.parse" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2742,7 +2922,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.parse" class="doc doc-headin
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../../../dataset/gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../../../datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2756,7 +2936,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.parse" class="doc doc-headin
         <tr>
           <td><code>lift</code></td>
           <td>
-                <code><span title="otg.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
+                <code><span title="gentropy.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2783,7 +2963,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.parse" class="doc doc-headin
     <tbody>
         <tr>
 <td><code>Intervals</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.intervals.Intervals" href="../../../dataset/intervals/#otg.dataset.intervals.Intervals">Intervals</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.intervals.Intervals" href="../../../datasets/intervals/#gentropy.dataset.intervals.Intervals">Intervals</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2795,7 +2975,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.parse" class="doc doc-headin
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/jung.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/jung.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 34</span>
 <span class="normal"> 35</span>
 <span class="normal"> 36</span>
@@ -2946,15 +3126,14 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.parse" class="doc doc-headin
 
 
 
-
-<h3 id="otg.datasource.intervals.jung.IntervalsJung.read" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.jung.IntervalsJung.read" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">read</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.jung.IntervalsJung.read" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.jung.IntervalsJung.read" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3030,7 +3209,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.read" class="doc doc-heading
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/jung.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/jung.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">21</span>
 <span class="normal">22</span>
 <span class="normal">23</span>
@@ -3066,6 +3245,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.read" class="doc doc-heading
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3089,7 +3269,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.read" class="doc doc-heading
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3156,7 +3336,7 @@ <h3 id="otg.datasource.intervals.jung.IntervalsJung.read" class="doc doc-heading
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/intervals/thurman/index.html b/python_api/datasources/intervals/thurman/index.html
similarity index 87%
rename from python_api/datasource/intervals/thurman/index.html
rename to python_api/datasources/intervals/thurman/index.html
index 4ebda556d..3ff08bc49 100644
--- a/python_api/datasource/intervals/thurman/index.html
+++ b/python_api/datasources/intervals/thurman/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Thurman et al. - Open Targets Genetics</title>
+        <title>Thurman et al. - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.intervals.thurman.IntervalsThurman" class="md-skip">
+        <a href="#gentropy.datasource.intervals.thurman.IntervalsThurman" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
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+  
+
+      </a>
+    </li>
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+  
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+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
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+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
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+            Datasets
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     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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@@ -1007,14 +1158,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
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+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1234,7 +1427,7 @@
         
         
         
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1373,7 +1566,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" checked>
         
           
           
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-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
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         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.thurman.IntervalsThurman" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.thurman.IntervalsThurman" class="md-nav__link">
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       IntervalsThurman
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@@ -1524,18 +1717,18 @@
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           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.thurman.IntervalsThurman.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.thurman.IntervalsThurman.parse" class="md-nav__link">
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 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.thurman.IntervalsThurman.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.thurman.IntervalsThurman.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -1579,7 +1772,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
@@ -1595,14 +1788,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1658,80 +1851,6 @@
 
               
             
-              
-                
-  
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-              
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-        
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-
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-  
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-              
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@@ -1756,32 +1875,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1792,11 +1911,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1813,11 +1932,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1834,11 +1953,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1855,11 +1974,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1876,11 +1995,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1897,11 +2016,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1927,12 +2046,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1943,14 +2062,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1963,7 +2082,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1984,7 +2103,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2005,7 +2124,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2026,7 +2145,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2072,32 +2191,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2108,11 +2227,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2129,11 +2248,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2150,11 +2269,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2171,11 +2290,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2192,11 +2311,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2213,11 +2332,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2234,11 +2353,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2255,11 +2374,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2276,11 +2395,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2297,11 +2416,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2318,11 +2437,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2339,11 +2458,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2360,11 +2479,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2381,11 +2500,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2435,7 +2617,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.thurman.IntervalsThurman" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.thurman.IntervalsThurman" class="md-nav__link">
     <span class="md-ellipsis">
       IntervalsThurman
     </span>
@@ -2445,18 +2627,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.thurman.IntervalsThurman.parse" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.thurman.IntervalsThurman.parse" class="md-nav__link">
     <span class="md-ellipsis">
-      parse()
+      parse
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.intervals.thurman.IntervalsThurman.read" class="md-nav__link">
+  <a href="#gentropy.datasource.intervals.thurman.IntervalsThurman.read" class="md-nav__link">
     <span class="md-ellipsis">
-      read()
+      read
     </span>
   </a>
   
@@ -2491,12 +2673,11 @@ <h1>Thurman et al.</h1>
 
 
 
-
-<h2 id="otg.datasource.intervals.thurman.IntervalsThurman" class="doc doc-heading">
-          <code>otg.datasource.intervals.thurman.IntervalsThurman</code>
+<h2 id="gentropy.datasource.intervals.thurman.IntervalsThurman" class="doc doc-heading">
+          <code>gentropy.datasource.intervals.thurman.IntervalsThurman</code>
 
 
-<a href="#otg.datasource.intervals.thurman.IntervalsThurman" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.intervals.thurman.IntervalsThurman" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2505,7 +2686,7 @@ <h2 id="otg.datasource.intervals.thurman.IntervalsThurman" class="doc doc-headin
       <p>Interval dataset from Thurman et al. 2012.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/intervals/thurman.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/intervals/thurman.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 18</span>
 <span class="normal"> 19</span>
 <span class="normal"> 20</span>
@@ -2699,15 +2880,14 @@ <h2 id="otg.datasource.intervals.thurman.IntervalsThurman" class="doc doc-headin
 
 
 
-
-<h3 id="otg.datasource.intervals.thurman.IntervalsThurman.parse" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.thurman.IntervalsThurman.parse" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">parse</span><span class="p">(</span><span class="n">thurman_raw</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">:</span> <span class="n">GeneIndex</span><span class="p">,</span> <span class="n">lift</span><span class="p">:</span> <span class="n">LiftOverSpark</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Intervals</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.thurman.IntervalsThurman.parse" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.thurman.IntervalsThurman.parse" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2744,7 +2924,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.parse" class="doc doc-
         <tr>
           <td><code>gene_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../../../dataset/gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../../../datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2758,7 +2938,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.parse" class="doc doc-
         <tr>
           <td><code>lift</code></td>
           <td>
-                <code><span title="otg.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
+                <code><span title="gentropy.common.Liftover.LiftOverSpark">LiftOverSpark</span></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2785,7 +2965,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.parse" class="doc doc-
     <tbody>
         <tr>
 <td><code>Intervals</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.intervals.Intervals" href="../../../dataset/intervals/#otg.dataset.intervals.Intervals">Intervals</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.intervals.Intervals" href="../../../datasets/intervals/#gentropy.dataset.intervals.Intervals">Intervals</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2797,7 +2977,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.parse" class="doc doc-
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/thurman.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/thurman.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 46</span>
 <span class="normal"> 47</span>
 <span class="normal"> 48</span>
@@ -2926,15 +3106,14 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.parse" class="doc doc-
 
 
 
-
-<h3 id="otg.datasource.intervals.thurman.IntervalsThurman.read" class="doc doc-heading">
+<h3 id="gentropy.datasource.intervals.thurman.IntervalsThurman.read" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">read</span><span class="p">(</span><span class="n">spark</span><span class="p">:</span> <span class="n">SparkSession</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.datasource.intervals.thurman.IntervalsThurman.read" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.intervals.thurman.IntervalsThurman.read" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3010,7 +3189,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.read" class="doc doc-h
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/intervals/thurman.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/intervals/thurman.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">21</span>
 <span class="normal">22</span>
 <span class="normal">23</span>
@@ -3070,6 +3249,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.read" class="doc doc-h
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3093,7 +3273,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.read" class="doc doc-h
         <span class="icon twemoji">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3160,7 +3340,7 @@ <h3 id="otg.datasource.intervals.thurman.IntervalsThurman.read" class="doc doc-h
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/open_targets/_open_targets/index.html b/python_api/datasources/open_targets/_open_targets/index.html
similarity index 80%
rename from python_api/datasource/open_targets/_open_targets/index.html
rename to python_api/datasources/open_targets/_open_targets/index.html
index 58caffca5..a89aecd23 100644
--- a/python_api/datasource/open_targets/_open_targets/index.html
+++ b/python_api/datasources/open_targets/_open_targets/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Open Targets - Open Targets Genetics</title>
+        <title>Open Targets - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,7 +102,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -187,13 +187,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -228,7 +245,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -244,6 +261,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -304,22 +338,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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+    opentargets/gentropy
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@@ -333,11 +367,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -353,11 +387,11 @@
   
   
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-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -390,11 +424,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
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+    </li>
+  
+
+              
+            
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+      
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+  
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+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
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+  <span class="md-ellipsis">
+    Development
+  </span>
+  
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+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
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-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
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             Python API
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+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -670,7 +821,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -691,7 +842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -712,7 +863,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -733,7 +884,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -754,7 +905,7 @@
   
   
     <li class="md-nav__item">
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+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -796,7 +947,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -817,7 +968,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -941,32 +1092,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
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-    Datasource
+    Datasources
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -986,12 +1137,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1002,14 +1153,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1021,6 +1172,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1060,7 +1232,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1076,14 +1248,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1110,6 +1282,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1134,7 +1327,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1150,14 +1343,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1229,7 +1422,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1245,14 +1438,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1366,7 +1559,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1382,14 +1575,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1505,7 +1698,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" checked>
         
           
           
@@ -1521,14 +1714,14 @@
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1584,80 +1777,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1682,32 +1801,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1718,11 +1837,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1739,11 +1858,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1760,11 +1879,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1781,11 +1900,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1802,11 +1921,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1823,11 +1942,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1853,12 +1972,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1869,14 +1988,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1889,7 +2008,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1910,7 +2029,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1931,7 +2050,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1952,7 +2071,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1998,32 +2117,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,11 +2153,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2055,11 +2174,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2076,11 +2195,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2307,11 +2426,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2382,8 +2564,18 @@ <h1>Open targets</h1>
   }
 </style>
 
-<p>The Open Targets Platform is a comprehensive resource that aims to aggregate and harmonise various types of data to facilitate the identification, prioritisation, and validation of drug targets. By integrating publicly available datasets including data generated by the Open Targets consortium, the Platform builds and scores target-disease associations to assist in drug target identification and prioritisation. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships.</p>
-<p>Genomic data from Open Targets integrates human genome-wide association studies (GWAS) and functional genomics data including gene expression, protein abundance, chromatin interaction and conformation data from a wide range of cell types and tissues to make robust connections between GWAS-associated loci, variants and likely causal genes.</p>
+<p>The Open Targets Platform is a comprehensive resource that aims to aggregate and harmonize various types of data to facilitate the identification, prioritization, and validation of drug targets. By integrating publicly available datasets, including data generated by the Open Targets consortium, the Platform builds and scores target-disease associations to assist in drug target identification and prioritization. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships.</p>
+<p>Within our analyses, we utilize Open Targets to infer two datasets:</p>
+<ol>
+<li>
+<p><strong>The list of targets:</strong>
+   This dataset provides a compilation of targets. In the Open Targets Platform, a target is understood as any naturally-occurring molecule that can be targeted by a medicinal product. The EMBL-EBI Ensembl database serves as the source for human targets in the Platform, with the Ensembl gene ID as the primary identifier. For more details, refer to <a href="https://platform-docs.opentargets.org/target">this link</a>.</p>
+</li>
+<li>
+<p><strong>The list of Gold Standard Positives:</strong>
+   We use this dataset for training the Locus-to-Gene model. The current list contains 496 Gold Standard Positives.</p>
+</li>
+</ol>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2406,7 +2598,7 @@ <h1>Open targets</h1>
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
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               target="_blank"
               ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
-          </li><li>
-            <a
-              href="https://github.com/apps/pre-commit-ci"
-              title="pre-commit-ci[bot]"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/in/68672?v=4" alt="pre-commit-ci[bot]"
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-          </li><li>
-            <a
-              href="https://github.com/hlnicholls"
-              title="hlnicholls"
-              data-bi-name="contributorprofile"
-              target="_blank"
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@@ -2489,7 +2665,7 @@ <h1>Open targets</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/open_targets/l2g_gold_standard/index.html b/python_api/datasources/open_targets/l2g_gold_standard/index.html
similarity index 86%
rename from python_api/datasource/open_targets/l2g_gold_standard/index.html
rename to python_api/datasources/open_targets/l2g_gold_standard/index.html
index b45a2f8a6..327dc9c67 100644
--- a/python_api/datasource/open_targets/l2g_gold_standard/index.html
+++ b/python_api/datasources/open_targets/l2g_gold_standard/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Gold Standard - Open Targets Genetics</title>
+        <title>L2G Gold Standard - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="md-skip">
+        <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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         </div>
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@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
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+      </a>
+    </li>
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
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+    </li>
+  
+
+      
+        
+  
+  
+  
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       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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+    Open Targets Gentropy
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
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+    Home
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@@ -358,11 +392,11 @@
   
   
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+      <a href="../../../../installation/" class="md-nav__link">
         
   
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+    Installation
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
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+  
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+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+    Run step using YAML config
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+        
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+  <span class="md-ellipsis">
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+            <a href="../../../../development/_development/" class="md-nav__link ">
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+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
@@ -1155,14 +1348,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1234,7 +1427,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
@@ -1250,14 +1443,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1371,7 +1564,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1387,14 +1580,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1510,7 +1703,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" checked>
         
           
           
@@ -1526,14 +1719,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1588,7 +1781,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="md-nav__link">
     <span class="md-ellipsis">
       OpenTargetsL2GGoldStandard
     </span>
@@ -1598,27 +1791,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="md-nav__link">
     <span class="md-ellipsis">
-      as_l2g_gold_standard()
+      as_l2g_gold_standard
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="md-nav__link">
     <span class="md-ellipsis">
-      expand_gold_standard_with_negatives()
+      expand_gold_standard_with_negatives
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="md-nav__link">
     <span class="md-ellipsis">
-      parse_positive_curation()
+      parse_positive_curation
     </span>
   </a>
   
@@ -1667,80 +1860,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1765,32 +1884,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1801,11 +1920,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1822,11 +1941,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1843,11 +1962,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1864,11 +1983,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1885,11 +2004,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1906,11 +2025,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1936,12 +2055,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1952,14 +2071,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1972,7 +2091,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1993,7 +2112,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2014,7 +2133,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2035,7 +2154,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2081,32 +2200,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2117,11 +2236,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2138,11 +2257,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2159,11 +2278,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2180,11 +2299,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2201,11 +2320,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2222,11 +2341,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2243,11 +2362,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2264,11 +2383,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2285,11 +2404,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2306,11 +2425,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2327,11 +2446,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2348,11 +2467,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2369,11 +2488,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2390,11 +2509,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2444,7 +2626,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="md-nav__link">
     <span class="md-ellipsis">
       OpenTargetsL2GGoldStandard
     </span>
@@ -2454,27 +2636,27 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="md-nav__link">
     <span class="md-ellipsis">
-      as_l2g_gold_standard()
+      as_l2g_gold_standard
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="md-nav__link">
     <span class="md-ellipsis">
-      expand_gold_standard_with_negatives()
+      expand_gold_standard_with_negatives
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="md-nav__link">
     <span class="md-ellipsis">
-      parse_positive_curation()
+      parse_positive_curation
     </span>
   </a>
   
@@ -2509,12 +2691,11 @@ <h1>L2G Gold Standard</h1>
 
 
 
+<h2 id="gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="doc doc-heading">
+          <code>gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard</code>
 
-<h2 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="doc doc-heading">
-          <code>otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard</code>
 
-
-<a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2530,7 +2711,7 @@ <h2 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
 </ul>
 </details>
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 14</span>
 <span class="normal"> 15</span>
 <span class="normal"> 16</span>
@@ -2770,15 +2951,14 @@ <h2 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
 
 
 
-
-<h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="doc doc-heading">
+<h3 id="gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">as_l2g_gold_standard</span><span class="p">(</span><span class="n">gold_standard_curation</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GGoldStandard</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2815,7 +2995,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
         <tr>
           <td><code>v2g</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../../../dataset/variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../../../datasets/variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2842,7 +3022,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
     <tbody>
         <tr>
 <td><code>L2GGoldStandard</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_gold_standard.L2GGoldStandard" href="../../../dataset/l2g_gold_standard/#otg.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_gold_standard.L2GGoldStandard" href="../../../datasets/l2g_gold_standard/#gentropy.dataset.l2g_gold_standard.L2GGoldStandard">L2GGoldStandard</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2854,7 +3034,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">103</span>
 <span class="normal">104</span>
 <span class="normal">105</span>
@@ -2907,15 +3087,14 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
 
 
 
-
-<h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="doc doc-heading">
+<h3 id="gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">expand_gold_standard_with_negatives</span><span class="p">(</span><span class="n">positive_set</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2953,7 +3132,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
         <tr>
           <td><code>v2g</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.v2g.V2G" href="../../../dataset/variant_to_gene/#otg.dataset.v2g.V2G">V2G</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.v2g.V2G" href="../../../datasets/variant_to_gene/#gentropy.dataset.v2g.V2G">V2G</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2992,7 +3171,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 60</span>
 <span class="normal"> 61</span>
 <span class="normal"> 62</span>
@@ -3087,15 +3266,14 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
 
 
 
-
-<h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="doc doc-heading">
+<h3 id="gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">parse_positive_curation</span><span class="p">(</span><span class="n">gold_standard_curation</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3157,7 +3335,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">24</span>
 <span class="normal">25</span>
 <span class="normal">26</span>
@@ -3239,6 +3417,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3262,7 +3441,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
         <span class="icon twemoji">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3275,11 +3454,11 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
       <li class="contributors-holder">
         <ul class="contributors" data-bi-name="contributors"><li>
             <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
+              href="https://github.com/d0choa"
+              title="d0choa"
               data-bi-name="contributorprofile"
               target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
+              ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
           </li></ul>
       </li>
@@ -3329,7 +3508,7 @@ <h3 id="otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/datasource/open_targets/target/index.html b/python_api/datasources/open_targets/target/index.html
similarity index 85%
rename from python_api/datasource/open_targets/target/index.html
rename to python_api/datasources/open_targets/target/index.html
index 384d14cf0..e43df3397 100644
--- a/python_api/datasource/open_targets/target/index.html
+++ b/python_api/datasources/open_targets/target/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../l2g_gold_standard/">
       
       
-        <link rel="next" href="../../ukbiobank/_ukbiobank/">
+        <link rel="next" href="../../../methods/_methods/">
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Target - Open Targets Genetics</title>
+        <title>Target - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.datasource.open_targets.target.OpenTargetsTarget" class="md-skip">
+        <a href="#gentropy.datasource.open_targets.target.OpenTargetsTarget" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -946,32 +1097,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_datasource/" class="md-nav__link ">
+            <a href="../../_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
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@@ -991,12 +1142,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1007,14 +1158,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1026,6 +1177,27 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../../eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../../eqtl_catalogue/summary_stats/" class="md-nav__link">
         
@@ -1065,7 +1237,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
@@ -1081,14 +1253,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1115,6 +1287,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -1139,7 +1332,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
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             </a>
             
               
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+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1371,7 +1564,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
@@ -1387,14 +1580,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1510,7 +1703,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" checked>
         
           
           
@@ -1526,14 +1719,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1609,7 +1802,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.target.OpenTargetsTarget" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.target.OpenTargetsTarget" class="md-nav__link">
     <span class="md-ellipsis">
       OpenTargetsTarget
     </span>
@@ -1619,9 +1812,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="md-nav__link">
     <span class="md-ellipsis">
-      as_gene_index()
+      as_gene_index
     </span>
   </a>
   
@@ -1649,80 +1842,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1747,32 +1866,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/_method/" class="md-nav__link ">
+            <a href="../../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1783,11 +1902,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/clumping/" class="md-nav__link">
+      <a href="../../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1804,11 +1923,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/coloc/" class="md-nav__link">
+      <a href="../../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1825,11 +1944,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ecaviar/" class="md-nav__link">
+      <a href="../../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1846,11 +1965,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1867,11 +1986,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/pics/" class="md-nav__link">
+      <a href="../../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1888,11 +2007,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1918,12 +2037,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1934,14 +2053,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1954,7 +2073,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1975,7 +2094,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1996,7 +2115,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/model/" class="md-nav__link">
+      <a href="../../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2017,7 +2136,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2063,32 +2182,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2099,11 +2218,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2120,11 +2239,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2141,11 +2260,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2162,11 +2281,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2183,11 +2302,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2204,11 +2323,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2225,11 +2344,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2246,11 +2365,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2267,11 +2386,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2288,11 +2407,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2309,11 +2428,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2330,11 +2449,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2351,11 +2470,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2372,11 +2491,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2426,7 +2608,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.target.OpenTargetsTarget" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.target.OpenTargetsTarget" class="md-nav__link">
     <span class="md-ellipsis">
       OpenTargetsTarget
     </span>
@@ -2436,9 +2618,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="md-nav__link">
+  <a href="#gentropy.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="md-nav__link">
     <span class="md-ellipsis">
-      as_gene_index()
+      as_gene_index
     </span>
   </a>
   
@@ -2473,12 +2655,11 @@ <h1>Target</h1>
 
 
 
-
-<h2 id="otg.datasource.open_targets.target.OpenTargetsTarget" class="doc doc-heading">
-          <code>otg.datasource.open_targets.target.OpenTargetsTarget</code>
+<h2 id="gentropy.datasource.open_targets.target.OpenTargetsTarget" class="doc doc-heading">
+          <code>gentropy.datasource.open_targets.target.OpenTargetsTarget</code>
 
 
-<a href="#otg.datasource.open_targets.target.OpenTargetsTarget" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.datasource.open_targets.target.OpenTargetsTarget" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2491,7 +2672,7 @@ <h2 id="otg.datasource.open_targets.target.OpenTargetsTarget" class="doc doc-hea
 - Genes in alternative assemblies encoding for a reviewed protein product.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/datasource/open_targets/target.py</code></summary>
+              <summary>Source code in <code>src/gentropy/datasource/open_targets/target.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
 <span class="normal">11</span>
 <span class="normal">12</span>
@@ -2649,15 +2830,14 @@ <h2 id="otg.datasource.open_targets.target.OpenTargetsTarget" class="doc doc-hea
 
 
 
-
-<h3 id="otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="doc doc-heading">
+<h3 id="gentropy.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">as_gene_index</span><span class="p">(</span><span class="n">target_index</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">GeneIndex</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2707,7 +2887,7 @@ <h3 id="otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" clas
     <tbody>
         <tr>
 <td><code>GeneIndex</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.gene_index.GeneIndex" href="../../../dataset/gene_index/#otg.dataset.gene_index.GeneIndex">GeneIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.gene_index.GeneIndex" href="../../../datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex">GeneIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2719,7 +2899,7 @@ <h3 id="otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" clas
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/datasource/open_targets/target.py</code></summary>
+            <summary>Source code in <code>src/gentropy/datasource/open_targets/target.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">46</span>
 <span class="normal">47</span>
 <span class="normal">48</span>
@@ -2797,6 +2977,7 @@ <h3 id="otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index" clas
 
   </div>
 
+
 </div>
 <hr />
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-<h1 id="clumping">Clumping<a class="headerlink" href="#clumping" title="Permanent link">&para;</a></h1>
-<p>Clumping is a commonly used post-processing method that allows for identification of independent association signals from GWAS summary statistics and curated associations. This process is critical because of the complex linkage disequilibrium (LD) structure in human populations, which can result in multiple statistically significant associations within the same genomic region. Clumping methods help reduce redundancy in GWAS results and ensure that each reported association represents an independent signal.</p>
-<p>We have implemented 2 clumping methods:</p>
-
-
-<div class="doc doc-object doc-class">
-
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-
-
-<h2 id="otg.method.clump.LDclumping" class="doc doc-heading">
-          <code>otg.method.clump.LDclumping</code>
-
-
-<a href="#otg.method.clump.LDclumping" class="headerlink" title="Permanent link">&para;</a></h2>
-
-
-  <div class="doc doc-contents first">
-
-  
-      <p>LD clumping reports the most significant genetic associations in a region in terms of a smaller number of “clumps” of genetically linked SNPs.</p>
-
-            <details class="quote">
-              <summary>Source code in <code>src/otg/method/clump.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">17</span>
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-<span class="normal">75</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">LDclumping</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;LD clumping reports the most significant genetic associations in a region in terms of a smaller number of “clumps” of genetically linked SNPs.&quot;&quot;&quot;</span>
-
-    <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">_is_lead_linked</span><span class="p">(</span>
-        <span class="n">study_id</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
-        <span class="n">variant_id</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
-        <span class="n">p_value_exponent</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
-        <span class="n">p_value_mantissa</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
-        <span class="n">ld_set</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
-    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.</span>
-
-<span class="sd">        Args:</span>
-<span class="sd">            study_id (Column): studyId</span>
-<span class="sd">            variant_id (Column): Lead variant id</span>
-<span class="sd">            p_value_exponent (Column): p-value exponent</span>
-<span class="sd">            p_value_mantissa (Column): p-value mantissa</span>
-<span class="sd">            ld_set (Column): Array of variants in LD with the lead variant</span>
-
-<span class="sd">        Returns:</span>
-<span class="sd">            Column: Boolean in which True indicates that the lead is linked to another tag in the same dataset.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">leads_in_study</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">collect_set</span><span class="p">(</span><span class="n">variant_id</span><span class="p">)</span><span class="o">.</span><span class="n">over</span><span class="p">(</span><span class="n">Window</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="n">study_id</span><span class="p">))</span>
-        <span class="n">tags_in_studylocus</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">array_union</span><span class="p">(</span>
-            <span class="c1"># Get all tag variants from the credible set per studyLocusId</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">ld_set</span><span class="p">,</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">tagVariantId</span><span class="p">),</span>
-            <span class="c1"># And append the lead variant so that the intersection is the same for all studyLocusIds in a study</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">variant_id</span><span class="p">),</span>
-        <span class="p">)</span>
-        <span class="n">intersect_lead_tags</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">array_sort</span><span class="p">(</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">array_intersect</span><span class="p">(</span><span class="n">leads_in_study</span><span class="p">,</span> <span class="n">tags_in_studylocus</span><span class="p">)</span>
-        <span class="p">)</span>
-        <span class="k">return</span> <span class="p">(</span>
-            <span class="c1"># If the lead is in the credible set, we rank the peaks by p-value</span>
-            <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">intersect_lead_tags</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">,</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">row_number</span><span class="p">()</span><span class="o">.</span><span class="n">over</span><span class="p">(</span>
-                    <span class="n">Window</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="n">study_id</span><span class="p">,</span> <span class="n">intersect_lead_tags</span><span class="p">)</span><span class="o">.</span><span class="n">orderBy</span><span class="p">(</span>
-                        <span class="n">p_value_exponent</span><span class="p">,</span> <span class="n">p_value_mantissa</span>
-                    <span class="p">)</span>
-                <span class="p">)</span>
-                <span class="o">&gt;</span> <span class="mi">1</span><span class="p">,</span>
-            <span class="p">)</span>
-            <span class="c1"># If the intersection is empty (lead is not in the credible set or cred set is empty), the association is not linked</span>
-            <span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">))</span>
-        <span class="p">)</span>
-
-    <span class="nd">@classmethod</span>
-    <span class="k">def</span> <span class="nf">clump</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">LDclumping</span><span class="p">],</span> <span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Perform clumping on studyLocus dataset.</span>
-
-<span class="sd">        Args:</span>
-<span class="sd">            associations (StudyLocus): StudyLocus dataset</span>
-
-<span class="sd">        Returns:</span>
-<span class="sd">            StudyLocus: including flag and removing locus information for LD clumped loci.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="k">return</span> <span class="n">associations</span><span class="o">.</span><span class="n">clump</span><span class="p">()</span>
-</code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
-
-
-
-<div class="doc doc-object doc-function">
-
-
-
-
-<h3 id="otg.method.clump.LDclumping.clump" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">clump</span><span class="p">(</span><span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
-  </span>
-
-<a href="#otg.method.clump.LDclumping.clump" class="headerlink" title="Permanent link">&para;</a></h3>
-
-
-  <div class="doc doc-contents ">
-  
-      <p>Perform clumping on studyLocus dataset.</p>
-
-
-
-  <p><strong>Parameters:</strong></p>
-  <table>
-    <thead>
-      <tr>
-        <th>Name</th>
-        <th>Type</th>
-        <th>Description</th>
-        <th>Default</th>
-      </tr>
-    </thead>
-    <tbody>
-        <tr>
-          <td><code>associations</code></td>
-          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>StudyLocus dataset</p>
-            </div>
-          </td>
-          <td>
-              <em>required</em>
-          </td>
-        </tr>
-    </tbody>
-  </table>
-
-
-
-  <p><strong>Returns:</strong></p>
-  <table>
-    <thead>
-      <tr>
-<th>Name</th>        <th>Type</th>
-        <th>Description</th>
-      </tr>
-    </thead>
-    <tbody>
-        <tr>
-<td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>including flag and removing locus information for LD clumped loci.</p>
-            </div>
-          </td>
-        </tr>
-    </tbody>
-  </table>
-
-          <details class="quote">
-            <summary>Source code in <code>src/otg/method/clump.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">65</span>
-<span class="normal">66</span>
-<span class="normal">67</span>
-<span class="normal">68</span>
-<span class="normal">69</span>
-<span class="normal">70</span>
-<span class="normal">71</span>
-<span class="normal">72</span>
-<span class="normal">73</span>
-<span class="normal">74</span>
-<span class="normal">75</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
-<span class="k">def</span> <span class="nf">clump</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">LDclumping</span><span class="p">],</span> <span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Perform clumping on studyLocus dataset.</span>
-
-<span class="sd">    Args:</span>
-<span class="sd">        associations (StudyLocus): StudyLocus dataset</span>
-
-<span class="sd">    Returns:</span>
-<span class="sd">        StudyLocus: including flag and removing locus information for LD clumped loci.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">return</span> <span class="n">associations</span><span class="o">.</span><span class="n">clump</span><span class="p">()</span>
-</code></pre></div></td></tr></table></div>
-          </details>
-  </div>
-
-</div>
-
-
-
-  </div>
-
-  </div>
-
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-<hr />
-<div class="md-source-file">
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diff --git a/python_api/method/_method/index.html b/python_api/methods/_methods/index.html
similarity index 80%
rename from python_api/method/_method/index.html
rename to python_api/methods/_methods/index.html
index 787d628f5..af4eff24b 100644
--- a/python_api/method/_method/index.html
+++ b/python_api/methods/_methods/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../datasource/ukbiobank/study_index/">
+        <link rel="prev" href="../../datasources/open_targets/target/">
       
       
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+        <link rel="next" href="../carma/">
       
       
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+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Method - Open Targets Genetics</title>
+        <title>Methods - Open Targets Gentropy</title>
       
     
     
@@ -77,11 +77,6 @@
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     <div data-md-component="skip">
       
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@@ -94,7 +89,7 @@
 
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   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +102,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Method
+              Methods
             
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@@ -192,13 +187,13 @@
     
     
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-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -215,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
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@@ -233,7 +245,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +261,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
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@@ -309,22 +338,22 @@
 
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+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -338,11 +367,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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@@ -358,11 +387,11 @@
   
   
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+      <a href="../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +424,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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@@ -414,6 +443,123 @@
         
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+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
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+  <span class="md-ellipsis">
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+  
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
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+  <span class="md-ellipsis">
+    Run step using YAML config
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+  
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+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Roadmap
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+            <a href="../../../development/_development/" class="md-nav__link ">
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+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
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+            Datasets
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-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +779,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +800,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +821,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +842,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +863,7 @@
   
   
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-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +884,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +905,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +947,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +968,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +989,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1010,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1031,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1052,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -944,32 +1090,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
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     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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@@ -1063,12 +1230,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1246,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             Finngen
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     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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@@ -1137,12 +1325,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
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-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
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@@ -1194,7 +1382,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
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@@ -1232,12 +1420,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
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-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
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@@ -1248,14 +1436,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1456,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1477,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1498,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1519,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1557,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1573,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1593,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1614,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1635,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1656,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1694,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1710,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1730,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1751,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1773,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,7 +1799,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
@@ -1694,23 +1808,23 @@
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1835,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clumping/" class="md-nav__link">
+      <a href="../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1742,11 +1856,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../coloc/" class="md-nav__link">
+      <a href="../clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1763,11 +1877,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ecaviar/" class="md-nav__link">
+      <a href="../coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1898,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_annotator/" class="md-nav__link">
+      <a href="../ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1919,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1826,11 +1940,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../window_based_clumping/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1856,7 +1970,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
@@ -1872,14 +1986,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2001,32 +2115,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2151,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2172,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2193,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2214,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2121,11 +2235,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2142,11 +2256,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2163,11 +2277,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2184,11 +2298,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2205,11 +2319,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2226,11 +2340,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2247,11 +2361,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2268,11 +2382,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2289,11 +2403,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2310,11 +2424,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2356,8 +2533,6 @@
   
   
   
-    
-  
   
 </nav>
                   </div>
@@ -2375,8 +2550,9 @@
   
 
 
-<h1 id="method">Method<a class="headerlink" href="#method" title="Permanent link">&para;</a></h1>
-<p>TBC</p>
+  <h1>Methods</h1>
+
+<p>This section consists of all the methods available in the package. It provides detailed explanations and usage examples for each method. Developers can refer to this section to understand how to use the methods effectively in their code. The list of methods is constantly updated.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2399,7 +2575,7 @@ <h1 id="method">Method<a class="headerlink" href="#method" title="Permanent link
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2466,7 +2642,7 @@ <h1 id="method">Method<a class="headerlink" href="#method" title="Permanent link
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            Development
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/airflow/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Airflow configuration
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/contributing/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Contributing guidelines
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/troubleshooting/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Troubleshooting
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/workflows/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Pipeline workflows
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
+      
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+        
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../_python_api/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Python API
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
+            <span class="md-nav__icon md-icon"></span>
+            Python API
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
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+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
+            <span class="md-nav__icon md-icon"></span>
+            Datasets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Gene Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/intervals/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Prediction
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus Overlap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant-to-gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasources
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
+            <span class="md-nav__icon md-icon"></span>
+            Datasources
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Eqtl catalogue
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
+            <span class="md-nav__icon md-icon"></span>
+            Eqtl catalogue
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Stats
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Finngen
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
+            <span class="md-nav__icon md-icon"></span>
+            Finngen
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gnomad
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
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+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
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+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
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+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
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+        </nav>
+      
+    </li>
+  
+
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+            
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+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.method.carma.CARMA" class="md-nav__link">
+    <span class="md-ellipsis">
+      CARMA
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="CARMA">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.method.carma.CARMA.CARMA_spike_slab_noEM" class="md-nav__link">
+    <span class="md-ellipsis">
+      CARMA_spike_slab_noEM
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../coloc/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Coloc
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ecaviar/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_annotator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LDAnnotator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    PICS
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../l2g/_l2g/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    L2g
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
+            <span class="md-nav__icon md-icon"></span>
+            L2g
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/evaluator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    W&B evaluator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/feature_factory/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Factory
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/model/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Model
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/trainer/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Trainer
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
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+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../steps/_steps/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Steps
+  </span>
+  
+
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+            
+              
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
+            <span class="md-nav__icon md-icon"></span>
+            Steps
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.method.carma.CARMA" class="md-nav__link">
+    <span class="md-ellipsis">
+      CARMA
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="CARMA">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.method.carma.CARMA.CARMA_spike_slab_noEM" class="md-nav__link">
+    <span class="md-ellipsis">
+      CARMA_spike_slab_noEM
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+  <h1>CARMA</h1>
+
+<p>CARMA is the method of the fine-mapping and outlier detection, originally implemented in R (<a href="https://github.com/ZikunY/CARMA">CARMA on GitHub</a>).</p>
+<p>The full repository for the reimplementation of CARMA in Python can be found <a href="https://github.com/hlnicholls/carmapy/tree/0.1.0">here</a>.</p>
+<p>This is a simplified version of CARMA with the following features:</p>
+<ol>
+<li>It uses only Spike-slab effect size priors and Poisson model priors.</li>
+<li>C++ is re-implemented in Python.</li>
+<li>The way of storing the configuration list is changed. It uses a string with the list of indexes for causal SNPs instead of a sparse matrix.</li>
+<li>Fixed bugs in PIP calculation.</li>
+<li>No credible models.</li>
+<li>No credible sets, only PIPs.</li>
+<li>No functional annotations.</li>
+<li>Removed unnecessary parameters.</li>
+</ol>
+
+
+<div class="doc doc-object doc-class">
+
+
+
+<h2 id="gentropy.method.carma.CARMA" class="doc doc-heading">
+          <code>gentropy.method.carma.CARMA</code>
+
+
+<a href="#gentropy.method.carma.CARMA" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
+
+  
+      <p>Implementation of CARMA outlier detection method.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/method/carma.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 14</span>
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+<span class="normal">857</span>
+<span class="normal">858</span>
+<span class="normal">859</span>
+<span class="normal">860</span>
+<span class="normal">861</span>
+<span class="normal">862</span>
+<span class="normal">863</span>
+<span class="normal">864</span>
+<span class="normal">865</span>
+<span class="normal">866</span>
+<span class="normal">867</span>
+<span class="normal">868</span>
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+<span class="normal">870</span>
+<span class="normal">871</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">CARMA</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Implementation of CARMA outlier detection method.&quot;&quot;&quot;</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">CARMA_spike_slab_noEM</span><span class="p">(</span>
+        <span class="n">z</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">ld</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">lambda_val</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="n">Max_Model_Dim</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">200_000</span><span class="p">,</span>
+        <span class="n">all_iter</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="n">all_inner_iter</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+        <span class="n">epsilon_threshold</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-5</span><span class="p">,</span>
+        <span class="n">num_causal</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+        <span class="n">tau</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.04</span><span class="p">,</span>
+        <span class="n">outlier_switch</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">outlier_BF_index</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="mf">3.2</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Perform CARMA analysis using a Spike-and-Slab prior without Expectation-Maximization (EM).</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            z (np.ndarray): Numeric vector representing z-scores.</span>
+<span class="sd">            ld (np.ndarray): Numeric matrix representing the linkage disequilibrium (LD) matrix.</span>
+<span class="sd">            lambda_val (float): Regularization parameter controlling the strength of the L1 penalty.</span>
+<span class="sd">            Max_Model_Dim (int): Maximum allowed dimension for the causal models.</span>
+<span class="sd">            all_iter (int): The total number of iterations to run the CARMA analysis.</span>
+<span class="sd">            all_inner_iter (int): The number of inner iterations in each CARMA iteration.</span>
+<span class="sd">            epsilon_threshold (float): Threshold for convergence in CARMA iterations.</span>
+<span class="sd">            num_causal (int): Maximal number of causal variants to be selected in the final model.</span>
+<span class="sd">            tau (float): Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.</span>
+<span class="sd">            outlier_switch (bool): Whether to consider outlier detection in the analysis.</span>
+<span class="sd">            outlier_BF_index (float): Bayes Factor threshold for identifying outliers.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            dict[str, Any]: A dictionary containing the following results:</span>
+<span class="sd">                - PIPs: A numeric vector of posterior inclusion probabilities (PIPs) for all SNPs.</span>
+<span class="sd">                - B_list: A dataframe containing the marginal likelihoods and the corresponding model space.</span>
+<span class="sd">                - Outliers: A list of outlier SNPs.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">p_snp</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">z</span><span class="p">)</span>
+        <span class="n">epsilon_list</span> <span class="o">=</span> <span class="n">epsilon_threshold</span> <span class="o">*</span> <span class="n">p_snp</span>
+        <span class="n">all_epsilon_threshold</span> <span class="o">=</span> <span class="n">epsilon_threshold</span> <span class="o">*</span> <span class="n">p_snp</span>
+
+        <span class="c1"># Zero step</span>
+        <span class="n">all_C_list</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_MCS_modified</span><span class="p">(</span>
+            <span class="n">z</span><span class="o">=</span><span class="n">z</span><span class="p">,</span>
+            <span class="n">ld_matrix</span><span class="o">=</span><span class="n">ld</span><span class="p">,</span>
+            <span class="n">epsilon</span><span class="o">=</span><span class="n">epsilon_list</span><span class="p">,</span>
+            <span class="n">Max_Model_Dim</span><span class="o">=</span><span class="n">Max_Model_Dim</span><span class="p">,</span>
+            <span class="n">lambda_val</span><span class="o">=</span><span class="n">lambda_val</span><span class="p">,</span>
+            <span class="n">outlier_switch</span><span class="o">=</span><span class="n">outlier_switch</span><span class="p">,</span>
+            <span class="n">tau</span><span class="o">=</span><span class="n">tau</span><span class="p">,</span>
+            <span class="n">num_causal</span><span class="o">=</span><span class="n">num_causal</span><span class="p">,</span>
+            <span class="n">inner_all_iter</span><span class="o">=</span><span class="n">all_inner_iter</span><span class="p">,</span>
+            <span class="n">outlier_BF_index</span><span class="o">=</span><span class="n">outlier_BF_index</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Main steps</span>
+        <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">all_iter</span><span class="p">):</span>
+            <span class="n">ac1</span> <span class="o">=</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">]</span>
+            <span class="n">previous_result</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">ac1</span><span class="p">[</span><span class="mi">0</span> <span class="p">:</span> <span class="nb">round</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ac1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">4</span><span class="p">)])</span>
+
+            <span class="n">all_C_list</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_MCS_modified</span><span class="p">(</span>
+                <span class="n">z</span><span class="o">=</span><span class="n">z</span><span class="p">,</span>
+                <span class="n">ld_matrix</span><span class="o">=</span><span class="n">ld</span><span class="p">,</span>
+                <span class="n">input_conditional_S_list</span><span class="o">=</span><span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;conditional_S_list&quot;</span><span class="p">],</span>
+                <span class="n">Max_Model_Dim</span><span class="o">=</span><span class="n">Max_Model_Dim</span><span class="p">,</span>
+                <span class="n">num_causal</span><span class="o">=</span><span class="n">num_causal</span><span class="p">,</span>
+                <span class="n">epsilon</span><span class="o">=</span><span class="n">epsilon_list</span><span class="p">,</span>
+                <span class="n">outlier_switch</span><span class="o">=</span><span class="n">outlier_switch</span><span class="p">,</span>
+                <span class="n">tau</span><span class="o">=</span><span class="n">tau</span><span class="p">,</span>
+                <span class="n">lambda_val</span><span class="o">=</span><span class="n">lambda_val</span><span class="p">,</span>
+                <span class="n">inner_all_iter</span><span class="o">=</span><span class="n">all_inner_iter</span><span class="p">,</span>
+                <span class="n">outlier_BF_index</span><span class="o">=</span><span class="n">outlier_BF_index</span><span class="p">,</span>
+            <span class="p">)</span>
+
+            <span class="n">ac1</span> <span class="o">=</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">]</span>
+            <span class="n">difference</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">previous_result</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">ac1</span><span class="p">[</span><span class="mi">0</span> <span class="p">:</span> <span class="nb">round</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ac1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">4</span><span class="p">)]))</span>
+            <span class="k">if</span> <span class="n">difference</span> <span class="o">&lt;</span> <span class="n">all_epsilon_threshold</span><span class="p">:</span>
+                <span class="k">break</span>
+
+        <span class="c1"># Calculate PIPs and Credible Set</span>
+        <span class="n">pip</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_PIP_func</span><span class="p">(</span>
+            <span class="n">likeli</span><span class="o">=</span><span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">],</span>
+            <span class="n">model_space</span><span class="o">=</span><span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;matrix_gamma&quot;</span><span class="p">],</span>
+            <span class="n">p</span><span class="o">=</span><span class="n">p_snp</span><span class="p">,</span>
+            <span class="n">num_causal</span><span class="o">=</span><span class="n">num_causal</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">results_list</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="s2">&quot;PIPs&quot;</span><span class="p">:</span> <span class="n">pip</span><span class="p">,</span>
+            <span class="s2">&quot;B_list&quot;</span><span class="p">:</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">],</span>
+            <span class="s2">&quot;Outliers&quot;</span><span class="p">:</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;conditional_S_list&quot;</span><span class="p">],</span>
+        <span class="p">}</span>
+
+
+        <span class="k">return</span> <span class="n">results_list</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_ind_normal_sigma_fixed_marginal_fun_indi</span><span class="p">(</span>
+        <span class="n">zSigmaz_S</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">tau</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">p_S</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">det_S</span><span class="p">:</span> <span class="nb">float</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Internal function for calculating the marginal likelihood of configuration model.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            zSigmaz_S (np.ndarray): The zSigmaz_S value.</span>
+<span class="sd">            tau (float): The tau value.</span>
+<span class="sd">            p_S (int): The number of SNPs.</span>
+<span class="sd">            det_S (float): The det_S value.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            float: The marginal likelihood of a model.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">            &gt;&gt;&gt; zSigmaz_S = 0.1</span>
+<span class="sd">            &gt;&gt;&gt; tau = 1 / 0.05**2</span>
+<span class="sd">            &gt;&gt;&gt; p_S = 3</span>
+<span class="sd">            &gt;&gt;&gt; det_S = 0.1</span>
+<span class="sd">            &gt;&gt;&gt; np.round(CARMA._ind_normal_sigma_fixed_marginal_fun_indi(zSigmaz_S, tau, p_S, det_S),decimals=5)</span>
+<span class="sd">            10.18849</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">p_S</span> <span class="o">/</span> <span class="mf">2.0</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">tau</span><span class="p">)</span> <span class="o">-</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">det_S</span><span class="p">)</span> <span class="o">+</span> <span class="n">zSigmaz_S</span> <span class="o">/</span> <span class="mf">2.0</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_ind_Normal_fixed_sigma_marginal_external</span><span class="p">(</span>
+        <span class="n">index_vec_input</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">Sigma</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">z</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">tau</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+        <span class="n">p_S</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Marginal likelihood of configuration model.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            index_vec_input (np.ndarray): The index vector.</span>
+<span class="sd">            Sigma (np.ndarray): The Sigma matrix.</span>
+<span class="sd">            z (np.ndarray): The z vector.</span>
+<span class="sd">            tau (float): The tau value.</span>
+<span class="sd">            p_S (int): The number of SNPs.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            float: The marginal likelihood of a model.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">            &gt;&gt;&gt; index_vec_input = np.array([1, 2])</span>
+<span class="sd">            &gt;&gt;&gt; Sigma = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])</span>
+<span class="sd">            &gt;&gt;&gt; z = np.array([10, 11, 10])</span>
+<span class="sd">            &gt;&gt;&gt; tau = 1</span>
+<span class="sd">            &gt;&gt;&gt; p_S = 2</span>
+<span class="sd">            &gt;&gt;&gt; np.round(CARMA._ind_Normal_fixed_sigma_marginal_external(index_vec_input, Sigma, z, tau, p_S),decimals=5)</span>
+<span class="sd">            43.60579</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">index_vec</span> <span class="o">=</span> <span class="n">index_vec_input</span> <span class="o">-</span> <span class="mi">1</span>
+        <span class="n">Sigma_S</span> <span class="o">=</span> <span class="n">Sigma</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">index_vec</span><span class="p">,</span> <span class="n">index_vec</span><span class="p">)]</span>
+        <span class="n">A</span> <span class="o">=</span> <span class="n">tau</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="n">p_S</span><span class="p">)</span>
+
+        <span class="n">det_S</span> <span class="o">=</span> <span class="n">det</span><span class="p">(</span><span class="n">Sigma_S</span> <span class="o">+</span> <span class="n">A</span><span class="p">)</span>
+        <span class="n">Sigma_S_inv</span> <span class="o">=</span> <span class="n">inv</span><span class="p">(</span><span class="n">Sigma_S</span> <span class="o">+</span> <span class="n">A</span><span class="p">)</span>
+
+        <span class="n">sub_z</span> <span class="o">=</span> <span class="n">z</span><span class="p">[</span><span class="n">index_vec</span><span class="p">]</span>
+        <span class="n">zSigmaz_S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">sub_z</span><span class="o">.</span><span class="n">T</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">Sigma_S_inv</span><span class="p">,</span> <span class="n">sub_z</span><span class="p">))</span>
+
+        <span class="n">b</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_ind_normal_sigma_fixed_marginal_fun_indi</span><span class="p">(</span><span class="n">zSigmaz_S</span><span class="p">,</span> <span class="n">tau</span><span class="p">,</span> <span class="n">p_S</span><span class="p">,</span> <span class="n">det_S</span><span class="p">)</span>
+
+        <span class="n">results</span> <span class="o">=</span> <span class="n">b</span>
+
+        <span class="k">return</span> <span class="n">results</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_outlier_ind_Normal_marginal_external</span><span class="p">(</span>
+        <span class="n">index_vec_input</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">Sigma</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">z</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">tau</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+        <span class="n">p_S</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Likehood of outlier model.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            index_vec_input (np.ndarray): The index vector.</span>
+<span class="sd">            Sigma (np.ndarray): The Sigma matrix.</span>
+<span class="sd">            z (np.ndarray): The z vector.</span>
+<span class="sd">            tau (float): The tau value.</span>
+<span class="sd">            p_S (int): The number of SNPs.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            float: The likelihood of a model.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">            &gt;&gt;&gt; index_vec_input = np.array([1, 2, 3])</span>
+<span class="sd">            &gt;&gt;&gt; Sigma = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])</span>
+<span class="sd">            &gt;&gt;&gt; z = np.array([0.1, 0.2, 0.3])</span>
+<span class="sd">            &gt;&gt;&gt; tau = 1 / 0.05**2</span>
+<span class="sd">            &gt;&gt;&gt; p_S = 3</span>
+<span class="sd">            &gt;&gt;&gt; np.round(CARMA._outlier_ind_Normal_marginal_external(index_vec_input, Sigma, z, tau, p_S),decimals=5)</span>
+<span class="sd">            -8.8497</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">index_vec</span> <span class="o">=</span> <span class="n">index_vec_input</span> <span class="o">-</span> <span class="mi">1</span>
+
+        <span class="n">Sigma_S</span> <span class="o">=</span> <span class="n">Sigma</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">index_vec</span><span class="p">,</span> <span class="n">index_vec</span><span class="p">)]</span>
+        <span class="n">A</span> <span class="o">=</span> <span class="n">tau</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="n">p_S</span><span class="p">)</span>
+
+        <span class="n">Sigma_S_I_inv</span> <span class="o">=</span> <span class="n">pinv</span><span class="p">(</span><span class="n">Sigma_S</span> <span class="o">+</span> <span class="n">A</span><span class="p">,</span> <span class="n">rtol</span><span class="o">=</span><span class="mf">0.00001</span><span class="p">)</span>
+        <span class="n">Sigma_S_inv</span> <span class="o">=</span> <span class="n">pinv</span><span class="p">(</span><span class="n">Sigma_S</span><span class="p">,</span> <span class="n">rtol</span><span class="o">=</span><span class="mf">0.00001</span><span class="p">)</span>
+
+        <span class="n">det_S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">det</span><span class="p">(</span><span class="n">Sigma_S_inv</span><span class="p">))</span>
+        <span class="n">det_I_S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">det</span><span class="p">(</span><span class="n">Sigma_S_I_inv</span><span class="p">))</span>
+
+        <span class="n">sub_z</span> <span class="o">=</span> <span class="n">z</span><span class="p">[</span><span class="n">index_vec</span><span class="p">]</span>
+        <span class="n">zSigmaz_S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">sub_z</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">Sigma_S_inv</span><span class="p">,</span> <span class="n">sub_z</span><span class="p">))</span>
+        <span class="n">zSigmaz_I_S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">sub_z</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">dot</span><span class="p">(</span><span class="n">Sigma_S_I_inv</span><span class="p">,</span> <span class="n">sub_z</span><span class="p">))</span>
+
+        <span class="n">b</span> <span class="o">=</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">det_S</span><span class="p">)</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">det_I_S</span><span class="p">))</span> <span class="o">-</span> <span class="mf">0.5</span> <span class="o">*</span> <span class="p">(</span><span class="n">zSigmaz_S</span> <span class="o">-</span> <span class="n">zSigmaz_I_S</span><span class="p">)</span>
+        <span class="n">results</span> <span class="o">=</span> <span class="n">b</span>
+
+        <span class="k">return</span> <span class="n">results</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_add_function</span><span class="p">(</span><span class="n">S_sub</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">Any</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Concatenate two arrays and sort the result.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            S_sub (np.ndarray): The first array.</span>
+<span class="sd">            y (Any): The second array.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            np.ndarray: The concatenated and sorted array.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">            &gt;&gt;&gt; S_sub = np.array([3, 4])</span>
+<span class="sd">            &gt;&gt;&gt; y = np.array([1, 2])</span>
+<span class="sd">            &gt;&gt;&gt; CARMA._add_function(S_sub, y)</span>
+<span class="sd">            array([[1, 2, 3],</span>
+<span class="sd">                   [1, 2, 4]])</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(([</span><span class="n">x</span><span class="p">],</span> <span class="n">y</span><span class="p">)))</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">S_sub</span><span class="p">])</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_set_gamma_func_base</span><span class="p">(</span><span class="n">S</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span> <span class="n">p</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Creates a dictionary of sets of configurations assuming no conditional set.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            S (Any): The input set.</span>
+<span class="sd">            p (int): The number of SNPs.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            dict[int, np.ndarray]: A dictionary of sets of configurations.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; S = [0,1]</span>
+<span class="sd">        &gt;&gt;&gt; p = 4</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._set_gamma_func_base(S, p)</span>
+<span class="sd">        {0: array([[0],</span>
+<span class="sd">               [1]]), 1: array([[0, 1, 2],</span>
+<span class="sd">               [0, 1, 3]]), 2: array([[0, 2],</span>
+<span class="sd">               [0, 3],</span>
+<span class="sd">               [1, 2],</span>
+<span class="sd">               [1, 3]])}</span>
+
+<span class="sd">        &gt;&gt;&gt; S = [0]</span>
+<span class="sd">        &gt;&gt;&gt; p = 2</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._set_gamma_func_base(S, p)</span>
+<span class="sd">        {0: None, 1: array([[0, 1]]), 2: array([[1]])}</span>
+
+<span class="sd">        &gt;&gt;&gt; S = []</span>
+<span class="sd">        &gt;&gt;&gt; p = 2</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._set_gamma_func_base(S, p)</span>
+<span class="sd">        {0: None, 1: array([[0],</span>
+<span class="sd">               [1]]), 2: None}</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">set_gamma</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">p</span><span class="p">)</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="n">S_sub</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">p</span><span class="p">),</span> <span class="n">S</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_add_function</span><span class="p">(</span><span class="n">S_sub</span><span class="p">,</span> <span class="n">S</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">S_sub</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="n">S_sub</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">p</span><span class="p">),</span> <span class="n">S</span><span class="p">)</span>
+            <span class="n">S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">S</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">combinations</span><span class="p">(</span><span class="n">S</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)))</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_add_function</span><span class="p">(</span><span class="n">S_sub</span><span class="p">,</span> <span class="n">S</span><span class="p">)</span>
+            <span class="n">xs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">CARMA</span><span class="o">.</span><span class="n">_add_function</span><span class="p">(</span><span class="n">S_sub</span><span class="p">,</span> <span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">xs</span>
+
+        <span class="k">return</span> <span class="n">set_gamma</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_set_gamma_func_conditional</span><span class="p">(</span>
+        <span class="n">input_S</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span> <span class="n">condition_index</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">],</span> <span class="n">p</span><span class="p">:</span> <span class="nb">int</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Creates a dictionary of sets of configurations assuming conditional set.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            input_S (Any): The input set.</span>
+<span class="sd">            condition_index (list[int]): The conditional set.</span>
+<span class="sd">            p (int): The number of SNPs.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            dict[int, np.ndarray]: A dictionary of sets of configurations.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; input_S = [0,1,2]</span>
+<span class="sd">        &gt;&gt;&gt; condition_index = [2]</span>
+<span class="sd">        &gt;&gt;&gt; p = 4</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._set_gamma_func_conditional(input_S, condition_index, p)</span>
+<span class="sd">        {0: array([[0],</span>
+<span class="sd">               [1]]), 1: array([[0, 1, 3]]), 2: array([[0, 3],</span>
+<span class="sd">               [1, 3]])}</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">set_gamma</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="p">{}</span>
+        <span class="n">S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">input_S</span><span class="p">,</span> <span class="n">condition_index</span><span class="p">)</span>
+
+        <span class="c1"># set of gamma-</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">S_sub</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">p</span><span class="p">),</span> <span class="n">condition_index</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">S_sub</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="n">S_sub</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">p</span><span class="p">),</span> <span class="n">input_S</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_add_function</span><span class="p">(</span><span class="n">S_sub</span><span class="p">,</span> <span class="n">S</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">S_sub</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="o">-</span><span class="mi">1</span><span class="p">,</span> <span class="mi">1</span><span class="p">)</span>
+
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+            <span class="n">S_sub</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">p</span><span class="p">),</span> <span class="n">input_S</span><span class="p">)</span>
+            <span class="n">S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">S</span><span class="p">)</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="nb">list</span><span class="p">(</span><span class="n">combinations</span><span class="p">(</span><span class="n">S</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">S</span><span class="p">)</span> <span class="o">-</span> <span class="mi">1</span><span class="p">)))</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_add_function</span><span class="p">(</span><span class="n">S_sub</span><span class="p">,</span> <span class="n">S</span><span class="p">)</span>
+            <span class="n">xs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">vstack</span><span class="p">([</span><span class="n">CARMA</span><span class="o">.</span><span class="n">_add_function</span><span class="p">(</span><span class="n">S_sub</span><span class="p">,</span> <span class="n">row</span><span class="p">)</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">set_gamma</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+            <span class="n">set_gamma</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">xs</span>
+
+        <span class="k">return</span> <span class="n">set_gamma</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_set_gamma_func</span><span class="p">(</span>
+        <span class="n">input_S</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span> <span class="n">p</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">condition_index</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Creates a dictionary of sets of configurations.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            input_S (Any): The input set.</span>
+<span class="sd">            p (int): The number of SNPs.</span>
+<span class="sd">            condition_index (list[int] | None): The conditional set. Defaults to None.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            dict[int, np.ndarray]: A dictionary of sets of configurations.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; input_S = [0,1,2]</span>
+<span class="sd">        &gt;&gt;&gt; condition_index=[2]</span>
+<span class="sd">        &gt;&gt;&gt; p = 4</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._set_gamma_func(input_S, p, condition_index)</span>
+<span class="sd">        {0: array([[0],</span>
+<span class="sd">               [1]]), 1: array([[0, 1, 3]]), 2: array([[0, 3],</span>
+<span class="sd">               [1, 3]])}</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">if</span> <span class="n">condition_index</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">results</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_set_gamma_func_base</span><span class="p">(</span><span class="n">input_S</span><span class="p">,</span> <span class="n">p</span><span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">results</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_set_gamma_func_conditional</span><span class="p">(</span><span class="n">input_S</span><span class="p">,</span> <span class="n">condition_index</span><span class="p">,</span> <span class="n">p</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">results</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_index_fun_internal</span><span class="p">(</span><span class="n">x</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">str</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Convert an array of causal SNP indexes to comma-separated string.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            x (np.ndarray): The input array.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            str: The comma-separated string.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; x = np.array([1,2,3])</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._index_fun_internal(x)</span>
+<span class="sd">        &#39;1,2,3&#39;</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">y</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">x</span><span class="p">)</span>
+        <span class="n">y</span> <span class="o">=</span> <span class="n">y</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">str</span><span class="p">)</span>
+        <span class="k">return</span> <span class="s2">&quot;,&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">y</span><span class="p">)</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_index_fun</span><span class="p">(</span><span class="n">y</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Convert an array of causal SNP indexes to comma-separated string.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            y (np.ndarray): The input array.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            np.ndarray: The comma-separated string.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; y = np.array([[1,2,3],[4,5,6]])</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._index_fun(y)</span>
+<span class="sd">        array([&#39;1,2,3&#39;, &#39;4,5,6&#39;], dtype=&#39;&lt;U5&#39;)</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">([</span><span class="n">CARMA</span><span class="o">.</span><span class="n">_index_fun_internal</span><span class="p">(</span><span class="n">x</span><span class="p">)</span> <span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">y</span><span class="p">])</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_ridge_fun</span><span class="p">(</span>
+        <span class="n">x</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+        <span class="n">Sigma</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">modi_ld_S</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">test_S</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">z</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">outlier_tau</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span>
+        <span class="n">outlier_likelihood</span><span class="p">:</span> <span class="n">Any</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Estimate the matrix shrinkage parameter for outlier detection.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            x (float): The input parameter.</span>
+<span class="sd">            Sigma (np.ndarray): The Sigma matrix.</span>
+<span class="sd">            modi_ld_S (np.ndarray): The modi_ld_S matrix.</span>
+<span class="sd">            test_S (np.ndarray): The test_S matrix.</span>
+<span class="sd">            z (np.ndarray): The z vector.</span>
+<span class="sd">            outlier_tau (float): The outlier_tau value.</span>
+<span class="sd">            outlier_likelihood (Any): The outlier_likelihood function.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            float: The estimated matrix shrinkage parameter.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; x = 0.5</span>
+<span class="sd">        &gt;&gt;&gt; Sigma = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])</span>
+<span class="sd">        &gt;&gt;&gt; modi_ld_S = np.array([[1, 0.5], [0.5, 1]])</span>
+<span class="sd">        &gt;&gt;&gt; test_S = np.array([1, 2])</span>
+<span class="sd">        &gt;&gt;&gt; z = np.array([0.1, 0.2, 0.3])</span>
+<span class="sd">        &gt;&gt;&gt; outlier_tau = 1 / 0.05**2</span>
+<span class="sd">        &gt;&gt;&gt; outlier_likelihood = CARMA._outlier_ind_Normal_marginal_external</span>
+<span class="sd">        &gt;&gt;&gt; np.round(CARMA._ridge_fun(x, Sigma, modi_ld_S, test_S, z, outlier_tau, outlier_likelihood),decimals=5)</span>
+<span class="sd">        6.01486</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">temp_Sigma</span> <span class="o">=</span> <span class="n">Sigma</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+        <span class="n">temp_ld_S</span> <span class="o">=</span> <span class="n">x</span> <span class="o">*</span> <span class="n">modi_ld_S</span> <span class="o">+</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">x</span><span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">modi_ld_S</span><span class="p">))</span>
+        <span class="n">temp_Sigma</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">test_S</span><span class="p">,</span> <span class="n">test_S</span><span class="p">)]</span> <span class="o">=</span> <span class="n">temp_ld_S</span>
+        <span class="k">return</span> <span class="o">-</span><span class="n">outlier_likelihood</span><span class="p">(</span>
+            <span class="n">index_vec_input</span><span class="o">=</span><span class="n">test_S</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="n">Sigma</span><span class="o">=</span><span class="n">temp_Sigma</span><span class="p">,</span>
+            <span class="n">z</span><span class="o">=</span><span class="n">z</span><span class="p">,</span>
+            <span class="n">tau</span><span class="o">=</span><span class="n">outlier_tau</span><span class="p">,</span>
+            <span class="n">p_S</span><span class="o">=</span><span class="nb">len</span><span class="p">(</span><span class="n">test_S</span><span class="p">),</span>
+        <span class="p">)</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_prior_dist</span><span class="p">(</span><span class="n">t</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">lambda_val</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">p</span><span class="p">:</span> <span class="nb">int</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Estimate the priors for the given configurations.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            t (str): The input string for the given configuration.</span>
+<span class="sd">            lambda_val (float): The lambda value.</span>
+<span class="sd">            p (int): The number of SNPs.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            float: The estimated prior.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; t = &quot;1,2,3&quot;</span>
+<span class="sd">        &gt;&gt;&gt; lambda_val = 1</span>
+<span class="sd">        &gt;&gt;&gt; p = 4</span>
+<span class="sd">        &gt;&gt;&gt; np.round(CARMA._prior_dist(t, lambda_val, p),decimals=5)</span>
+<span class="sd">        -3.17805</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">index_array</span> <span class="o">=</span> <span class="n">t</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;,&quot;</span><span class="p">)</span>
+        <span class="n">dim_model</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">index_array</span><span class="p">)</span>
+        <span class="k">if</span> <span class="n">t</span> <span class="o">==</span> <span class="s2">&quot;&quot;</span><span class="p">:</span>
+            <span class="n">dim_model</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="n">dim_model</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">lambda_val</span><span class="p">)</span> <span class="o">+</span> <span class="n">lgamma</span><span class="p">(</span><span class="n">p</span> <span class="o">-</span> <span class="n">dim_model</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span> <span class="o">-</span> <span class="n">lgamma</span><span class="p">(</span><span class="n">p</span> <span class="o">+</span> <span class="mi">1</span><span class="p">)</span>
+        <span class="p">)</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_PIP_func</span><span class="p">(</span>
+        <span class="n">likeli</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">model_space</span><span class="p">:</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">,</span> <span class="n">p</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">num_causal</span><span class="p">:</span> <span class="nb">int</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Estimates the posterior inclusion probabilities (PIPs) for all SNPs.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            likeli (pd.DataFrame): The marginal likelihoods.</span>
+<span class="sd">            model_space (pd.DataFrame): The corresponding model space.</span>
+<span class="sd">            p (int): The number of SNPs.</span>
+<span class="sd">            num_causal (int): The maximal number of causal SNPs.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            np.ndarray: The posterior inclusion probabilities (PIPs) for all SNPs.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; likeli = pd.DataFrame([10, 10, 5,11,0], columns=[&#39;likeli&#39;]).squeeze()</span>
+<span class="sd">        &gt;&gt;&gt; model_space = pd.DataFrame([&#39;0&#39;, &#39;1&#39;, &#39;2&#39;,&#39;0,1&#39;,&#39;&#39;], columns=[&#39;config&#39;]).squeeze()</span>
+<span class="sd">        &gt;&gt;&gt; p = 3</span>
+<span class="sd">        &gt;&gt;&gt; num_causal = 2</span>
+<span class="sd">        &gt;&gt;&gt; CARMA._PIP_func(likeli, model_space, p, num_causal)</span>
+<span class="sd">        array([0.7869271, 0.7869271, 0.001426 ])</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">likeli</span> <span class="o">=</span> <span class="n">likeli</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="n">model_space</span> <span class="o">=</span> <span class="n">model_space</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+        <span class="n">model_space_matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">((</span><span class="nb">len</span><span class="p">(</span><span class="n">model_space</span><span class="p">),</span> <span class="n">p</span><span class="p">),</span> <span class="n">dtype</span><span class="o">=</span><span class="nb">int</span><span class="p">)</span>
+
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">model_space</span><span class="p">)):</span>
+            <span class="k">if</span> <span class="n">model_space</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">!=</span> <span class="s2">&quot;&quot;</span><span class="p">:</span>
+                <span class="n">ind</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">model_space</span><span class="o">.</span><span class="n">iloc</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;,&quot;</span><span class="p">)))</span>
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                    <span class="n">model_space_matrix</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">ind</span><span class="p">]</span> <span class="o">=</span> <span class="mi">1</span>
+
+        <span class="n">infi_index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">isinf</span><span class="p">(</span><span class="n">likeli</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">infi_index</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">likeli</span> <span class="o">=</span> <span class="n">likeli</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">infi_index</span><span class="p">)</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+            <span class="n">model_space_matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">model_space_matrix</span><span class="p">,</span> <span class="n">infi_index</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+
+        <span class="n">na_index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">where</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">isnan</span><span class="p">(</span><span class="n">likeli</span><span class="p">))[</span><span class="mi">0</span><span class="p">]</span>
+        <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">na_index</span><span class="p">)</span> <span class="o">!=</span> <span class="mi">0</span><span class="p">:</span>
+            <span class="n">likeli</span> <span class="o">=</span> <span class="n">likeli</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">na_index</span><span class="p">)</span><span class="o">.</span><span class="n">reset_index</span><span class="p">(</span><span class="n">drop</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+            <span class="n">model_space_matrix</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span><span class="n">model_space_matrix</span><span class="p">,</span> <span class="n">na_index</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">)</span>
+
+        <span class="n">row_sums</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">model_space_matrix</span><span class="p">,</span> <span class="n">axis</span><span class="o">=</span><span class="mi">1</span><span class="p">)</span>
+        <span class="n">model_space_matrix</span> <span class="o">=</span> <span class="n">model_space_matrix</span><span class="p">[</span><span class="n">row_sums</span> <span class="o">&lt;=</span> <span class="n">num_causal</span><span class="p">]</span>
+        <span class="n">likeli</span> <span class="o">=</span> <span class="n">likeli</span><span class="p">[</span><span class="n">row_sums</span> <span class="o">&lt;=</span> <span class="n">num_causal</span><span class="p">]</span>
+
+        <span class="n">aa</span> <span class="o">=</span> <span class="n">likeli</span> <span class="o">-</span> <span class="nb">max</span><span class="p">(</span><span class="n">likeli</span><span class="p">)</span>
+        <span class="n">prob_sum</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">))</span>
+
+        <span class="n">result_prob</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">zeros</span><span class="p">(</span><span class="n">p</span><span class="p">)</span>
+        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">p</span><span class="p">):</span>
+            <span class="n">result_prob</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">[</span><span class="n">model_space_matrix</span><span class="p">[:,</span> <span class="n">i</span><span class="p">]</span> <span class="o">==</span> <span class="mi">1</span><span class="p">]))</span> <span class="o">/</span> <span class="n">prob_sum</span>
+            <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">result_prob</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_MCS_modified</span><span class="p">(</span>  <span class="c1"># noqa: C901</span>
+        <span class="n">z</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">ld_matrix</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+        <span class="n">Max_Model_Dim</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10_000</span><span class="p">,</span>
+        <span class="n">lambda_val</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+        <span class="n">num_causal</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+        <span class="n">outlier_switch</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+        <span class="n">input_conditional_S_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">int</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">tau</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="mf">0.05</span><span class="o">**</span><span class="mi">2</span><span class="p">,</span>
+        <span class="n">epsilon</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-3</span><span class="p">,</span>
+        <span class="n">inner_all_iter</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+        <span class="n">outlier_BF_index</span><span class="p">:</span> <span class="nb">float</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Modified Monte Carlo shotgun sampling (MCS) algorithm.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            z (np.ndarray): Numeric vector representing z-scores.</span>
+<span class="sd">            ld_matrix (np.ndarray): Numeric matrix representing the linkage disequilibrium (LD) matrix.</span>
+<span class="sd">            Max_Model_Dim (int): Maximum allowed dimension for the causal models.</span>
+<span class="sd">            lambda_val (float): Regularization parameter controlling the strength of the L1 penalty.</span>
+<span class="sd">            num_causal (int): Maximal number of causal variants to be selected in the final model.</span>
+<span class="sd">            outlier_switch (bool): Whether to consider outlier detection in the analysis.</span>
+<span class="sd">            input_conditional_S_list (list[int] | None): The conditional set. Defaults to None.</span>
+<span class="sd">            tau (float): Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.</span>
+<span class="sd">            epsilon (float): Threshold for convergence in CARMA iterations.</span>
+<span class="sd">            inner_all_iter (int): The number of inner iterations in each CARMA iteration.</span>
+<span class="sd">            outlier_BF_index (float | None): Bayes Factor threshold for identifying outliers. Defaults to None.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            dict[str, Any]: A dictionary containing the following results:</span>
+<span class="sd">                - B_list: A dataframe containing the marginal likelihoods and the corresponding model space.</span>
+<span class="sd">                - conditional_S_list: A list of outliers.</span>
+
+<span class="sd">        Examples:</span>
+<span class="sd">        &gt;&gt;&gt; z = np.array([0.1, 0.2, 0.3])</span>
+<span class="sd">        &gt;&gt;&gt; ld_matrix = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])</span>
+<span class="sd">        &gt;&gt;&gt; Max_Model_Dim = 10_000</span>
+<span class="sd">        &gt;&gt;&gt; lambda_val = 1</span>
+
+<span class="sd">        &gt;&gt;&gt; num_causal = 10</span>
+<span class="sd">        &gt;&gt;&gt; outlier_switch = True</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">p</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">z</span><span class="p">)</span>
+        <span class="n">marginal_likelihood</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_ind_Normal_fixed_sigma_marginal_external</span>
+        <span class="n">tau_sample</span> <span class="o">=</span> <span class="n">tau</span>
+        <span class="k">if</span> <span class="n">outlier_switch</span><span class="p">:</span>
+            <span class="n">outlier_likelihood</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_outlier_ind_Normal_marginal_external</span>
+            <span class="n">outlier_tau</span> <span class="o">=</span> <span class="n">tau</span>
+
+        <span class="n">B</span> <span class="o">=</span> <span class="n">Max_Model_Dim</span>
+        <span class="n">stored_bf</span> <span class="o">=</span> <span class="mi">0</span>
+        <span class="n">Sigma</span> <span class="o">=</span> <span class="n">ld_matrix</span>
+
+        <span class="n">S</span> <span class="o">=</span> <span class="p">[]</span>
+
+        <span class="n">null_model</span> <span class="o">=</span> <span class="s2">&quot;&quot;</span>
+        <span class="n">null_margin</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_prior_dist</span><span class="p">(</span><span class="n">null_model</span><span class="p">,</span> <span class="n">lambda_val</span><span class="o">=</span><span class="n">lambda_val</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">p</span><span class="p">)</span>
+
+        <span class="n">B_list</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">({</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">:</span> <span class="p">[</span><span class="n">null_margin</span><span class="p">],</span> <span class="s2">&quot;matrix_gamma&quot;</span><span class="p">:</span> <span class="p">[</span><span class="s2">&quot;&quot;</span><span class="p">]})</span>
+
+        <span class="k">if</span> <span class="n">input_conditional_S_list</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+            <span class="n">conditional_S</span> <span class="o">=</span> <span class="p">[]</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="n">conditional_S</span> <span class="o">=</span> <span class="n">input_conditional_S_list</span>
+            <span class="n">S</span> <span class="o">=</span> <span class="n">conditional_S</span>
+
+        <span class="k">for</span> <span class="n">_i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">inner_all_iter</span><span class="p">):</span>
+            <span class="k">for</span> <span class="n">_j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">10</span><span class="p">):</span>
+                <span class="n">set_gamma</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_set_gamma_func</span><span class="p">(</span>
+                    <span class="n">input_S</span><span class="o">=</span><span class="n">S</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">p</span><span class="p">,</span> <span class="n">condition_index</span><span class="o">=</span><span class="n">conditional_S</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="n">conditional_S</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+                    <span class="n">working_S</span> <span class="o">=</span> <span class="n">S</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">working_S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">sort</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">S</span><span class="p">,</span> <span class="n">conditional_S</span><span class="p">))</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span>
+
+                <span class="n">set_gamma_margin</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span>
+                <span class="n">set_gamma_prior</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span>
+                <span class="n">matrix_gamma</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">,</span> <span class="kc">None</span><span class="p">]</span>
+
+                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">set_gamma</span><span class="p">)):</span>
+                    <span class="k">if</span> <span class="n">set_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                        <span class="n">matrix_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_index_fun</span><span class="p">(</span><span class="n">set_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">])</span>
+                        <span class="n">p_S</span> <span class="o">=</span> <span class="n">set_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                        <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">apply_along_axis</span><span class="p">(</span>
+                            <span class="n">marginal_likelihood</span><span class="p">,</span>
+                            <span class="mi">1</span><span class="p">,</span>
+                            <span class="n">set_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+                            <span class="n">Sigma</span><span class="o">=</span><span class="n">Sigma</span><span class="p">,</span>
+                            <span class="n">z</span><span class="o">=</span><span class="n">z</span><span class="p">,</span>
+                            <span class="n">tau</span><span class="o">=</span><span class="n">tau_sample</span><span class="p">,</span>
+                            <span class="n">p_S</span><span class="o">=</span><span class="n">p_S</span><span class="p">,</span>
+                        <span class="p">)</span>
+                        <span class="n">set_gamma_prior</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
+                            <span class="p">[</span>
+                                <span class="n">CARMA</span><span class="o">.</span><span class="n">_prior_dist</span><span class="p">(</span><span class="n">model</span><span class="p">,</span> <span class="n">lambda_val</span><span class="o">=</span><span class="n">lambda_val</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">p</span><span class="p">)</span>
+                                <span class="k">for</span> <span class="n">model</span> <span class="ow">in</span> <span class="n">matrix_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+                            <span class="p">]</span>
+                        <span class="p">)</span>
+                        <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">set_gamma_prior</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">+</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">null_margin</span><span class="p">)</span>
+                        <span class="n">set_gamma_prior</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+                        <span class="n">matrix_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">null_model</span><span class="p">)</span>
+
+                <span class="n">columns</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">,</span> <span class="s2">&quot;matrix_gamma&quot;</span><span class="p">]</span>
+                <span class="n">add_B</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span><span class="n">columns</span><span class="o">=</span><span class="n">columns</span><span class="p">)</span>
+
+                <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">set_gamma</span><span class="p">)):</span>
+                    <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span> <span class="nb">list</span><span class="p">):</span>
+                        <span class="n">new_row</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                            <span class="p">{</span>
+                                <span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">:</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span>
+                                <span class="s2">&quot;matrix_gamma&quot;</span><span class="p">:</span> <span class="n">matrix_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">(),</span>
+                            <span class="p">}</span>
+                        <span class="p">)</span>
+                        <span class="n">add_B</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">add_B</span><span class="p">,</span> <span class="n">new_row</span><span class="p">],</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="n">new_row</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                            <span class="p">{</span>
+                                <span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">:</span> <span class="p">[</span><span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()],</span>
+                                <span class="s2">&quot;matrix_gamma&quot;</span><span class="p">:</span> <span class="p">[</span><span class="n">matrix_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()],</span>
+                            <span class="p">}</span>
+                        <span class="p">)</span>
+                        <span class="n">add_B</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">add_B</span><span class="p">,</span> <span class="n">new_row</span><span class="p">],</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+                <span class="c1"># Add visited models into the storage space of models</span>
+                <span class="n">B_list</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">concat</span><span class="p">([</span><span class="n">B_list</span><span class="p">,</span> <span class="n">add_B</span><span class="p">],</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+                <span class="n">B_list</span> <span class="o">=</span> <span class="n">B_list</span><span class="o">.</span><span class="n">drop_duplicates</span><span class="p">(</span>
+                    <span class="n">subset</span><span class="o">=</span><span class="s2">&quot;matrix_gamma&quot;</span><span class="p">,</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span>
+                <span class="p">)</span>
+                <span class="n">B_list</span> <span class="o">=</span> <span class="n">B_list</span><span class="o">.</span><span class="n">sort_values</span><span class="p">(</span>
+                    <span class="n">by</span><span class="o">=</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">,</span> <span class="n">ignore_index</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">ascending</span><span class="o">=</span><span class="kc">False</span>
+                <span class="p">)</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">working_S</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
+                    <span class="c1"># Create a DataFrame set.star</span>
+                    <span class="n">set_star</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                        <span class="p">{</span>
+                            <span class="s2">&quot;set_index&quot;</span><span class="p">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span>
+                            <span class="s2">&quot;gamma_set_index&quot;</span><span class="p">:</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">],</span>
+                            <span class="s2">&quot;margin&quot;</span><span class="p">:</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">],</span>
+                        <span class="p">}</span>
+                    <span class="p">)</span>
+
+                    <span class="c1"># Assuming set.gamma.margin and current.log.margin are defined</span>
+                    <span class="n">aa</span> <span class="o">=</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="n">aa</span> <span class="o">=</span> <span class="n">aa</span> <span class="o">-</span> <span class="n">aa</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">aa</span><span class="p">)]</span>
+
+                    <span class="n">min_half_len</span> <span class="o">=</span> <span class="nb">min</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">aa</span><span class="p">),</span> <span class="n">floor</span><span class="p">(</span><span class="n">p</span> <span class="o">/</span> <span class="mi">2</span><span class="p">))</span>
+                    <span class="n">decr_ind</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">argsort</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">))[::</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
+                    <span class="n">decr_half_ind</span> <span class="o">=</span> <span class="n">decr_ind</span><span class="p">[:</span><span class="n">min_half_len</span><span class="p">]</span>
+
+                    <span class="n">probs</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">)[</span><span class="n">decr_half_ind</span><span class="p">]</span>
+
+                    <span class="n">chosen_index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span>
+                        <span class="n">decr_half_ind</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">probs</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">probs</span><span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="s2">&quot;gamma_set_index&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">chosen_index</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span>
+                    <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="s2">&quot;margin&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">chosen_index</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span>
+
+                    <span class="n">S</span> <span class="o">=</span> <span class="n">set_gamma</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="n">chosen_index</span><span class="p">[</span><span class="mi">0</span><span class="p">]]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">set_star</span> <span class="o">=</span> <span class="n">pd</span><span class="o">.</span><span class="n">DataFrame</span><span class="p">(</span>
+                        <span class="p">{</span>
+                            <span class="s2">&quot;set_index&quot;</span><span class="p">:</span> <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span>
+                            <span class="s2">&quot;gamma_set_index&quot;</span><span class="p">:</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">],</span>
+                            <span class="s2">&quot;margin&quot;</span><span class="p">:</span> <span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">nan</span><span class="p">],</span>
+                        <span class="p">}</span>
+                    <span class="p">)</span>
+                    <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">):</span>
+                        <span class="n">aa</span> <span class="o">=</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+                        <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">aa</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                            <span class="n">aa</span> <span class="o">=</span> <span class="n">aa</span> <span class="o">-</span> <span class="n">aa</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">aa</span><span class="p">)]</span>
+                            <span class="n">chosen_index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span>
+                                <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">])),</span>
+                                <span class="mi">1</span><span class="p">,</span>
+                                <span class="n">p</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">)),</span>
+                            <span class="p">)</span>
+                            <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="s2">&quot;gamma_set_index&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">chosen_index</span>
+                            <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="s2">&quot;margin&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="n">chosen_index</span><span class="p">]</span>
+                        <span class="k">else</span><span class="p">:</span>
+                            <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="s2">&quot;gamma_set_index&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="mi">0</span>
+                            <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="s2">&quot;margin&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+
+                    <span class="k">if</span> <span class="n">outlier_switch</span><span class="p">:</span>
+                        <span class="k">for</span> <span class="n">i</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">set_gamma</span><span class="p">)):</span>
+                            <span class="n">test_log_BF</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">100</span>
+                            <span class="k">while</span> <span class="kc">True</span><span class="p">:</span>
+                                <span class="n">aa</span> <span class="o">=</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span>
+                                <span class="n">aa</span> <span class="o">=</span> <span class="n">aa</span> <span class="o">-</span> <span class="n">aa</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">argmax</span><span class="p">(</span><span class="n">aa</span><span class="p">)]</span>
+                                <span class="n">chosen_index</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span>
+                                    <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">])),</span>
+                                    <span class="mi">1</span><span class="p">,</span>
+                                    <span class="n">p</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">)),</span>
+                                <span class="p">)</span>
+                                <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="s2">&quot;gamma_set_index&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">chosen_index</span>
+                                <span class="n">set_star</span><span class="o">.</span><span class="n">at</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="s2">&quot;margin&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">][</span>
+                                    <span class="n">chosen_index</span>
+                                <span class="p">]</span>
+
+                                <span class="n">test_S</span> <span class="o">=</span> <span class="n">set_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="nb">int</span><span class="p">(</span><span class="n">chosen_index</span><span class="p">),</span> <span class="p">:]</span>
+
+                                <span class="n">modi_Sigma</span> <span class="o">=</span> <span class="n">Sigma</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+                                <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">test_S</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">1</span><span class="p">:</span>
+                                    <span class="n">modi_ld_S</span> <span class="o">=</span> <span class="n">modi_Sigma</span><span class="p">[</span><span class="n">test_S</span><span class="p">][:,</span> <span class="n">test_S</span><span class="p">]</span>
+
+                                    <span class="n">result</span> <span class="o">=</span> <span class="n">minimize_scalar</span><span class="p">(</span>
+                                        <span class="n">CARMA</span><span class="o">.</span><span class="n">_ridge_fun</span><span class="p">,</span>
+                                        <span class="n">bounds</span><span class="o">=</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span>
+                                        <span class="n">args</span><span class="o">=</span><span class="p">(</span>
+                                            <span class="n">Sigma</span><span class="p">,</span>
+                                            <span class="n">modi_ld_S</span><span class="p">,</span>
+                                            <span class="n">test_S</span><span class="p">,</span>
+                                            <span class="n">z</span><span class="p">,</span>
+                                            <span class="n">outlier_tau</span><span class="p">,</span>
+                                            <span class="n">outlier_likelihood</span><span class="p">,</span>
+                                        <span class="p">),</span>
+                                        <span class="n">method</span><span class="o">=</span><span class="s2">&quot;bounded&quot;</span><span class="p">,</span>
+                                    <span class="p">)</span>
+                                    <span class="n">modi_ld_S</span> <span class="o">=</span> <span class="n">result</span><span class="o">.</span><span class="n">x</span> <span class="o">*</span> <span class="n">modi_ld_S</span> <span class="o">+</span> <span class="p">(</span>
+                                        <span class="mi">1</span> <span class="o">-</span> <span class="n">result</span><span class="o">.</span><span class="n">x</span>
+                                    <span class="p">)</span> <span class="o">*</span> <span class="n">np</span><span class="o">.</span><span class="n">eye</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">modi_ld_S</span><span class="p">))</span>
+
+                                    <span class="n">modi_Sigma</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">ix_</span><span class="p">(</span><span class="n">test_S</span><span class="p">,</span> <span class="n">test_S</span><span class="p">)]</span> <span class="o">=</span> <span class="n">modi_ld_S</span>
+
+                                    <span class="n">test_log_BF</span> <span class="o">=</span> <span class="n">outlier_likelihood</span><span class="p">(</span>
+                                        <span class="n">test_S</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Sigma</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">outlier_tau</span><span class="p">,</span> <span class="nb">len</span><span class="p">(</span><span class="n">test_S</span><span class="p">)</span>
+                                    <span class="p">)</span> <span class="o">-</span> <span class="n">outlier_likelihood</span><span class="p">(</span>
+                                        <span class="n">test_S</span> <span class="o">+</span> <span class="mi">1</span><span class="p">,</span>
+                                        <span class="n">modi_Sigma</span><span class="p">,</span>
+                                        <span class="n">z</span><span class="p">,</span>
+                                        <span class="n">outlier_tau</span><span class="p">,</span>
+                                        <span class="nb">len</span><span class="p">(</span><span class="n">test_S</span><span class="p">),</span>
+                                    <span class="p">)</span>
+                                    <span class="n">test_log_BF</span> <span class="o">=</span> <span class="o">-</span><span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">test_log_BF</span><span class="p">)</span>
+
+                                <span class="k">if</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">test_log_BF</span><span class="p">)</span> <span class="o">&lt;</span> <span class="n">outlier_BF_index</span><span class="p">:</span>
+                                    <span class="n">set_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span>
+                                        <span class="n">set_gamma</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                                        <span class="nb">int</span><span class="p">(</span><span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;gamma_set_index&quot;</span><span class="p">][</span><span class="n">i</span><span class="p">]),</span>
+                                        <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
+                                    <span class="p">)</span>
+                                    <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">delete</span><span class="p">(</span>
+                                        <span class="n">set_gamma_margin</span><span class="p">[</span><span class="n">i</span><span class="p">],</span>
+                                        <span class="nb">int</span><span class="p">(</span><span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;gamma_set_index&quot;</span><span class="p">][</span><span class="n">i</span><span class="p">]),</span>
+                                        <span class="n">axis</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span>
+                                    <span class="p">)</span>
+                                    <span class="n">conditional_S</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">concatenate</span><span class="p">(</span>
+                                        <span class="p">[</span><span class="n">conditional_S</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">setdiff1d</span><span class="p">(</span><span class="n">test_S</span><span class="p">,</span> <span class="n">working_S</span><span class="p">)]</span>
+                                    <span class="p">)</span>
+                                    <span class="n">conditional_S</span> <span class="o">=</span> <span class="p">(</span>
+                                        <span class="n">np</span><span class="o">.</span><span class="n">unique</span><span class="p">(</span><span class="n">conditional_S</span><span class="p">)</span><span class="o">.</span><span class="n">astype</span><span class="p">(</span><span class="nb">int</span><span class="p">)</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+                                    <span class="p">)</span>
+                                <span class="k">else</span><span class="p">:</span>
+                                    <span class="k">break</span>
+
+                    <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">working_S</span><span class="p">)</span> <span class="o">==</span> <span class="n">num_causal</span><span class="p">:</span>
+                        <span class="n">set_star</span> <span class="o">=</span> <span class="n">set_star</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
+                        <span class="n">aa</span> <span class="o">=</span> <span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;margin&quot;</span><span class="p">]</span> <span class="o">-</span> <span class="nb">max</span><span class="p">(</span><span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;margin&quot;</span><span class="p">])</span>
+                        <span class="n">sec_sample</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span>
+                            <span class="p">[</span><span class="mi">0</span><span class="p">,</span> <span class="mi">2</span><span class="p">],</span> <span class="mi">1</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">))</span>
+                        <span class="p">)</span>
+                        <span class="n">ind_sec</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span>
+                            <span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;gamma_set_index&quot;</span><span class="p">][</span>
+                                <span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;set_index&quot;</span><span class="p">]</span> <span class="o">==</span> <span class="nb">int</span><span class="p">(</span><span class="n">sec_sample</span><span class="p">)</span>
+                            <span class="p">]</span>
+                        <span class="p">)</span>
+                        <span class="n">S</span> <span class="o">=</span> <span class="n">set_gamma</span><span class="p">[</span><span class="n">sec_sample</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span><span class="n">ind_sec</span><span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+                    <span class="k">else</span><span class="p">:</span>
+                        <span class="n">aa</span> <span class="o">=</span> <span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;margin&quot;</span><span class="p">]</span> <span class="o">-</span> <span class="nb">max</span><span class="p">(</span><span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;margin&quot;</span><span class="p">])</span>
+                        <span class="n">sec_sample</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">random</span><span class="o">.</span><span class="n">choice</span><span class="p">(</span>
+                            <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="mi">1</span><span class="p">,</span> <span class="n">p</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">)</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">aa</span><span class="p">))</span>
+                        <span class="p">)</span>
+                        <span class="n">S</span> <span class="o">=</span> <span class="n">set_gamma</span><span class="p">[</span><span class="n">sec_sample</span><span class="p">[</span><span class="mi">0</span><span class="p">]][</span>
+                            <span class="nb">int</span><span class="p">(</span><span class="n">set_star</span><span class="p">[</span><span class="s2">&quot;gamma_set_index&quot;</span><span class="p">][</span><span class="n">sec_sample</span><span class="p">[</span><span class="mi">0</span><span class="p">]])</span>
+                        <span class="p">]</span><span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+
+                <span class="k">for</span> <span class="n">item</span> <span class="ow">in</span> <span class="n">conditional_S</span><span class="p">:</span>
+                    <span class="k">if</span> <span class="n">item</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">S</span><span class="p">:</span>
+                        <span class="n">S</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">item</span><span class="p">)</span>
+            <span class="c1"># END h_ind loop</span>
+            <span class="c1">#</span>
+            <span class="k">if</span> <span class="n">conditional_S</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">all_c_index</span> <span class="o">=</span> <span class="p">[]</span>
+                <span class="n">index_array</span> <span class="o">=</span> <span class="p">[</span><span class="n">s</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;,&quot;</span><span class="p">)</span> <span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="n">B_list</span><span class="p">[</span><span class="s2">&quot;matrix_gamma&quot;</span><span class="p">]]</span>
+                <span class="k">for</span> <span class="n">tt</span> <span class="ow">in</span> <span class="n">conditional_S</span><span class="p">:</span>
+                    <span class="n">tt_str</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">tt</span><span class="p">)</span>
+                    <span class="n">ind</span> <span class="o">=</span> <span class="p">[</span>
+                        <span class="n">i</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">sublist</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">index_array</span><span class="p">)</span> <span class="k">if</span> <span class="n">tt_str</span> <span class="ow">in</span> <span class="n">sublist</span>
+                    <span class="p">]</span>
+                    <span class="n">all_c_index</span><span class="o">.</span><span class="n">extend</span><span class="p">(</span><span class="n">ind</span><span class="p">)</span>
+
+                <span class="n">all_c_index</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="nb">set</span><span class="p">(</span><span class="n">all_c_index</span><span class="p">))</span>
+
+                <span class="k">if</span> <span class="nb">len</span><span class="p">(</span><span class="n">all_c_index</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">:</span>
+                    <span class="n">temp_B_list</span> <span class="o">=</span> <span class="n">B_list</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+                    <span class="n">temp_B_list</span> <span class="o">=</span> <span class="n">B_list</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="n">all_c_index</span><span class="p">)</span>
+                <span class="k">else</span><span class="p">:</span>
+                    <span class="n">temp_B_list</span> <span class="o">=</span> <span class="n">B_list</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">temp_B_list</span> <span class="o">=</span> <span class="n">B_list</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span>
+
+            <span class="n">result_B_list</span> <span class="o">=</span> <span class="n">temp_B_list</span><span class="p">[:</span> <span class="nb">min</span><span class="p">(</span><span class="nb">int</span><span class="p">(</span><span class="n">B</span><span class="p">),</span> <span class="nb">len</span><span class="p">(</span><span class="n">temp_B_list</span><span class="p">))]</span>
+
+            <span class="n">rb1</span> <span class="o">=</span> <span class="n">result_B_list</span><span class="p">[</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">]</span>
+
+            <span class="n">difference</span> <span class="o">=</span> <span class="nb">abs</span><span class="p">(</span><span class="n">rb1</span><span class="p">[:</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">rb1</span><span class="p">)</span> <span class="o">//</span> <span class="mi">4</span><span class="p">)]</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span> <span class="o">-</span> <span class="n">stored_bf</span><span class="p">)</span>
+
+            <span class="k">if</span> <span class="n">difference</span> <span class="o">&lt;</span> <span class="n">epsilon</span><span class="p">:</span>
+                <span class="k">break</span>
+            <span class="k">else</span><span class="p">:</span>
+                <span class="n">stored_bf</span> <span class="o">=</span> <span class="n">rb1</span><span class="p">[:</span> <span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">rb1</span><span class="p">)</span> <span class="o">//</span> <span class="mi">4</span><span class="p">)]</span><span class="o">.</span><span class="n">mean</span><span class="p">()</span>
+
+        <span class="n">out</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;B_list&quot;</span><span class="p">:</span> <span class="n">result_B_list</span><span class="p">,</span> <span class="s2">&quot;conditional_S_list&quot;</span><span class="p">:</span> <span class="n">conditional_S</span><span class="p">}</span>
+
+        <span class="k">return</span> <span class="n">out</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.method.carma.CARMA.CARMA_spike_slab_noEM" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">CARMA_spike_slab_noEM</span><span class="p">(</span><span class="n">z</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">ld</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="n">lambda_val</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">Max_Model_Dim</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">200000</span><span class="p">,</span> <span class="n">all_iter</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="n">all_inner_iter</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">epsilon_threshold</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-05</span><span class="p">,</span> <span class="n">num_causal</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span> <span class="n">tau</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.04</span><span class="p">,</span> <span class="n">outlier_switch</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span> <span class="n">outlier_BF_index</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="mf">3.2</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span></code>
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
+  </span>
+
+<a href="#gentropy.method.carma.CARMA.CARMA_spike_slab_noEM" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Perform CARMA analysis using a Spike-and-Slab prior without Expectation-Maximization (EM).</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>z</code></td>
+          <td>
+                <code><span title="numpy.ndarray">ndarray</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Numeric vector representing z-scores.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>ld</code></td>
+          <td>
+                <code><span title="numpy.ndarray">ndarray</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Numeric matrix representing the linkage disequilibrium (LD) matrix.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>lambda_val</code></td>
+          <td>
+                <code>float</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Regularization parameter controlling the strength of the L1 penalty.</p>
+            </div>
+          </td>
+          <td>
+                <code>1</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>Max_Model_Dim</code></td>
+          <td>
+                <code>int</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Maximum allowed dimension for the causal models.</p>
+            </div>
+          </td>
+          <td>
+                <code>200000</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>all_iter</code></td>
+          <td>
+                <code>int</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>The total number of iterations to run the CARMA analysis.</p>
+            </div>
+          </td>
+          <td>
+                <code>1</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>all_inner_iter</code></td>
+          <td>
+                <code>int</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>The number of inner iterations in each CARMA iteration.</p>
+            </div>
+          </td>
+          <td>
+                <code>10</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>epsilon_threshold</code></td>
+          <td>
+                <code>float</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Threshold for convergence in CARMA iterations.</p>
+            </div>
+          </td>
+          <td>
+                <code>1e-05</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>num_causal</code></td>
+          <td>
+                <code>int</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Maximal number of causal variants to be selected in the final model.</p>
+            </div>
+          </td>
+          <td>
+                <code>10</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>tau</code></td>
+          <td>
+                <code>float</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.</p>
+            </div>
+          </td>
+          <td>
+                <code>0.04</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>outlier_switch</code></td>
+          <td>
+                <code>bool</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Whether to consider outlier detection in the analysis.</p>
+            </div>
+          </td>
+          <td>
+                <code>True</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>outlier_BF_index</code></td>
+          <td>
+                <code>float</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Bayes Factor threshold for identifying outliers.</p>
+            </div>
+          </td>
+          <td>
+                <code>1 / 3.2</code>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td>
+                <code>dict[str, <span title="typing.Any">Any</span>]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>dict[str, Any]: A dictionary containing the following results:
+- PIPs: A numeric vector of posterior inclusion probabilities (PIPs) for all SNPs.
+- B_list: A dataframe containing the marginal likelihoods and the corresponding model space.
+- Outliers: A list of outlier SNPs.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/method/carma.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 17</span>
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+<span class="normal">109</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+<span class="k">def</span> <span class="nf">CARMA_spike_slab_noEM</span><span class="p">(</span>
+    <span class="n">z</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+    <span class="n">ld</span><span class="p">:</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span>
+    <span class="n">lambda_val</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+    <span class="n">Max_Model_Dim</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">200_000</span><span class="p">,</span>
+    <span class="n">all_iter</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span>
+    <span class="n">all_inner_iter</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+    <span class="n">epsilon_threshold</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-5</span><span class="p">,</span>
+    <span class="n">num_causal</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">10</span><span class="p">,</span>
+    <span class="n">tau</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.04</span><span class="p">,</span>
+    <span class="n">outlier_switch</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">True</span><span class="p">,</span>
+    <span class="n">outlier_BF_index</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mi">1</span> <span class="o">/</span> <span class="mf">3.2</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Perform CARMA analysis using a Spike-and-Slab prior without Expectation-Maximization (EM).</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        z (np.ndarray): Numeric vector representing z-scores.</span>
+<span class="sd">        ld (np.ndarray): Numeric matrix representing the linkage disequilibrium (LD) matrix.</span>
+<span class="sd">        lambda_val (float): Regularization parameter controlling the strength of the L1 penalty.</span>
+<span class="sd">        Max_Model_Dim (int): Maximum allowed dimension for the causal models.</span>
+<span class="sd">        all_iter (int): The total number of iterations to run the CARMA analysis.</span>
+<span class="sd">        all_inner_iter (int): The number of inner iterations in each CARMA iteration.</span>
+<span class="sd">        epsilon_threshold (float): Threshold for convergence in CARMA iterations.</span>
+<span class="sd">        num_causal (int): Maximal number of causal variants to be selected in the final model.</span>
+<span class="sd">        tau (float): Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.</span>
+<span class="sd">        outlier_switch (bool): Whether to consider outlier detection in the analysis.</span>
+<span class="sd">        outlier_BF_index (float): Bayes Factor threshold for identifying outliers.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        dict[str, Any]: A dictionary containing the following results:</span>
+<span class="sd">            - PIPs: A numeric vector of posterior inclusion probabilities (PIPs) for all SNPs.</span>
+<span class="sd">            - B_list: A dataframe containing the marginal likelihoods and the corresponding model space.</span>
+<span class="sd">            - Outliers: A list of outlier SNPs.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">p_snp</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">z</span><span class="p">)</span>
+    <span class="n">epsilon_list</span> <span class="o">=</span> <span class="n">epsilon_threshold</span> <span class="o">*</span> <span class="n">p_snp</span>
+    <span class="n">all_epsilon_threshold</span> <span class="o">=</span> <span class="n">epsilon_threshold</span> <span class="o">*</span> <span class="n">p_snp</span>
+
+    <span class="c1"># Zero step</span>
+    <span class="n">all_C_list</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_MCS_modified</span><span class="p">(</span>
+        <span class="n">z</span><span class="o">=</span><span class="n">z</span><span class="p">,</span>
+        <span class="n">ld_matrix</span><span class="o">=</span><span class="n">ld</span><span class="p">,</span>
+        <span class="n">epsilon</span><span class="o">=</span><span class="n">epsilon_list</span><span class="p">,</span>
+        <span class="n">Max_Model_Dim</span><span class="o">=</span><span class="n">Max_Model_Dim</span><span class="p">,</span>
+        <span class="n">lambda_val</span><span class="o">=</span><span class="n">lambda_val</span><span class="p">,</span>
+        <span class="n">outlier_switch</span><span class="o">=</span><span class="n">outlier_switch</span><span class="p">,</span>
+        <span class="n">tau</span><span class="o">=</span><span class="n">tau</span><span class="p">,</span>
+        <span class="n">num_causal</span><span class="o">=</span><span class="n">num_causal</span><span class="p">,</span>
+        <span class="n">inner_all_iter</span><span class="o">=</span><span class="n">all_inner_iter</span><span class="p">,</span>
+        <span class="n">outlier_BF_index</span><span class="o">=</span><span class="n">outlier_BF_index</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Main steps</span>
+    <span class="k">for</span> <span class="n">_</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">all_iter</span><span class="p">):</span>
+        <span class="n">ac1</span> <span class="o">=</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">]</span>
+        <span class="n">previous_result</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">ac1</span><span class="p">[</span><span class="mi">0</span> <span class="p">:</span> <span class="nb">round</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ac1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">4</span><span class="p">)])</span>
+
+        <span class="n">all_C_list</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_MCS_modified</span><span class="p">(</span>
+            <span class="n">z</span><span class="o">=</span><span class="n">z</span><span class="p">,</span>
+            <span class="n">ld_matrix</span><span class="o">=</span><span class="n">ld</span><span class="p">,</span>
+            <span class="n">input_conditional_S_list</span><span class="o">=</span><span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;conditional_S_list&quot;</span><span class="p">],</span>
+            <span class="n">Max_Model_Dim</span><span class="o">=</span><span class="n">Max_Model_Dim</span><span class="p">,</span>
+            <span class="n">num_causal</span><span class="o">=</span><span class="n">num_causal</span><span class="p">,</span>
+            <span class="n">epsilon</span><span class="o">=</span><span class="n">epsilon_list</span><span class="p">,</span>
+            <span class="n">outlier_switch</span><span class="o">=</span><span class="n">outlier_switch</span><span class="p">,</span>
+            <span class="n">tau</span><span class="o">=</span><span class="n">tau</span><span class="p">,</span>
+            <span class="n">lambda_val</span><span class="o">=</span><span class="n">lambda_val</span><span class="p">,</span>
+            <span class="n">inner_all_iter</span><span class="o">=</span><span class="n">all_inner_iter</span><span class="p">,</span>
+            <span class="n">outlier_BF_index</span><span class="o">=</span><span class="n">outlier_BF_index</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">ac1</span> <span class="o">=</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">]</span>
+        <span class="n">difference</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span><span class="n">previous_result</span> <span class="o">-</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">ac1</span><span class="p">[</span><span class="mi">0</span> <span class="p">:</span> <span class="nb">round</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">ac1</span><span class="p">)</span> <span class="o">/</span> <span class="mi">4</span><span class="p">)]))</span>
+        <span class="k">if</span> <span class="n">difference</span> <span class="o">&lt;</span> <span class="n">all_epsilon_threshold</span><span class="p">:</span>
+            <span class="k">break</span>
+
+    <span class="c1"># Calculate PIPs and Credible Set</span>
+    <span class="n">pip</span> <span class="o">=</span> <span class="n">CARMA</span><span class="o">.</span><span class="n">_PIP_func</span><span class="p">(</span>
+        <span class="n">likeli</span><span class="o">=</span><span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;set_gamma_margin&quot;</span><span class="p">],</span>
+        <span class="n">model_space</span><span class="o">=</span><span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">][</span><span class="s2">&quot;matrix_gamma&quot;</span><span class="p">],</span>
+        <span class="n">p</span><span class="o">=</span><span class="n">p_snp</span><span class="p">,</span>
+        <span class="n">num_causal</span><span class="o">=</span><span class="n">num_causal</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="n">results_list</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="s2">&quot;PIPs&quot;</span><span class="p">:</span> <span class="n">pip</span><span class="p">,</span>
+        <span class="s2">&quot;B_list&quot;</span><span class="p">:</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;B_list&quot;</span><span class="p">],</span>
+        <span class="s2">&quot;Outliers&quot;</span><span class="p">:</span> <span class="n">all_C_list</span><span class="p">[</span><span class="s2">&quot;conditional_S_list&quot;</span><span class="p">],</span>
+    <span class="p">}</span>
+
+
+    <span class="k">return</span> <span class="n">results_list</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+
+  </div>
+
+  </div>
+
+
+</div>
+<hr />
+<div class="md-source-file">
+  <small>
+    <ul
+      class="metadata page-metadata"
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+        </span>
+        <span class="label"> Contributors </span>
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+        <ul class="contributors" data-bi-name="contributors"><li>
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+</div>
+
+
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+                
+              </article>
+            </div>
+          
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+        </div>
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+          <button type="button" class="md-top md-icon" data-md-component="top" hidden>
+  
+  <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8v12Z"/></svg>
+  Back to top
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diff --git a/python_api/method/window_based_clumping/index.html b/python_api/methods/clumping/index.html
similarity index 82%
rename from python_api/method/window_based_clumping/index.html
rename to python_api/methods/clumping/index.html
index 785030d76..d322256bb 100644
--- a/python_api/method/window_based_clumping/index.html
+++ b/python_api/methods/clumping/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../pics/">
+        <link rel="prev" href="../carma/">
       
       
-        <link rel="next" href="../l2g/_l2g/">
+        <link rel="next" href="../coloc/">
       
       
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Window-based clumping - Open Targets Genetics</title>
+        <title>Clumping - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.window_based_clumping.WindowBasedClumping" class="md-skip">
+        <a href="#clumping" class="md-skip">
           Skip to content
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@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Window-based clumping
+              Clumping
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
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+  
+
+      
+        
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+  
+  
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@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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@@ -358,11 +392,11 @@
   
   
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+      <a href="../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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@@ -414,6 +448,123 @@
         
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+          <ul class="md-nav__list" data-md-scrollfix>
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
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+    </li>
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+            
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+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
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+  
+
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+            
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+        </nav>
+      
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+  
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+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+  
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+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
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-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
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-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
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-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
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-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
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-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
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-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,32 +1804,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_method/" class="md-nav__link ">
+            <a href="../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clumping/" class="md-nav__link">
+      <a href="../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1739,18 +1858,28 @@
                 
   
   
+    
   
   
-    <li class="md-nav__item">
-      <a href="../coloc/" class="md-nav__link">
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+        
+      
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
       </a>
+      
     </li>
   
 
@@ -1763,11 +1892,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ecaviar/" class="md-nav__link">
+      <a href="../coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1913,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_annotator/" class="md-nav__link">
+      <a href="../ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1934,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1823,87 +1952,18 @@
                 
   
   
-    
-  
-  
-  
-    <li class="md-nav__item md-nav__item--active">
-      
-      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
-      
-      
-      
-        <label class="md-nav__link md-nav__link--active" for="__toc">
-          
   
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
   
-
-          <span class="md-nav__icon md-icon"></span>
-        </label>
-      
-      <a href="./" class="md-nav__link md-nav__link--active">
+    <li class="md-nav__item">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
       </a>
-      
-        
-
-<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
-  
-  
-  
-  
-    <label class="md-nav__title" for="__toc">
-      <span class="md-nav__icon md-icon"></span>
-      Table of contents
-    </label>
-    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
-      
-        <li class="md-nav__item">
-  <a href="#otg.method.window_based_clumping.WindowBasedClumping" class="md-nav__link">
-    <span class="md-ellipsis">
-      WindowBasedClumping
-    </span>
-  </a>
-  
-    <nav class="md-nav" aria-label="WindowBasedClumping">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#otg.method.window_based_clumping.WindowBasedClumping.clump" class="md-nav__link">
-    <span class="md-ellipsis">
-      clump()
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" class="md-nav__link">
-    <span class="md-ellipsis">
-      clump_with_locus()
-    </span>
-  </a>
-  
-</li>
-        
-      </ul>
-    </nav>
-  
-</li>
-      
-    </ul>
-  
-</nav>
-      
     </li>
   
 
@@ -1925,7 +1985,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
@@ -1941,14 +2001,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2070,32 +2130,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2106,11 +2166,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2127,11 +2187,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2148,11 +2208,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2169,11 +2229,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2190,11 +2250,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2211,11 +2271,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2232,11 +2292,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2253,11 +2313,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2274,11 +2334,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2295,11 +2355,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2316,11 +2376,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2337,11 +2397,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2358,11 +2418,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2379,11 +2439,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2425,47 +2548,8 @@
   
   
   
+    
   
-    <label class="md-nav__title" for="__toc">
-      <span class="md-nav__icon md-icon"></span>
-      Table of contents
-    </label>
-    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
-      
-        <li class="md-nav__item">
-  <a href="#otg.method.window_based_clumping.WindowBasedClumping" class="md-nav__link">
-    <span class="md-ellipsis">
-      WindowBasedClumping
-    </span>
-  </a>
-  
-    <nav class="md-nav" aria-label="WindowBasedClumping">
-      <ul class="md-nav__list">
-        
-          <li class="md-nav__item">
-  <a href="#otg.method.window_based_clumping.WindowBasedClumping.clump" class="md-nav__link">
-    <span class="md-ellipsis">
-      clump()
-    </span>
-  </a>
-  
-</li>
-        
-          <li class="md-nav__item">
-  <a href="#otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" class="md-nav__link">
-    <span class="md-ellipsis">
-      clump_with_locus()
-    </span>
-  </a>
-  
-</li>
-        
-      </ul>
-    </nav>
-  
-</li>
-      
-    </ul>
   
 </nav>
                   </div>
@@ -2483,18 +2567,26 @@
   
 
 
-  <h1>Window-based clumping</h1>
+<h1 id="clumping">Clumping<a class="headerlink" href="#clumping" title="Permanent link">&para;</a></h1>
+<p>Clumping is a commonly used post-processing method that allows for the identification of independent association signals from GWAS summary statistics and curated associations. This process is critical because of the complex linkage disequilibrium (LD) structure in human populations, which can result in multiple statistically significant associations within the same genomic region. Clumping methods help reduce redundancy in GWAS results and ensure that each reported association represents an independent signal.</p>
+<p>We have implemented two clumping methods:</p>
+<ol>
+<li><strong>Distance-based clumping:</strong> Uses genomic window to clump the significant SNPs into one hit.</li>
+<li><strong>LD-based clumping:</strong> Uses genomic window and LD to clump the significant SNPs into one hit.</li>
+</ol>
+<p>The algorithmic logic is similar to classic clumping approaches from PLINK (Reference: <a href="https://zzz.bwh.harvard.edu/plink/clump.shtml">PLINK Clump Documentation</a>). See details below:</p>
+<h1 id="distance-based-clumping">Distance-based clumping<a class="headerlink" href="#distance-based-clumping" title="Permanent link">&para;</a></h1>
 
-<div class="doc doc-object doc-class">
 
+<div class="doc doc-object doc-class">
 
 
 
-<h2 id="otg.method.window_based_clumping.WindowBasedClumping" class="doc doc-heading">
-          <code>otg.method.window_based_clumping.WindowBasedClumping</code>
+<h2 id="gentropy.method.window_based_clumping.WindowBasedClumping" class="doc doc-heading">
+          <code>gentropy.method.window_based_clumping.WindowBasedClumping</code>
 
 
-<a href="#otg.method.window_based_clumping.WindowBasedClumping" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.window_based_clumping.WindowBasedClumping" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2503,7 +2595,7 @@ <h2 id="otg.method.window_based_clumping.WindowBasedClumping" class="doc doc-hea
       <p>Get semi-lead snps from summary statistics using a window based function.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/window_based_clumping.py</code></summary>
+              <summary>Source code in <code>src/gentropy/method/window_based_clumping.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 23</span>
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@@ -3149,15 +3241,14 @@ <h2 id="otg.method.window_based_clumping.WindowBasedClumping" class="doc doc-hea
 
 
 
-
-<h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump" class="doc doc-heading">
+<h3 id="gentropy.method.window_based_clumping.WindowBasedClumping.clump" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">clump</span><span class="p">(</span><span class="n">summary_stats</span><span class="p">:</span> <span class="n">SummaryStatistics</span><span class="p">,</span> <span class="n">window_length</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">p_value_significance</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">5e-08</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.window_based_clumping.WindowBasedClumping.clump" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.window_based_clumping.WindowBasedClumping.clump" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3180,7 +3271,7 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump" class="doc d
         <tr>
           <td><code>summary_stats</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="../../dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.summary_statistics.SummaryStatistics" href="../../datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3235,7 +3326,7 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump" class="doc d
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3247,7 +3338,7 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump" class="doc d
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/window_based_clumping.py</code></summary>
+            <summary>Source code in <code>src/gentropy/method/window_based_clumping.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">154</span>
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@@ -3446,15 +3537,14 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump" class="doc d
 
 
 
-
-<h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" class="doc doc-heading">
+<h3 id="gentropy.method.window_based_clumping.WindowBasedClumping.clump_with_locus" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">clump_with_locus</span><span class="p">(</span><span class="n">summary_stats</span><span class="p">:</span> <span class="n">SummaryStatistics</span><span class="p">,</span> <span class="n">window_length</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">p_value_significance</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">5e-08</span><span class="p">,</span> <span class="n">p_value_baseline</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.05</span><span class="p">,</span> <span class="n">locus_window_length</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.window_based_clumping.WindowBasedClumping.clump_with_locus" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3477,7 +3567,7 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" c
         <tr>
           <td><code>summary_stats</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.summary_statistics.SummaryStatistics" href="../../dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.summary_statistics.SummaryStatistics" href="../../datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics">SummaryStatistics</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3560,7 +3650,7 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" c
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3572,7 +3662,7 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" c
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/window_based_clumping.py</code></summary>
+            <summary>Source code in <code>src/gentropy/method/window_based_clumping.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">249</span>
 <span class="normal">250</span>
 <span class="normal">251</span>
@@ -3758,6 +3848,269 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" c
 
   </div>
 
+
+</div><h1 id="ld-based-clumping">LD-based clumping:<a class="headerlink" href="#ld-based-clumping" title="Permanent link">&para;</a></h1>
+
+
+<div class="doc doc-object doc-class">
+
+
+
+<h2 id="gentropy.method.clump.LDclumping" class="doc doc-heading">
+          <code>gentropy.method.clump.LDclumping</code>
+
+
+<a href="#gentropy.method.clump.LDclumping" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
+
+  
+      <p>LD clumping reports the most significant genetic associations in a region in terms of a smaller number of “clumps” of genetically linked SNPs.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/method/clump.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">17</span>
+<span class="normal">18</span>
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+<span class="normal">74</span>
+<span class="normal">75</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">LDclumping</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;LD clumping reports the most significant genetic associations in a region in terms of a smaller number of “clumps” of genetically linked SNPs.&quot;&quot;&quot;</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_is_lead_linked</span><span class="p">(</span>
+        <span class="n">study_id</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
+        <span class="n">variant_id</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
+        <span class="n">p_value_exponent</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
+        <span class="n">p_value_mantissa</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
+        <span class="n">ld_set</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Column</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            study_id (Column): studyId</span>
+<span class="sd">            variant_id (Column): Lead variant id</span>
+<span class="sd">            p_value_exponent (Column): p-value exponent</span>
+<span class="sd">            p_value_mantissa (Column): p-value mantissa</span>
+<span class="sd">            ld_set (Column): Array of variants in LD with the lead variant</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            Column: Boolean in which True indicates that the lead is linked to another tag in the same dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">leads_in_study</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">collect_set</span><span class="p">(</span><span class="n">variant_id</span><span class="p">)</span><span class="o">.</span><span class="n">over</span><span class="p">(</span><span class="n">Window</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="n">study_id</span><span class="p">))</span>
+        <span class="n">tags_in_studylocus</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">array_union</span><span class="p">(</span>
+            <span class="c1"># Get all tag variants from the credible set per studyLocusId</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span><span class="n">ld_set</span><span class="p">,</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">tagVariantId</span><span class="p">),</span>
+            <span class="c1"># And append the lead variant so that the intersection is the same for all studyLocusIds in a study</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">variant_id</span><span class="p">),</span>
+        <span class="p">)</span>
+        <span class="n">intersect_lead_tags</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="n">array_sort</span><span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">array_intersect</span><span class="p">(</span><span class="n">leads_in_study</span><span class="p">,</span> <span class="n">tags_in_studylocus</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="k">return</span> <span class="p">(</span>
+            <span class="c1"># If the lead is in the credible set, we rank the peaks by p-value</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">when</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">intersect_lead_tags</span><span class="p">)</span> <span class="o">&gt;</span> <span class="mi">0</span><span class="p">,</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">row_number</span><span class="p">()</span><span class="o">.</span><span class="n">over</span><span class="p">(</span>
+                    <span class="n">Window</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="n">study_id</span><span class="p">,</span> <span class="n">intersect_lead_tags</span><span class="p">)</span><span class="o">.</span><span class="n">orderBy</span><span class="p">(</span>
+                        <span class="n">p_value_exponent</span><span class="p">,</span> <span class="n">p_value_mantissa</span>
+                    <span class="p">)</span>
+                <span class="p">)</span>
+                <span class="o">&gt;</span> <span class="mi">1</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="c1"># If the intersection is empty (lead is not in the credible set or cred set is empty), the association is not linked</span>
+            <span class="o">.</span><span class="n">otherwise</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="kc">False</span><span class="p">))</span>
+        <span class="p">)</span>
+
+    <span class="nd">@classmethod</span>
+    <span class="k">def</span> <span class="nf">clump</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">LDclumping</span><span class="p">],</span> <span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Perform clumping on studyLocus dataset.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            associations (StudyLocus): StudyLocus dataset</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            StudyLocus: including flag and removing locus information for LD clumped loci.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">associations</span><span class="o">.</span><span class="n">clump</span><span class="p">()</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.method.clump.LDclumping.clump" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">clump</span><span class="p">(</span><span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
+  </span>
+
+<a href="#gentropy.method.clump.LDclumping.clump" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Perform clumping on studyLocus dataset.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>associations</code></td>
+          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>StudyLocus dataset</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>StudyLocus</code></td>          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>including flag and removing locus information for LD clumped loci.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/method/clump.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">65</span>
+<span class="normal">66</span>
+<span class="normal">67</span>
+<span class="normal">68</span>
+<span class="normal">69</span>
+<span class="normal">70</span>
+<span class="normal">71</span>
+<span class="normal">72</span>
+<span class="normal">73</span>
+<span class="normal">74</span>
+<span class="normal">75</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="k">def</span> <span class="nf">clump</span><span class="p">(</span><span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">LDclumping</span><span class="p">],</span> <span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Perform clumping on studyLocus dataset.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        associations (StudyLocus): StudyLocus dataset</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        StudyLocus: including flag and removing locus information for LD clumped loci.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">associations</span><span class="o">.</span><span class="n">clump</span><span class="p">()</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+
+  </div>
+
+  </div>
+
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3774,14 +4127,14 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" c
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-07-08T15:19:37+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-07-08</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-07-10T14:20:31+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-07-10</span> </span>
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         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3848,7 +4201,7 @@ <h3 id="otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus" c
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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     </a>
   
diff --git a/python_api/method/coloc/index.html b/python_api/methods/coloc/index.html
similarity index 81%
rename from python_api/method/coloc/index.html
rename to python_api/methods/coloc/index.html
index 302cb3f9b..98dd87efa 100644
--- a/python_api/method/coloc/index.html
+++ b/python_api/methods/coloc/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Coloc - Open Targets Genetics</title>
+        <title>Coloc - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.colocalisation.Coloc" class="md-skip">
+        <a href="#gentropy.method.colocalisation.Coloc" class="md-skip">
           Skip to content
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@@ -94,7 +94,7 @@
 
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-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
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@@ -107,7 +107,7 @@
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-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
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-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
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@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,10 +1778,20 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
   
+    
+  
   
   
     
@@ -1596,37 +1799,37 @@
     
     
     
-    <li class="md-nav__item md-nav__item--nested">
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
       
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1637,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1651,69 +1854,6 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-    
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1784,7 +1924,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.Coloc" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.Coloc" class="md-nav__link">
     <span class="md-ellipsis">
       Coloc
     </span>
@@ -1794,9 +1934,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.Coloc.colocalise" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.Coloc.colocalise" class="md-nav__link">
     <span class="md-ellipsis">
-      colocalise()
+      colocalise
     </span>
   </a>
   
@@ -1885,27 +2025,6 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     
     
     
@@ -1916,7 +2035,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
@@ -1932,14 +2051,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2061,32 +2180,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2307,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2328,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2349,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2370,11 +2489,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2424,7 +2606,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.Coloc" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.Coloc" class="md-nav__link">
     <span class="md-ellipsis">
       Coloc
     </span>
@@ -2434,9 +2616,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.Coloc.colocalise" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.Coloc.colocalise" class="md-nav__link">
     <span class="md-ellipsis">
-      colocalise()
+      colocalise
     </span>
   </a>
   
@@ -2471,12 +2653,11 @@ <h1>Coloc</h1>
 
 
 
+<h2 id="gentropy.method.colocalisation.Coloc" class="doc doc-heading">
+          <code>gentropy.method.colocalisation.Coloc</code>
 
-<h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
-          <code>otg.method.colocalisation.Coloc</code>
 
-
-<a href="#otg.method.colocalisation.Coloc" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.colocalisation.Coloc" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2515,12 +2696,12 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
 </tbody>
 </table>
 <div class="admonition warning">
-<p class="admonition-title">Approximate Bayes factors required</p>
-<p>Coloc requires the availability of approximate Bayes factors (ABF) for each variant in the credible set (<code>logABF</code> column).</p>
+<p class="admonition-title">Bayes factors required</p>
+<p>Coloc requires the availability of Bayes factors (BF) for each variant in the credible set (<code>logBF</code> column).</p>
 </div>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/colocalisation.py</code></summary>
+              <summary>Source code in <code>src/gentropy/method/colocalisation.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 89</span>
 <span class="normal"> 90</span>
 <span class="normal"> 91</span>
@@ -2706,7 +2887,8 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
 <span class="normal">271</span>
 <span class="normal">272</span>
 <span class="normal">273</span>
-<span class="normal">274</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">Coloc</span><span class="p">:</span>
+<span class="normal">274</span>
+<span class="normal">275</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">Coloc</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Calculate bayesian colocalisation based on overlapping signals from credible sets.</span>
 
 <span class="sd">    Based on the [R COLOC package](https://github.com/chr1swallace/coloc/blob/main/R/claudia.R), which uses the Bayes factors from the credible set to estimate the posterior probability of colocalisation. This method makes the simplifying assumption that **only one single causal variant** exists for any given trait in any genomic region.</span>
@@ -2719,20 +2901,21 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
 <span class="sd">    | H&lt;sub&gt;3&lt;/sub&gt; | both traits are associated, but have different single causal variants |</span>
 <span class="sd">    | H&lt;sub&gt;4&lt;/sub&gt; | both traits are associated and share the same single causal variant   |</span>
 
-<span class="sd">    !!! warning &quot;Approximate Bayes factors required&quot;</span>
-<span class="sd">        Coloc requires the availability of approximate Bayes factors (ABF) for each variant in the credible set (`logABF` column).</span>
+<span class="sd">    !!! warning &quot;Bayes factors required&quot;</span>
+
+<span class="sd">        Coloc requires the availability of Bayes factors (BF) for each variant in the credible set (`logBF` column).</span>
 
 <span class="sd">    &quot;&quot;&quot;</span>
 
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">_get_logsum</span><span class="p">(</span><span class="n">log_abf</span><span class="p">:</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
+    <span class="k">def</span> <span class="nf">_get_logsum</span><span class="p">(</span><span class="n">log_bf</span><span class="p">:</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="nb">float</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Calculates logsum of vector.</span>
 
 <span class="sd">        This function calculates the log of the sum of the exponentiated</span>
 <span class="sd">        logs taking out the max, i.e. insuring that the sum is not Inf</span>
 
 <span class="sd">        Args:</span>
-<span class="sd">            log_abf (NDArray[np.float64]): log approximate bayes factor</span>
+<span class="sd">            log_bf (NDArray[np.float64]): log bayes factor</span>
 
 <span class="sd">        Returns:</span>
 <span class="sd">            float: logsum</span>
@@ -2742,16 +2925,16 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
 <span class="sd">            &gt;&gt;&gt; round(Coloc._get_logsum(l), 6)</span>
 <span class="sd">            1.476557</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">themax</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">log_abf</span><span class="p">)</span>
-        <span class="n">result</span> <span class="o">=</span> <span class="n">themax</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">log_abf</span> <span class="o">-</span> <span class="n">themax</span><span class="p">)))</span>
+        <span class="n">themax</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">log_bf</span><span class="p">)</span>
+        <span class="n">result</span> <span class="o">=</span> <span class="n">themax</span> <span class="o">+</span> <span class="n">np</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">sum</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">log_bf</span> <span class="o">-</span> <span class="n">themax</span><span class="p">)))</span>
         <span class="k">return</span> <span class="nb">float</span><span class="p">(</span><span class="n">result</span><span class="p">)</span>
 
     <span class="nd">@staticmethod</span>
-    <span class="k">def</span> <span class="nf">_get_posteriors</span><span class="p">(</span><span class="n">all_abfs</span><span class="p">:</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">DenseVector</span><span class="p">:</span>
+    <span class="k">def</span> <span class="nf">_get_posteriors</span><span class="p">(</span><span class="n">all_bfs</span><span class="p">:</span> <span class="n">NDArray</span><span class="p">[</span><span class="n">np</span><span class="o">.</span><span class="n">float64</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">DenseVector</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Calculate posterior probabilities for each hypothesis.</span>
 
 <span class="sd">        Args:</span>
-<span class="sd">            all_abfs (NDArray[np.float64]): h0-h4 bayes factors</span>
+<span class="sd">            all_bfs (NDArray[np.float64]): h0-h4 bayes factors</span>
 
 <span class="sd">        Returns:</span>
 <span class="sd">            DenseVector: Posterior</span>
@@ -2761,9 +2944,9 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
 <span class="sd">            &gt;&gt;&gt; Coloc._get_posteriors(l)</span>
 <span class="sd">            DenseVector([0.279, 0.2524, 0.2401, 0.2284])</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">diff</span> <span class="o">=</span> <span class="n">all_abfs</span> <span class="o">-</span> <span class="n">Coloc</span><span class="o">.</span><span class="n">_get_logsum</span><span class="p">(</span><span class="n">all_abfs</span><span class="p">)</span>
-        <span class="n">abfs_posteriors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">diff</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">Vectors</span><span class="o">.</span><span class="n">dense</span><span class="p">(</span><span class="n">abfs_posteriors</span><span class="p">)</span>
+        <span class="n">diff</span> <span class="o">=</span> <span class="n">all_bfs</span> <span class="o">-</span> <span class="n">Coloc</span><span class="o">.</span><span class="n">_get_logsum</span><span class="p">(</span><span class="n">all_bfs</span><span class="p">)</span>
+        <span class="n">bfs_posteriors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">exp</span><span class="p">(</span><span class="n">diff</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">Vectors</span><span class="o">.</span><span class="n">dense</span><span class="p">(</span><span class="n">bfs_posteriors</span><span class="p">)</span>
 
     <span class="nd">@classmethod</span>
     <span class="k">def</span> <span class="nf">colocalise</span><span class="p">(</span>
@@ -2790,31 +2973,31 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
         <span class="k">return</span> <span class="n">Colocalisation</span><span class="p">(</span>
             <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
                 <span class="n">overlapping_signals</span><span class="o">.</span><span class="n">df</span>
-                <span class="c1"># Before summing log_abf columns nulls need to be filled with 0:</span>
-                <span class="o">.</span><span class="n">fillna</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;statistics.left_logABF&quot;</span><span class="p">,</span> <span class="s2">&quot;statistics.right_logABF&quot;</span><span class="p">])</span>
-                <span class="c1"># Sum of log_abfs for each pair of signals</span>
+                <span class="c1"># Before summing log_BF columns nulls need to be filled with 0:</span>
+                <span class="o">.</span><span class="n">fillna</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;statistics.left_logBF&quot;</span><span class="p">,</span> <span class="s2">&quot;statistics.right_logBF&quot;</span><span class="p">])</span>
+                <span class="c1"># Sum of log_BFs for each pair of signals</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                    <span class="s2">&quot;sum_log_abf&quot;</span><span class="p">,</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logABF&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logABF&quot;</span><span class="p">),</span>
+                    <span class="s2">&quot;sum_log_bf&quot;</span><span class="p">,</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logBF&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logBF&quot;</span><span class="p">),</span>
                 <span class="p">)</span>
-                <span class="c1"># Group by overlapping peak and generating dense vectors of log_abf:</span>
+                <span class="c1"># Group by overlapping peak and generating dense vectors of log_BF:</span>
                 <span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">,</span> <span class="s2">&quot;leftStudyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;rightStudyLocusId&quot;</span><span class="p">)</span>
                 <span class="o">.</span><span class="n">agg</span><span class="p">(</span>
                     <span class="n">f</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s2">&quot;*&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;numberColocalisingVariants&quot;</span><span class="p">),</span>
                     <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logABF&quot;</span><span class="p">))</span>
-                    <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;left_logABF&quot;</span><span class="p">),</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logBF&quot;</span><span class="p">))</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;left_logBF&quot;</span><span class="p">),</span>
                     <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logABF&quot;</span><span class="p">))</span>
-                    <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;right_logABF&quot;</span><span class="p">),</span>
-                    <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_abf&quot;</span><span class="p">)))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                        <span class="s2">&quot;sum_log_abf&quot;</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logBF&quot;</span><span class="p">))</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;right_logBF&quot;</span><span class="p">),</span>
+                    <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_bf&quot;</span><span class="p">)))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+                        <span class="s2">&quot;sum_log_bf&quot;</span>
                     <span class="p">),</span>
                 <span class="p">)</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;left_logABF&quot;</span><span class="p">)))</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_logABF&quot;</span><span class="p">)))</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_abf&quot;</span><span class="p">)))</span>
-                <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;left_logABF&quot;</span><span class="p">,</span> <span class="s2">&quot;right_logABF&quot;</span><span class="p">,</span> <span class="s2">&quot;sum_log_abf&quot;</span><span class="p">)</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;left_logBF&quot;</span><span class="p">)))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_logBF&quot;</span><span class="p">)))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_bf&quot;</span><span class="p">)))</span>
+                <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;left_logBF&quot;</span><span class="p">,</span> <span class="s2">&quot;right_logBF&quot;</span><span class="p">,</span> <span class="s2">&quot;sum_log_bf&quot;</span><span class="p">)</span>
                 <span class="c1"># Add priors</span>
                 <span class="c1"># priorc1 Prior on variant being causal for trait 1</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">priorc1</span><span class="p">))</span>
@@ -2823,9 +3006,9 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
                 <span class="c1"># priorc12 Prior on variant being causal for traits 1 and 2</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;priorc12&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">priorc12</span><span class="p">))</span>
                 <span class="c1"># h0-h2</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH0abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH1abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">))</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH2abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc2&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH0bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH1bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH2bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc2&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">))</span>
                 <span class="c1"># h3</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;sumlogsum&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">))</span>
                 <span class="c1"># exclude null H3/H4s: due to sumlogsum == logsum12</span>
@@ -2842,33 +3025,33 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
                     <span class="p">),</span>
                 <span class="p">)</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                    <span class="s2">&quot;lH3abf&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;lH3bf&quot;</span><span class="p">,</span>
                     <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">))</span>
                     <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc2&quot;</span><span class="p">))</span>
                     <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logdiff&quot;</span><span class="p">),</span>
                 <span class="p">)</span>
                 <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;right_logsum&quot;</span><span class="p">,</span> <span class="s2">&quot;left_logsum&quot;</span><span class="p">,</span> <span class="s2">&quot;sumlogsum&quot;</span><span class="p">,</span> <span class="s2">&quot;max&quot;</span><span class="p">,</span> <span class="s2">&quot;logdiff&quot;</span><span class="p">)</span>
                 <span class="c1"># h4</span>
-                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH4abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc12&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">))</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH4bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc12&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">))</span>
                 <span class="c1"># cleaning</span>
                 <span class="o">.</span><span class="n">drop</span><span class="p">(</span>
                     <span class="s2">&quot;priorc1&quot;</span><span class="p">,</span> <span class="s2">&quot;priorc2&quot;</span><span class="p">,</span> <span class="s2">&quot;priorc12&quot;</span><span class="p">,</span> <span class="s2">&quot;logsum1&quot;</span><span class="p">,</span> <span class="s2">&quot;logsum2&quot;</span><span class="p">,</span> <span class="s2">&quot;logsum12&quot;</span>
                 <span class="p">)</span>
                 <span class="c1"># posteriors</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                    <span class="s2">&quot;allABF&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;allBF&quot;</span><span class="p">,</span>
                     <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span>
                         <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH0abf&quot;</span><span class="p">),</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH1abf&quot;</span><span class="p">),</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH2abf&quot;</span><span class="p">),</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH3abf&quot;</span><span class="p">),</span>
-                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH4abf&quot;</span><span class="p">),</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH0bf&quot;</span><span class="p">),</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH1bf&quot;</span><span class="p">),</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH2bf&quot;</span><span class="p">),</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH3bf&quot;</span><span class="p">),</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH4bf&quot;</span><span class="p">),</span>
                         <span class="p">)</span>
                     <span class="p">),</span>
                 <span class="p">)</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                    <span class="s2">&quot;posteriors&quot;</span><span class="p">,</span> <span class="n">fml</span><span class="o">.</span><span class="n">vector_to_array</span><span class="p">(</span><span class="n">posteriors</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;allABF&quot;</span><span class="p">)))</span>
+                    <span class="s2">&quot;posteriors&quot;</span><span class="p">,</span> <span class="n">fml</span><span class="o">.</span><span class="n">vector_to_array</span><span class="p">(</span><span class="n">posteriors</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;allBF&quot;</span><span class="p">)))</span>
                 <span class="p">)</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;h0&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;posteriors&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;h1&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;posteriors&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
@@ -2880,13 +3063,13 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
                 <span class="c1"># clean up</span>
                 <span class="o">.</span><span class="n">drop</span><span class="p">(</span>
                     <span class="s2">&quot;posteriors&quot;</span><span class="p">,</span>
-                    <span class="s2">&quot;allABF&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;allBF&quot;</span><span class="p">,</span>
                     <span class="s2">&quot;h4h3&quot;</span><span class="p">,</span>
-                    <span class="s2">&quot;lH0abf&quot;</span><span class="p">,</span>
-                    <span class="s2">&quot;lH1abf&quot;</span><span class="p">,</span>
-                    <span class="s2">&quot;lH2abf&quot;</span><span class="p">,</span>
-                    <span class="s2">&quot;lH3abf&quot;</span><span class="p">,</span>
-                    <span class="s2">&quot;lH4abf&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;lH0bf&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;lH1bf&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;lH2bf&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;lH3bf&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;lH4bf&quot;</span><span class="p">,</span>
                 <span class="p">)</span>
                 <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;colocalisationMethod&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;COLOC&quot;</span><span class="p">))</span>
             <span class="p">),</span>
@@ -2912,15 +3095,14 @@ <h2 id="otg.method.colocalisation.Coloc" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
+<h3 id="gentropy.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">colocalise</span><span class="p">(</span><span class="n">overlapping_signals</span><span class="p">:</span> <span class="n">StudyLocusOverlap</span><span class="p">,</span> <span class="n">priorc1</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.0001</span><span class="p">,</span> <span class="n">priorc2</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.0001</span><span class="p">,</span> <span class="n">priorc12</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-05</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Colocalisation</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.colocalisation.Coloc.colocalise" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.colocalisation.Coloc.colocalise" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2943,7 +3125,7 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
         <tr>
           <td><code>overlapping_signals</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus_overlap.StudyLocusOverlap" href="../../dataset/study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus_overlap.StudyLocusOverlap" href="../../datasets/study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3012,7 +3194,7 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>Colocalisation</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.colocalisation.Colocalisation" href="../../dataset/colocalisation/#otg.dataset.colocalisation.Colocalisation">Colocalisation</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.colocalisation.Colocalisation" href="../../datasets/colocalisation/#gentropy.dataset.colocalisation.Colocalisation">Colocalisation</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3024,9 +3206,8 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/colocalisation.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">148</span>
-<span class="normal">149</span>
+            <summary>Source code in <code>src/gentropy/method/colocalisation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">149</span>
 <span class="normal">150</span>
 <span class="normal">151</span>
 <span class="normal">152</span>
@@ -3151,7 +3332,8 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
 <span class="normal">271</span>
 <span class="normal">272</span>
 <span class="normal">273</span>
-<span class="normal">274</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">274</span>
+<span class="normal">275</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">colocalise</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">Coloc</span><span class="p">],</span>
     <span class="n">overlapping_signals</span><span class="p">:</span> <span class="n">StudyLocusOverlap</span><span class="p">,</span>
@@ -3176,31 +3358,31 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
     <span class="k">return</span> <span class="n">Colocalisation</span><span class="p">(</span>
         <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
             <span class="n">overlapping_signals</span><span class="o">.</span><span class="n">df</span>
-            <span class="c1"># Before summing log_abf columns nulls need to be filled with 0:</span>
-            <span class="o">.</span><span class="n">fillna</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;statistics.left_logABF&quot;</span><span class="p">,</span> <span class="s2">&quot;statistics.right_logABF&quot;</span><span class="p">])</span>
-            <span class="c1"># Sum of log_abfs for each pair of signals</span>
+            <span class="c1"># Before summing log_BF columns nulls need to be filled with 0:</span>
+            <span class="o">.</span><span class="n">fillna</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span> <span class="n">subset</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;statistics.left_logBF&quot;</span><span class="p">,</span> <span class="s2">&quot;statistics.right_logBF&quot;</span><span class="p">])</span>
+            <span class="c1"># Sum of log_BFs for each pair of signals</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="s2">&quot;sum_log_abf&quot;</span><span class="p">,</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logABF&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logABF&quot;</span><span class="p">),</span>
+                <span class="s2">&quot;sum_log_bf&quot;</span><span class="p">,</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logBF&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logBF&quot;</span><span class="p">),</span>
             <span class="p">)</span>
-            <span class="c1"># Group by overlapping peak and generating dense vectors of log_abf:</span>
+            <span class="c1"># Group by overlapping peak and generating dense vectors of log_BF:</span>
             <span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">,</span> <span class="s2">&quot;leftStudyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;rightStudyLocusId&quot;</span><span class="p">)</span>
             <span class="o">.</span><span class="n">agg</span><span class="p">(</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">count</span><span class="p">(</span><span class="s2">&quot;*&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;numberColocalisingVariants&quot;</span><span class="p">),</span>
                 <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logABF&quot;</span><span class="p">))</span>
-                <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;left_logABF&quot;</span><span class="p">),</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.left_logBF&quot;</span><span class="p">))</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;left_logBF&quot;</span><span class="p">),</span>
                 <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span>
-                    <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logABF&quot;</span><span class="p">))</span>
-                <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;right_logABF&quot;</span><span class="p">),</span>
-                <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_abf&quot;</span><span class="p">)))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
-                    <span class="s2">&quot;sum_log_abf&quot;</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;statistics.right_logBF&quot;</span><span class="p">))</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;right_logBF&quot;</span><span class="p">),</span>
+                <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">collect_list</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_bf&quot;</span><span class="p">)))</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+                    <span class="s2">&quot;sum_log_bf&quot;</span>
                 <span class="p">),</span>
             <span class="p">)</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;left_logABF&quot;</span><span class="p">)))</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_logABF&quot;</span><span class="p">)))</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_abf&quot;</span><span class="p">)))</span>
-            <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;left_logABF&quot;</span><span class="p">,</span> <span class="s2">&quot;right_logABF&quot;</span><span class="p">,</span> <span class="s2">&quot;sum_log_abf&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;left_logBF&quot;</span><span class="p">)))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_logBF&quot;</span><span class="p">)))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">,</span> <span class="n">logsum</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sum_log_bf&quot;</span><span class="p">)))</span>
+            <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;left_logBF&quot;</span><span class="p">,</span> <span class="s2">&quot;right_logBF&quot;</span><span class="p">,</span> <span class="s2">&quot;sum_log_bf&quot;</span><span class="p">)</span>
             <span class="c1"># Add priors</span>
             <span class="c1"># priorc1 Prior on variant being causal for trait 1</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">priorc1</span><span class="p">))</span>
@@ -3209,9 +3391,9 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
             <span class="c1"># priorc12 Prior on variant being causal for traits 1 and 2</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;priorc12&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">priorc12</span><span class="p">))</span>
             <span class="c1"># h0-h2</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH0abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH1abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">))</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH2abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc2&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH0bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH1bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH2bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc2&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">))</span>
             <span class="c1"># h3</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;sumlogsum&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum1&quot;</span><span class="p">)</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum2&quot;</span><span class="p">))</span>
             <span class="c1"># exclude null H3/H4s: due to sumlogsum == logsum12</span>
@@ -3228,33 +3410,33 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
                 <span class="p">),</span>
             <span class="p">)</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="s2">&quot;lH3abf&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;lH3bf&quot;</span><span class="p">,</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc1&quot;</span><span class="p">))</span>
                 <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc2&quot;</span><span class="p">))</span>
                 <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logdiff&quot;</span><span class="p">),</span>
             <span class="p">)</span>
             <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;right_logsum&quot;</span><span class="p">,</span> <span class="s2">&quot;left_logsum&quot;</span><span class="p">,</span> <span class="s2">&quot;sumlogsum&quot;</span><span class="p">,</span> <span class="s2">&quot;max&quot;</span><span class="p">,</span> <span class="s2">&quot;logdiff&quot;</span><span class="p">)</span>
             <span class="c1"># h4</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH4abf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc12&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;lH4bf&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">log</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;priorc12&quot;</span><span class="p">))</span> <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;logsum12&quot;</span><span class="p">))</span>
             <span class="c1"># cleaning</span>
             <span class="o">.</span><span class="n">drop</span><span class="p">(</span>
                 <span class="s2">&quot;priorc1&quot;</span><span class="p">,</span> <span class="s2">&quot;priorc2&quot;</span><span class="p">,</span> <span class="s2">&quot;priorc12&quot;</span><span class="p">,</span> <span class="s2">&quot;logsum1&quot;</span><span class="p">,</span> <span class="s2">&quot;logsum2&quot;</span><span class="p">,</span> <span class="s2">&quot;logsum12&quot;</span>
             <span class="p">)</span>
             <span class="c1"># posteriors</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="s2">&quot;allABF&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;allBF&quot;</span><span class="p">,</span>
                 <span class="n">fml</span><span class="o">.</span><span class="n">array_to_vector</span><span class="p">(</span>
                     <span class="n">f</span><span class="o">.</span><span class="n">array</span><span class="p">(</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH0abf&quot;</span><span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH1abf&quot;</span><span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH2abf&quot;</span><span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH3abf&quot;</span><span class="p">),</span>
-                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH4abf&quot;</span><span class="p">),</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH0bf&quot;</span><span class="p">),</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH1bf&quot;</span><span class="p">),</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH2bf&quot;</span><span class="p">),</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH3bf&quot;</span><span class="p">),</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;lH4bf&quot;</span><span class="p">),</span>
                     <span class="p">)</span>
                 <span class="p">),</span>
             <span class="p">)</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="s2">&quot;posteriors&quot;</span><span class="p">,</span> <span class="n">fml</span><span class="o">.</span><span class="n">vector_to_array</span><span class="p">(</span><span class="n">posteriors</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;allABF&quot;</span><span class="p">)))</span>
+                <span class="s2">&quot;posteriors&quot;</span><span class="p">,</span> <span class="n">fml</span><span class="o">.</span><span class="n">vector_to_array</span><span class="p">(</span><span class="n">posteriors</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;allBF&quot;</span><span class="p">)))</span>
             <span class="p">)</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;h0&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;posteriors&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">0</span><span class="p">))</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;h1&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;posteriors&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">getItem</span><span class="p">(</span><span class="mi">1</span><span class="p">))</span>
@@ -3266,13 +3448,13 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
             <span class="c1"># clean up</span>
             <span class="o">.</span><span class="n">drop</span><span class="p">(</span>
                 <span class="s2">&quot;posteriors&quot;</span><span class="p">,</span>
-                <span class="s2">&quot;allABF&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;allBF&quot;</span><span class="p">,</span>
                 <span class="s2">&quot;h4h3&quot;</span><span class="p">,</span>
-                <span class="s2">&quot;lH0abf&quot;</span><span class="p">,</span>
-                <span class="s2">&quot;lH1abf&quot;</span><span class="p">,</span>
-                <span class="s2">&quot;lH2abf&quot;</span><span class="p">,</span>
-                <span class="s2">&quot;lH3abf&quot;</span><span class="p">,</span>
-                <span class="s2">&quot;lH4abf&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;lH0bf&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;lH1bf&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;lH2bf&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;lH3bf&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;lH4bf&quot;</span><span class="p">,</span>
             <span class="p">)</span>
             <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;colocalisationMethod&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;COLOC&quot;</span><span class="p">))</span>
         <span class="p">),</span>
@@ -3290,6 +3472,7 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3313,7 +3496,7 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3380,7 +3563,7 @@ <h3 id="otg.method.colocalisation.Coloc.colocalise" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/method/ecaviar/index.html b/python_api/methods/ecaviar/index.html
similarity index 83%
rename from python_api/method/ecaviar/index.html
rename to python_api/methods/ecaviar/index.html
index 94c95af31..08ffddae1 100644
--- a/python_api/method/ecaviar/index.html
+++ b/python_api/methods/ecaviar/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>eCAVIAR - Open Targets Genetics</title>
+        <title>eCAVIAR - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.colocalisation.ECaviar" class="md-skip">
+        <a href="#gentropy.method.colocalisation.ECaviar" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-    How-to
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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-    Development
+    How-to
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
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+  
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step in CLI
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+  
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+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Run step using YAML config
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
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@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
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@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
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+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
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-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
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-    Datasource
+    Datasources
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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             Eqtl catalogue
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     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
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             Finngen
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     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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@@ -1153,14 +1346,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             Gnomad
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@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
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@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
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@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
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@@ -1248,14 +1441,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
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@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
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@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
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@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
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@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
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@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
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@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
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@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
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@@ -1447,7 +1640,7 @@
   
   
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-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
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@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
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@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
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@@ -1522,14 +1715,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,10 +1778,20 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
   
+    
+  
   
   
     
@@ -1596,37 +1799,37 @@
     
     
     
-    <li class="md-nav__item md-nav__item--nested">
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
       
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1637,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1651,69 +1854,6 @@
 
               
             
-          </ul>
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-      
-    </li>
-  
-
-              
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-      
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-  
-
-              
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-  
-  <span class="md-ellipsis">
-    Method
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-  
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-            Method
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-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1805,7 +1945,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.ECaviar" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.ECaviar" class="md-nav__link">
     <span class="md-ellipsis">
       ECaviar
     </span>
@@ -1815,9 +1955,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.ECaviar.colocalise" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.ECaviar.colocalise" class="md-nav__link">
     <span class="md-ellipsis">
-      colocalise()
+      colocalise
     </span>
   </a>
   
@@ -1885,27 +2025,6 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     
     
     
@@ -1916,7 +2035,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
@@ -1932,14 +2051,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2061,32 +2180,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2307,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2328,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2349,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2370,11 +2489,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2424,7 +2606,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.ECaviar" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.ECaviar" class="md-nav__link">
     <span class="md-ellipsis">
       ECaviar
     </span>
@@ -2434,9 +2616,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.colocalisation.ECaviar.colocalise" class="md-nav__link">
+  <a href="#gentropy.method.colocalisation.ECaviar.colocalise" class="md-nav__link">
     <span class="md-ellipsis">
-      colocalise()
+      colocalise
     </span>
   </a>
   
@@ -2471,12 +2653,11 @@ <h1>eCAVIAR</h1>
 
 
 
-
-<h2 id="otg.method.colocalisation.ECaviar" class="doc doc-heading">
-          <code>otg.method.colocalisation.ECaviar</code>
+<h2 id="gentropy.method.colocalisation.ECaviar" class="doc doc-heading">
+          <code>gentropy.method.colocalisation.ECaviar</code>
 
 
-<a href="#otg.method.colocalisation.ECaviar" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.colocalisation.ECaviar" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2486,7 +2667,7 @@ <h2 id="otg.method.colocalisation.ECaviar" class="doc doc-heading">
 <p>It extends <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142122/#bib18">CAVIAR</a> framework to explicitly estimate the posterior probability that the same variant is causal in 2 studies while accounting for the uncertainty of LD. eCAVIAR computes the colocalization posterior probability (<strong>CLPP</strong>) by utilizing the marginal posterior probabilities. This framework allows for <strong>multiple variants to be causal</strong> in a single locus.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/colocalisation.py</code></summary>
+              <summary>Source code in <code>src/gentropy/method/colocalisation.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">22</span>
 <span class="normal">23</span>
 <span class="normal">24</span>
@@ -2636,15 +2817,14 @@ <h2 id="otg.method.colocalisation.ECaviar" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
+<h3 id="gentropy.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">colocalise</span><span class="p">(</span><span class="n">overlapping_signals</span><span class="p">:</span> <span class="n">StudyLocusOverlap</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Colocalisation</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.colocalisation.ECaviar.colocalise" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.colocalisation.ECaviar.colocalise" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2667,7 +2847,7 @@ <h3 id="otg.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
         <tr>
           <td><code>overlapping_signals</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus_overlap.StudyLocusOverlap" href="../../dataset/study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus_overlap.StudyLocusOverlap" href="../../datasets/study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap">StudyLocusOverlap</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2694,7 +2874,7 @@ <h3 id="otg.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>Colocalisation</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.colocalisation.Colocalisation" href="../../dataset/colocalisation/#otg.dataset.colocalisation.Colocalisation">Colocalisation</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.colocalisation.Colocalisation" href="../../datasets/colocalisation/#gentropy.dataset.colocalisation.Colocalisation">Colocalisation</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2706,7 +2886,7 @@ <h3 id="otg.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/colocalisation.py</code></summary>
+            <summary>Source code in <code>src/gentropy/method/colocalisation.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">57</span>
 <span class="normal">58</span>
 <span class="normal">59</span>
@@ -2778,6 +2958,7 @@ <h3 id="otg.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
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@@ -2801,7 +2982,7 @@ <h3 id="otg.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2868,7 +3049,7 @@ <h3 id="otg.method.colocalisation.ECaviar.colocalise" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/method/l2g/_l2g/index.html b/python_api/methods/l2g/_l2g/index.html
similarity index 77%
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rename to python_api/methods/l2g/_l2g/index.html
index 7fb4dbd90..413275199 100644
--- a/python_api/method/l2g/_l2g/index.html
+++ b/python_api/methods/l2g/_l2g/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../window_based_clumping/">
+        <link rel="prev" href="../../pics/">
       
       
         <link rel="next" href="../evaluator/">
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Locus to Gene (L2G) classifier - Open Targets Genetics</title>
+        <title>Locus to Gene (L2G) model - Open Targets Gentropy</title>
       
     
     
@@ -89,7 +89,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -102,13 +102,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Locus to Gene (L2G) classifier
+              Locus to Gene (L2G) model
             
           </span>
         </div>
@@ -187,13 +187,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -210,6 +210,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
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+      
+        
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+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -228,7 +245,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -244,6 +261,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -304,22 +338,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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+    opentargets/gentropy
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@@ -333,11 +367,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -353,11 +387,11 @@
   
   
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-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
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+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
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+    
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+  
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+  
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+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
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+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
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+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -939,32 +1090,32 @@
         
         
         
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+            <a href="../../../datasources/_datasources/" class="md-nav__link ">
               
   
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1020,7 +1171,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1058,12 +1230,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1074,14 +1246,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1094,7 +1266,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1132,12 +1325,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1148,14 +1341,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1168,7 +1361,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1189,7 +1382,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1227,12 +1420,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1243,14 +1436,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1263,7 +1456,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1284,7 +1477,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1305,7 +1498,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1326,7 +1519,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1364,12 +1557,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1380,14 +1573,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1400,7 +1593,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1421,7 +1614,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1442,7 +1635,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1463,7 +1656,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1501,12 +1694,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1517,14 +1710,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1537,7 +1730,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1558,7 +1751,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1580,80 +1773,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1680,32 +1799,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_method/" class="md-nav__link ">
+            <a href="../../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1716,11 +1835,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../clumping/" class="md-nav__link">
+      <a href="../../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1737,11 +1856,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../coloc/" class="md-nav__link">
+      <a href="../../clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1758,11 +1877,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ecaviar/" class="md-nav__link">
+      <a href="../../coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1779,11 +1898,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ld_annotator/" class="md-nav__link">
+      <a href="../../ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1800,11 +1919,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../pics/" class="md-nav__link">
+      <a href="../../ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1821,11 +1940,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../window_based_clumping/" class="md-nav__link">
+      <a href="../../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1853,7 +1972,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" checked>
         
           
           
@@ -1869,14 +1988,14 @@
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1998,32 +2117,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,11 +2153,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2055,11 +2174,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2076,11 +2195,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2307,11 +2426,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2372,7 +2554,26 @@
 
   <h1>L2g</h1>
 
-<p>TBC</p>
+<p>The <strong>“locus-to-gene” (L2G)</strong> model derives features to prioritize likely causal genes at each GWAS locus based on genetic and functional genomics features. The main categories of predictive features are:</p>
+<ul>
+<li><strong>Distance:</strong> (from credible set variants to gene)</li>
+<li><strong>Molecular QTL Colocalization</strong></li>
+<li><strong>Chromatin Interaction:</strong> (e.g., promoter-capture Hi-C)</li>
+<li><strong>Variant Pathogenicity:</strong> (from VEP)</li>
+</ul>
+<p>The L2G model is distinct from the variant-to-gene (V2G) pipeline in that it:</p>
+<ul>
+<li>Uses a machine-learning model to learn the weights of each evidence source based on a gold standard of previously identified causal genes.</li>
+<li>Relies upon fine-mapping and colocalization data.</li>
+</ul>
+<p>Some of the predictive features weight variant-to-gene (or genomic region-to-gene) evidence based on the posterior probability that the variant is causal, determined through fine-mapping of the GWAS association.</p>
+<p>Details of the L2G model are provided in our Nature Genetics publication (ref - <a href="https://www.nature.com/articles/s41588-021-00945-5">Nature Genetics Publication</a>):</p>
+<ul>
+<li><strong>Title:</strong> An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci.</li>
+<li><strong>Authors:</strong> Mountjoy, E., Schmidt, E.M., Carmona, M. et al.</li>
+<li><strong>Journal:</strong> Nat Genet 53, 1527–1533 (2021).</li>
+<li><strong>DOI:</strong> <a href="https://doi.org/10.1038/s41588-021-00945-5">10.1038/s41588-021-00945-5</a></li>
+</ul>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2395,7 +2596,7 @@ <h1>L2g</h1>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T15:56:05+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2408,11 +2609,11 @@ <h1>L2g</h1>
       <li class="contributors-holder">
         <ul class="contributors" data-bi-name="contributors"><li>
             <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
+              href="https://github.com/d0choa"
+              title="d0choa"
               data-bi-name="contributorprofile"
               target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
+              ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
           </li></ul>
       </li>
@@ -2462,7 +2663,7 @@ <h1>L2g</h1>
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/method/l2g/evaluator/index.html b/python_api/methods/l2g/evaluator/index.html
similarity index 78%
rename from python_api/method/l2g/evaluator/index.html
rename to python_api/methods/l2g/evaluator/index.html
index 4567fafe6..b66007eed 100644
--- a/python_api/method/l2g/evaluator/index.html
+++ b/python_api/methods/l2g/evaluator/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>W&B evaluator - Open Targets Genetics</title>
+        <title>W&B evaluator - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.l2g.evaluator.WandbEvaluator" class="md-skip">
+        <a href="#gentropy.method.l2g.evaluator.WandbEvaluator" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
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         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
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+      
+        
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+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
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+    
+      
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
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-    Dataset
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,32 +1804,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_method/" class="md-nav__link ">
+            <a href="../../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../clumping/" class="md-nav__link">
+      <a href="../../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1742,11 +1861,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../coloc/" class="md-nav__link">
+      <a href="../../clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1763,11 +1882,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ecaviar/" class="md-nav__link">
+      <a href="../../coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1903,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ld_annotator/" class="md-nav__link">
+      <a href="../../ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1924,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../pics/" class="md-nav__link">
+      <a href="../../ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1826,11 +1945,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../window_based_clumping/" class="md-nav__link">
+      <a href="../../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1858,7 +1977,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" checked>
         
           
           
@@ -1874,14 +1993,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1936,7 +2055,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator" class="md-nav__link">
     <span class="md-ellipsis">
       WandbEvaluator
     </span>
@@ -1946,54 +2065,63 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.__init__" class="md-nav__link">
     <span class="md-ellipsis">
-      getlabel_values()
+      __init__
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="md-nav__link">
     <span class="md-ellipsis">
-      getspark_ml_evaluator()
+      getlabel_values
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="md-nav__link">
     <span class="md-ellipsis">
-      getwandb_project_name()
+      getspark_ml_evaluator
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="md-nav__link">
     <span class="md-ellipsis">
-      getwandb_run()
+      getwandb_project_name
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="md-nav__link">
     <span class="md-ellipsis">
-      setlabel_values()
+      getwandb_run
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="md-nav__link">
     <span class="md-ellipsis">
-      setspark_ml_evaluator()
+      setlabel_values
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="md-nav__link">
+    <span class="md-ellipsis">
+      setspark_ml_evaluator
     </span>
   </a>
   
@@ -2108,32 +2236,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2144,11 +2272,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2165,11 +2293,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2186,11 +2314,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2207,11 +2335,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2228,11 +2356,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2249,11 +2377,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2270,11 +2398,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2291,11 +2419,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2312,11 +2440,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2333,11 +2461,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2354,11 +2482,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2375,11 +2503,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2396,11 +2524,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2417,11 +2545,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2471,7 +2662,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator" class="md-nav__link">
     <span class="md-ellipsis">
       WandbEvaluator
     </span>
@@ -2481,54 +2672,63 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="md-nav__link">
     <span class="md-ellipsis">
-      getlabel_values()
+      getlabel_values
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="md-nav__link">
     <span class="md-ellipsis">
-      getspark_ml_evaluator()
+      getspark_ml_evaluator
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="md-nav__link">
     <span class="md-ellipsis">
-      getwandb_project_name()
+      getwandb_project_name
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="md-nav__link">
     <span class="md-ellipsis">
-      getwandb_run()
+      getwandb_run
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="md-nav__link">
     <span class="md-ellipsis">
-      setlabel_values()
+      setlabel_values
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="md-nav__link">
+  <a href="#gentropy.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="md-nav__link">
     <span class="md-ellipsis">
-      setspark_ml_evaluator()
+      setspark_ml_evaluator
     </span>
   </a>
   
@@ -2563,12 +2763,11 @@ <h1>W&B evaluator</h1>
 
 
 
-
-<h2 id="otg.method.l2g.evaluator.WandbEvaluator" class="doc doc-heading">
-          <code>otg.method.l2g.evaluator.WandbEvaluator</code>
+<h2 id="gentropy.method.l2g.evaluator.WandbEvaluator" class="doc doc-heading">
+          <code>gentropy.method.l2g.evaluator.WandbEvaluator</code>
 
 
-<a href="#otg.method.l2g.evaluator.WandbEvaluator" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2579,8 +2778,9 @@ <h2 id="otg.method.l2g.evaluator.WandbEvaluator" class="doc doc-heading">
       <p>Wrapper for pyspark Evaluators. It is expected that the user will provide an Evaluators, and this wrapper will log metrics from said evaluator to W&amp;B.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/l2g/evaluator.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 21</span>
+              <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 20</span>
+<span class="normal"> 21</span>
 <span class="normal"> 22</span>
 <span class="normal"> 23</span>
 <span class="normal"> 24</span>
@@ -2763,8 +2963,7 @@ <h2 id="otg.method.l2g.evaluator.WandbEvaluator" class="doc doc-heading">
 <span class="normal">201</span>
 <span class="normal">202</span>
 <span class="normal">203</span>
-<span class="normal">204</span>
-<span class="normal">205</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">WandbEvaluator</span><span class="p">(</span><span class="n">Evaluator</span><span class="p">):</span>
+<span class="normal">204</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">WandbEvaluator</span><span class="p">(</span><span class="n">Evaluator</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Wrapper for pyspark Evaluators. It is expected that the user will provide an Evaluators, and this wrapper will log metrics from said evaluator to W&amp;B.&quot;&quot;&quot;</span>
 
     <span class="n">spark_ml_evaluator</span><span class="p">:</span> <span class="n">Param</span><span class="p">[</span><span class="n">Evaluator</span><span class="p">]</span> <span class="o">=</span> <span class="n">Param</span><span class="p">(</span>
@@ -2870,11 +3069,11 @@ <h2 id="otg.method.l2g.evaluator.WandbEvaluator" class="doc doc-heading">
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOrDefault</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">spark_ml_evaluator</span><span class="p">)</span>
 
-    <span class="k">def</span> <span class="nf">getwandb_run</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">wandb</span><span class="o">.</span><span class="n">sdk</span><span class="o">.</span><span class="n">wandb_run</span><span class="o">.</span><span class="n">Run</span><span class="p">:</span>
+    <span class="k">def</span> <span class="nf">getwandb_run</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Run</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Get the wandb_run parameter.</span>
 
 <span class="sd">        Returns:</span>
-<span class="sd">            wandb.sdk.wandb_run.Run: Wandb run object.</span>
+<span class="sd">            Run: Wandb run object.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOrDefault</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">wandb_run</span><span class="p">)</span>
 
@@ -2969,11 +3168,158 @@ <h2 id="otg.method.l2g.evaluator.WandbEvaluator" class="doc doc-heading">
 
 
 
+<h3 id="gentropy.method.l2g.evaluator.WandbEvaluator.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">label_values</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="n">BinaryClassificationEvaluator</span> <span class="o">|</span> <span class="n">MulticlassClassificationEvaluator</span> <span class="o">|</span> <span class="n">Run</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
 
-<h3 id="otg.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="doc doc-heading">
+
+  <div class="doc doc-contents ">
+  
+      <p>Initialize a WandbEvaluator.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>label_values</code></td>
+          <td>
+                <code>list[str] | None</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of label values.</p>
+            </div>
+          </td>
+          <td>
+                <code>None</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>**kwargs</code></td>
+          <td>
+                <code><span title="pyspark.ml.evaluation.BinaryClassificationEvaluator">BinaryClassificationEvaluator</span> | <span title="pyspark.ml.evaluation.MulticlassClassificationEvaluator">MulticlassClassificationEvaluator</span> | <span title="wandb.sdk.wandb_run.Run">Run</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Keyword arguments.</p>
+            </div>
+          </td>
+          <td>
+                <code>{}</code>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 60</span>
+<span class="normal"> 61</span>
+<span class="normal"> 62</span>
+<span class="normal"> 63</span>
+<span class="normal"> 64</span>
+<span class="normal"> 65</span>
+<span class="normal"> 66</span>
+<span class="normal"> 67</span>
+<span class="normal"> 68</span>
+<span class="normal"> 69</span>
+<span class="normal"> 70</span>
+<span class="normal"> 71</span>
+<span class="normal"> 72</span>
+<span class="normal"> 73</span>
+<span class="normal"> 74</span>
+<span class="normal"> 75</span>
+<span class="normal"> 76</span>
+<span class="normal"> 77</span>
+<span class="normal"> 78</span>
+<span class="normal"> 79</span>
+<span class="normal"> 80</span>
+<span class="normal"> 81</span>
+<span class="normal"> 82</span>
+<span class="normal"> 83</span>
+<span class="normal"> 84</span>
+<span class="normal"> 85</span>
+<span class="normal"> 86</span>
+<span class="normal"> 87</span>
+<span class="normal"> 88</span>
+<span class="normal"> 89</span>
+<span class="normal"> 90</span>
+<span class="normal"> 91</span>
+<span class="normal"> 92</span>
+<span class="normal"> 93</span>
+<span class="normal"> 94</span>
+<span class="normal"> 95</span>
+<span class="normal"> 96</span>
+<span class="normal"> 97</span>
+<span class="normal"> 98</span>
+<span class="normal"> 99</span>
+<span class="normal">100</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@keyword_only</span>
+<span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">,</span>
+    <span class="n">label_values</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="o">**</span><span class="n">kwargs</span><span class="p">:</span> <span class="n">BinaryClassificationEvaluator</span>
+    <span class="o">|</span> <span class="n">MulticlassClassificationEvaluator</span>
+    <span class="o">|</span> <span class="n">Run</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Initialize a WandbEvaluator.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        label_values (list[str] | None): List of label values.</span>
+<span class="sd">        **kwargs (BinaryClassificationEvaluator | MulticlassClassificationEvaluator | Run): Keyword arguments.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">if</span> <span class="n">label_values</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
+        <span class="n">label_values</span> <span class="o">=</span> <span class="p">[]</span>
+    <span class="nb">super</span><span class="p">(</span><span class="n">Evaluator</span><span class="p">,</span> <span class="bp">self</span><span class="p">)</span><span class="o">.</span><span class="fm">__init__</span><span class="p">()</span>
+
+    <span class="bp">self</span><span class="o">.</span><span class="n">metrics</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="n">MulticlassClassificationEvaluator</span><span class="p">:</span> <span class="p">[</span>
+            <span class="s2">&quot;f1&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;accuracy&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;weightedPrecision&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;weightedRecall&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;weightedTruePositiveRate&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;weightedFalsePositiveRate&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;weightedFMeasure&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;truePositiveRateByLabel&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;falsePositiveRateByLabel&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;precisionByLabel&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;recallByLabel&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;fMeasureByLabel&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;logLoss&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;hammingLoss&quot;</span><span class="p">,</span>
+        <span class="p">],</span>
+        <span class="n">BinaryClassificationEvaluator</span><span class="p">:</span> <span class="p">[</span><span class="s2">&quot;areaUnderROC&quot;</span><span class="p">,</span> <span class="s2">&quot;areaUnderPR&quot;</span><span class="p">],</span>
+    <span class="p">}</span>
+
+    <span class="bp">self</span><span class="o">.</span><span class="n">_setDefault</span><span class="p">(</span><span class="n">label_values</span><span class="o">=</span><span class="p">[])</span>
+    <span class="n">kwargs</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">_input_kwargs</span>
+    <span class="bp">self</span><span class="o">.</span><span class="n">_set</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">getlabel_values</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span></code>
 
-<a href="#otg.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3005,14 +3351,14 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="doc doc-
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/evaluator.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">143</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">142</span>
+<span class="normal">143</span>
 <span class="normal">144</span>
 <span class="normal">145</span>
 <span class="normal">146</span>
 <span class="normal">147</span>
-<span class="normal">148</span>
-<span class="normal">149</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getlabel_values</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>
+<span class="normal">148</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getlabel_values</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Get the label_values parameter.</span>
 
 <span class="sd">    Returns:</span>
@@ -3030,11 +3376,10 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getlabel_values" class="doc doc-
 
 
 
-
-<h3 id="otg.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">getspark_ml_evaluator</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Evaluator</span></code>
 
-<a href="#otg.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3066,14 +3411,14 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="do
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/evaluator.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">119</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">118</span>
+<span class="normal">119</span>
 <span class="normal">120</span>
 <span class="normal">121</span>
 <span class="normal">122</span>
 <span class="normal">123</span>
-<span class="normal">124</span>
-<span class="normal">125</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getspark_ml_evaluator</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Evaluator</span><span class="p">:</span>
+<span class="normal">124</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getspark_ml_evaluator</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Evaluator</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Get the spark_ml_evaluator parameter.</span>
 
 <span class="sd">    Returns:</span>
@@ -3091,11 +3436,10 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator" class="do
 
 
 
-
-<h3 id="otg.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">getwandb_project_name</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Any</span></code>
 
-<a href="#otg.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3127,14 +3471,14 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="do
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/evaluator.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">135</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">134</span>
+<span class="normal">135</span>
 <span class="normal">136</span>
 <span class="normal">137</span>
 <span class="normal">138</span>
 <span class="normal">139</span>
-<span class="normal">140</span>
-<span class="normal">141</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getwandb_project_name</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Any</span><span class="p">:</span>
+<span class="normal">140</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getwandb_project_name</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Any</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Get the wandb_project_name parameter.</span>
 
 <span class="sd">    Returns:</span>
@@ -3152,11 +3496,10 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getwandb_project_name" class="do
 
 
 
+<h3 id="gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">getwandb_run</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">Run</span></code>
 
-<h3 id="otg.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="doc doc-heading">
-          <code class="highlight language-python"><span class="n">getwandb_run</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="n">wandb</span><span class="o">.</span><span class="n">sdk</span><span class="o">.</span><span class="n">wandb_run</span><span class="o">.</span><span class="n">Run</span></code>
-
-<a href="#otg.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3169,18 +3512,18 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="doc doc-hea
   <table>
     <thead>
       <tr>
-        <th>Type</th>
+<th>Name</th>        <th>Type</th>
         <th>Description</th>
       </tr>
     </thead>
     <tbody>
         <tr>
-          <td>
+<td><code>Run</code></td>          <td>
                 <code><span title="wandb.sdk.wandb_run.Run">Run</span></code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>wandb.sdk.wandb_run.Run: Wandb run object.</p>
+              <p>Wandb run object.</p>
             </div>
           </td>
         </tr>
@@ -3188,18 +3531,18 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="doc doc-hea
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/evaluator.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">127</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">126</span>
+<span class="normal">127</span>
 <span class="normal">128</span>
 <span class="normal">129</span>
 <span class="normal">130</span>
 <span class="normal">131</span>
-<span class="normal">132</span>
-<span class="normal">133</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getwandb_run</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">wandb</span><span class="o">.</span><span class="n">sdk</span><span class="o">.</span><span class="n">wandb_run</span><span class="o">.</span><span class="n">Run</span><span class="p">:</span>
+<span class="normal">132</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">getwandb_run</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Run</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Get the wandb_run parameter.</span>
 
 <span class="sd">    Returns:</span>
-<span class="sd">        wandb.sdk.wandb_run.Run: Wandb run object.</span>
+<span class="sd">        Run: Wandb run object.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">getOrDefault</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">wandb_run</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
@@ -3213,11 +3556,10 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.getwandb_run" class="doc doc-hea
 
 
 
-
-<h3 id="otg.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">setlabel_values</span><span class="p">(</span><span class="n">value</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
 
-<a href="#otg.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3255,14 +3597,14 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="doc doc-
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/evaluator.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">111</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">110</span>
+<span class="normal">111</span>
 <span class="normal">112</span>
 <span class="normal">113</span>
 <span class="normal">114</span>
 <span class="normal">115</span>
-<span class="normal">116</span>
-<span class="normal">117</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">setlabel_values</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="normal">116</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">setlabel_values</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Set the label_values parameter.</span>
 
 <span class="sd">    Args:</span>
@@ -3280,11 +3622,10 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setlabel_values" class="doc doc-
 
 
 
-
-<h3 id="otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">setspark_ml_evaluator</span><span class="p">(</span><span class="n">value</span><span class="p">:</span> <span class="n">Evaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
 
-<a href="#otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3322,14 +3663,14 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="do
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/evaluator.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">103</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/evaluator.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">102</span>
+<span class="normal">103</span>
 <span class="normal">104</span>
 <span class="normal">105</span>
 <span class="normal">106</span>
 <span class="normal">107</span>
-<span class="normal">108</span>
-<span class="normal">109</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">setspark_ml_evaluator</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="n">Evaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="normal">108</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">setspark_ml_evaluator</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">WandbEvaluator</span><span class="p">,</span> <span class="n">value</span><span class="p">:</span> <span class="n">Evaluator</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Set the spark_ml_evaluator parameter.</span>
 
 <span class="sd">    Args:</span>
@@ -3348,6 +3689,7 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="do
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3371,7 +3713,7 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="do
         <span class="icon twemoji">
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         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T15:56:05+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3384,11 +3726,11 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="do
       <li class="contributors-holder">
         <ul class="contributors" data-bi-name="contributors"><li>
             <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
+              href="https://github.com/d0choa"
+              title="d0choa"
               data-bi-name="contributorprofile"
               target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
+              ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
             /></a>
           </li></ul>
       </li>
@@ -3438,7 +3780,7 @@ <h3 id="otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator" class="do
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/method/l2g/feature_factory/index.html b/python_api/methods/l2g/feature_factory/index.html
similarity index 63%
rename from python_api/method/l2g/feature_factory/index.html
rename to python_api/methods/l2g/feature_factory/index.html
index 9072c6896..3cf4a77ae 100644
--- a/python_api/method/l2g/feature_factory/index.html
+++ b/python_api/methods/l2g/feature_factory/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Feature Factory - Open Targets Genetics</title>
+        <title>L2G Feature Factory - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.l2g.feature_factory.ColocalisationFactory" class="md-skip">
+        <a href="#gentropy.method.l2g.feature_factory.ColocalisationFactory" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
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+      
+        
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+  
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       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
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-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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@@ -414,6 +448,123 @@
         
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+            <span class="md-nav__icon md-icon"></span>
+            How-to
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
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+                
+  
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+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
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+    </li>
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+
+              
+            
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+                
+  
+  
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+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
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+  
+
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+            
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+        </nav>
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+  
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+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+    </li>
+  
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+      
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+    
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+    
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+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
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+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -531,7 +682,7 @@
         
         
         
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
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-    Dataset
+    Datasets
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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@@ -612,7 +763,7 @@
   
   
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-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
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-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
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-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,32 +1804,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_method/" class="md-nav__link ">
+            <a href="../../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../clumping/" class="md-nav__link">
+      <a href="../../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1742,11 +1861,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../coloc/" class="md-nav__link">
+      <a href="../../clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1763,11 +1882,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ecaviar/" class="md-nav__link">
+      <a href="../../coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1903,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ld_annotator/" class="md-nav__link">
+      <a href="../../ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1924,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../pics/" class="md-nav__link">
+      <a href="../../ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1826,11 +1945,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../window_based_clumping/" class="md-nav__link">
+      <a href="../../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1858,7 +1977,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" checked>
         
           
           
@@ -1874,14 +1993,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1957,7 +2076,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.ColocalisationFactory" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.ColocalisationFactory" class="md-nav__link">
     <span class="md-ellipsis">
       ColocalisationFactory
     </span>
@@ -1966,7 +2085,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.StudyLocusFactory" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.StudyLocusFactory" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocusFactory
     </span>
@@ -2057,32 +2176,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2093,11 +2212,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2114,11 +2233,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2135,11 +2254,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2156,11 +2275,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2177,11 +2296,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2198,11 +2317,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2219,11 +2338,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2240,11 +2359,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2261,11 +2380,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2282,11 +2401,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2303,11 +2422,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2324,11 +2443,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2345,11 +2464,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2366,11 +2485,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2420,7 +2602,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.ColocalisationFactory" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.ColocalisationFactory" class="md-nav__link">
     <span class="md-ellipsis">
       ColocalisationFactory
     </span>
@@ -2429,7 +2611,7 @@
 </li>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.feature_factory.StudyLocusFactory" class="md-nav__link">
+  <a href="#gentropy.method.l2g.feature_factory.StudyLocusFactory" class="md-nav__link">
     <span class="md-ellipsis">
       StudyLocusFactory
     </span>
@@ -2461,12 +2643,11 @@ <h1>L2G Feature Factory</h1>
 
 
 
-
-<h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-heading">
-          <code>otg.method.l2g.feature_factory.ColocalisationFactory</code>
+<h2 id="gentropy.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-heading">
+          <code>gentropy.method.l2g.feature_factory.ColocalisationFactory</code>
 
 
-<a href="#otg.method.l2g.feature_factory.ColocalisationFactory" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.l2g.feature_factory.ColocalisationFactory" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2475,10 +2656,8 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
       <p>Feature extraction in colocalisation.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/l2g/feature_factory.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 22</span>
-<span class="normal"> 23</span>
-<span class="normal"> 24</span>
+              <summary>Source code in <code>src/gentropy/method/l2g/feature_factory.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 24</span>
 <span class="normal"> 25</span>
 <span class="normal"> 26</span>
 <span class="normal"> 27</span>
@@ -2639,7 +2818,41 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
 <span class="normal">182</span>
 <span class="normal">183</span>
 <span class="normal">184</span>
-<span class="normal">185</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">ColocalisationFactory</span><span class="p">:</span>
+<span class="normal">185</span>
+<span class="normal">186</span>
+<span class="normal">187</span>
+<span class="normal">188</span>
+<span class="normal">189</span>
+<span class="normal">190</span>
+<span class="normal">191</span>
+<span class="normal">192</span>
+<span class="normal">193</span>
+<span class="normal">194</span>
+<span class="normal">195</span>
+<span class="normal">196</span>
+<span class="normal">197</span>
+<span class="normal">198</span>
+<span class="normal">199</span>
+<span class="normal">200</span>
+<span class="normal">201</span>
+<span class="normal">202</span>
+<span class="normal">203</span>
+<span class="normal">204</span>
+<span class="normal">205</span>
+<span class="normal">206</span>
+<span class="normal">207</span>
+<span class="normal">208</span>
+<span class="normal">209</span>
+<span class="normal">210</span>
+<span class="normal">211</span>
+<span class="normal">212</span>
+<span class="normal">213</span>
+<span class="normal">214</span>
+<span class="normal">215</span>
+<span class="normal">216</span>
+<span class="normal">217</span>
+<span class="normal">218</span>
+<span class="normal">219</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">ColocalisationFactory</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Feature extraction in colocalisation.&quot;&quot;&quot;</span>
 
     <span class="nd">@staticmethod</span>
@@ -2669,17 +2882,17 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
             <span class="p">)</span>
         <span class="k">if</span> <span class="n">colocalisation_method</span> <span class="o">==</span> <span class="s2">&quot;COLOC&quot;</span><span class="p">:</span>
             <span class="n">coloc_score_col_name</span> <span class="o">=</span> <span class="s2">&quot;log2h4h3&quot;</span>
-            <span class="n">coloc_feature_col_template</span> <span class="o">=</span> <span class="s2">&quot;max_coloc_llr&quot;</span>
+            <span class="n">coloc_feature_col_template</span> <span class="o">=</span> <span class="s2">&quot;ColocLlrMaximum&quot;</span>
 
         <span class="k">elif</span> <span class="n">colocalisation_method</span> <span class="o">==</span> <span class="s2">&quot;eCAVIAR&quot;</span><span class="p">:</span>
             <span class="n">coloc_score_col_name</span> <span class="o">=</span> <span class="s2">&quot;clpp&quot;</span>
-            <span class="n">coloc_feature_col_template</span> <span class="o">=</span> <span class="s2">&quot;max_coloc_clpp&quot;</span>
+            <span class="n">coloc_feature_col_template</span> <span class="o">=</span> <span class="s2">&quot;ColocClppMaximum&quot;</span>
 
         <span class="n">colocalising_study_locus</span> <span class="o">=</span> <span class="p">(</span>
             <span class="n">study_locus</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
             <span class="c1"># annotate studyLoci with overlapping IDs on the left - to just keep GWAS associations</span>
             <span class="o">.</span><span class="n">join</span><span class="p">(</span>
-                <span class="n">colocalisation</span><span class="o">.</span><span class="n">_df</span><span class="o">.</span><span class="n">selectExpr</span><span class="p">(</span>
+                <span class="n">colocalisation</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">selectExpr</span><span class="p">(</span>
                     <span class="s2">&quot;leftStudyLocusId as studyLocusId&quot;</span><span class="p">,</span>
                     <span class="s2">&quot;rightStudyLocusId&quot;</span><span class="p">,</span>
                     <span class="s2">&quot;colocalisationMethod&quot;</span><span class="p">,</span>
@@ -2698,7 +2911,7 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
             <span class="p">)</span>
             <span class="o">.</span><span class="n">join</span><span class="p">(</span>
                 <span class="n">f</span><span class="o">.</span><span class="n">broadcast</span><span class="p">(</span>
-                    <span class="n">studies</span><span class="o">.</span><span class="n">_df</span><span class="o">.</span><span class="n">selectExpr</span><span class="p">(</span>
+                    <span class="n">studies</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">selectExpr</span><span class="p">(</span>
                         <span class="s2">&quot;studyId as right_studyId&quot;</span><span class="p">,</span>
                         <span class="s2">&quot;studyType as right_studyType&quot;</span><span class="p">,</span>
                         <span class="s2">&quot;geneId&quot;</span><span class="p">,</span>
@@ -2714,57 +2927,93 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
             <span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;right_studyType&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">,</span> <span class="s2">&quot;coloc_score&quot;</span><span class="p">)</span>
         <span class="p">)</span>
 
-        <span class="c1"># Max LLR calculation per studyLocus AND type of QTL</span>
+        <span class="c1"># Max PP calculation per studyLocus AND type of QTL</span>
         <span class="n">local_max</span> <span class="o">=</span> <span class="n">get_record_with_maximum_value</span><span class="p">(</span>
             <span class="n">colocalising_study_locus</span><span class="p">,</span>
             <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;right_studyType&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span>
             <span class="s2">&quot;coloc_score&quot;</span><span class="p">,</span>
-        <span class="p">)</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+
+        <span class="n">intercept</span> <span class="o">=</span> <span class="mf">0.0001</span>
         <span class="n">neighbourhood_max</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="n">get_record_with_maximum_value</span><span class="p">(</span>
-                <span class="n">colocalising_study_locus</span><span class="p">,</span>
-                <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;right_studyType&quot;</span><span class="p">],</span>
-                <span class="s2">&quot;coloc_score&quot;</span><span class="p">,</span>
-            <span class="p">)</span>
-            <span class="o">.</span><span class="n">join</span><span class="p">(</span>
-                <span class="n">local_max</span><span class="o">.</span><span class="n">selectExpr</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;coloc_score as coloc_local_max&quot;</span><span class="p">),</span>
-                <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
-                <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">,</span>
-            <span class="p">)</span>
-            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">_nbh&quot;</span><span class="p">,</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;coloc_local_max&quot;</span><span class="p">)</span> <span class="o">-</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;coloc_score&quot;</span><span class="p">),</span>
+            <span class="p">(</span>
+                <span class="n">local_max</span><span class="o">.</span><span class="n">selectExpr</span><span class="p">(</span>
+                    <span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;coloc_score as coloc_local_max&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="c1"># Add maximum in the neighborhood</span>
+                    <span class="n">get_record_with_maximum_value</span><span class="p">(</span>
+                        <span class="n">colocalising_study_locus</span><span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span>
+                            <span class="s2">&quot;coloc_score&quot;</span><span class="p">,</span> <span class="s2">&quot;coloc_neighborhood_max&quot;</span>
+                        <span class="p">),</span>
+                        <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;right_studyType&quot;</span><span class="p">],</span>
+                        <span class="s2">&quot;coloc_neighborhood_max&quot;</span><span class="p">,</span>
+                    <span class="p">)</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">),</span>
+                    <span class="n">on</span><span class="o">=</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                    <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">Neighborhood&quot;</span><span class="p">,</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">log10</span><span class="p">(</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">abs</span><span class="p">(</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;coloc_local_max&quot;</span><span class="p">)</span>
+                            <span class="o">-</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;coloc_neighborhood_max&quot;</span><span class="p">)</span>
+                            <span class="o">+</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="n">intercept</span><span class="p">)</span>
+                        <span class="p">)</span>
+                    <span class="p">),</span>
+                <span class="p">)</span>
             <span class="p">)</span>
+            <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;coloc_neighborhood_max&quot;</span><span class="p">,</span> <span class="s2">&quot;coloc_local_max&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">persist</span><span class="p">()</span>
         <span class="p">)</span>
 
         <span class="c1"># Split feature per molQTL</span>
         <span class="n">local_dfs</span> <span class="o">=</span> <span class="p">[]</span>
         <span class="n">nbh_dfs</span> <span class="o">=</span> <span class="p">[]</span>
-        <span class="k">for</span> <span class="n">qtl_type</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;eqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;sqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;pqtl&quot;</span><span class="p">]:</span>
-            <span class="n">local_max</span> <span class="o">=</span> <span class="n">local_max</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">)</span> <span class="o">==</span> <span class="n">qtl_type</span>
-            <span class="p">)</span><span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span>
-                <span class="s2">&quot;coloc_score&quot;</span><span class="p">,</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">qtl_type</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">_local&quot;</span>
+        <span class="n">qtl_types</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">colocalising_study_locus</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">distinct</span><span class="p">()</span>
+            <span class="o">.</span><span class="n">toPandas</span><span class="p">()[</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">]</span>
+            <span class="o">.</span><span class="n">tolist</span><span class="p">()</span>
+        <span class="p">)</span> <span class="ow">or</span> <span class="p">[</span><span class="s2">&quot;eqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;pqtl&quot;</span><span class="p">,</span> <span class="s2">&quot;sqtl&quot;</span><span class="p">]</span>
+        <span class="k">for</span> <span class="n">qtl_type</span> <span class="ow">in</span> <span class="n">qtl_types</span><span class="p">:</span>
+            <span class="n">filtered_local_max</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">local_max</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">)</span> <span class="o">==</span> <span class="n">qtl_type</span><span class="p">)</span>
+                <span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span>
+                    <span class="s2">&quot;coloc_score&quot;</span><span class="p">,</span>
+                    <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">qtl_type</span><span class="si">}{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">)</span>
             <span class="p">)</span>
-            <span class="n">local_dfs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">local_max</span><span class="p">)</span>
-
-            <span class="n">neighbourhood_max</span> <span class="o">=</span> <span class="n">neighbourhood_max</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
-                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">)</span> <span class="o">==</span> <span class="n">qtl_type</span>
-            <span class="p">)</span><span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">_nbh&quot;</span><span class="p">,</span>
-                <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">qtl_type</span><span class="si">}</span><span class="s2">_</span><span class="si">{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">_nbh&quot;</span><span class="p">,</span>
+            <span class="n">local_dfs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filtered_local_max</span><span class="p">)</span>
+
+            <span class="n">filtered_neighbourhood_max</span> <span class="o">=</span> <span class="p">(</span>
+                <span class="n">neighbourhood_max</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">)</span> <span class="o">==</span> <span class="n">qtl_type</span><span class="p">)</span>
+                <span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span>
+                    <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">Neighborhood&quot;</span><span class="p">,</span>
+                    <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="n">qtl_type</span><span class="si">}{</span><span class="n">coloc_feature_col_template</span><span class="si">}</span><span class="s2">Neighborhood&quot;</span><span class="p">,</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;right_studyType&quot;</span><span class="p">)</span>
             <span class="p">)</span>
-            <span class="n">nbh_dfs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">neighbourhood_max</span><span class="p">)</span>
+            <span class="n">nbh_dfs</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">filtered_neighbourhood_max</span><span class="p">)</span>
 
         <span class="n">wide_dfs</span> <span class="o">=</span> <span class="n">reduce</span><span class="p">(</span>
             <span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">allowMissingColumns</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
             <span class="n">local_dfs</span> <span class="o">+</span> <span class="n">nbh_dfs</span><span class="p">,</span>
-            <span class="n">colocalising_study_locus</span><span class="o">.</span><span class="n">limit</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span>
         <span class="p">)</span>
 
         <span class="k">return</span> <span class="n">L2GFeature</span><span class="p">(</span>
             <span class="n">_df</span><span class="o">=</span><span class="n">convert_from_wide_to_long</span><span class="p">(</span>
-                <span class="n">wide_dfs</span><span class="p">,</span>
+                <span class="n">wide_dfs</span><span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">agg</span><span class="p">(</span>
+                    <span class="o">*</span><span class="p">(</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">first</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="n">c</span><span class="p">),</span> <span class="n">ignorenulls</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>
+                        <span class="k">for</span> <span class="n">c</span> <span class="ow">in</span> <span class="n">wide_dfs</span><span class="o">.</span><span class="n">columns</span>
+                        <span class="k">if</span> <span class="n">c</span>
+                        <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span>
+                            <span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
+                            <span class="s2">&quot;geneId&quot;</span><span class="p">,</span>
+                        <span class="p">]</span>
+                    <span class="p">)</span>
+                <span class="p">),</span>
                 <span class="n">id_vars</span><span class="o">=</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">),</span>
                 <span class="n">var_name</span><span class="o">=</span><span class="s2">&quot;featureName&quot;</span><span class="p">,</span>
                 <span class="n">value_name</span><span class="o">=</span><span class="s2">&quot;featureValue&quot;</span><span class="p">,</span>
@@ -2778,6 +3027,8 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
     <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeature</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Calls _get_max_coloc_per_study_locus for both methods and concatenates the results.</span>
 
+<span class="sd">        !!! note &quot;Colocalisation features are only available for the eCAVIAR results for now.&quot;</span>
+
 <span class="sd">        Args:</span>
 <span class="sd">            study_locus (StudyLocus): Study locus dataset</span>
 <span class="sd">            studies (StudyIndex): Study index dataset</span>
@@ -2786,12 +3037,6 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
 <span class="sd">        Returns:</span>
 <span class="sd">            L2GFeature: Stores the features with the max coloc probabilities for each pair of study-locus</span>
 <span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">coloc_llr</span> <span class="o">=</span> <span class="n">ColocalisationFactory</span><span class="o">.</span><span class="n">_get_max_coloc_per_study_locus</span><span class="p">(</span>
-            <span class="n">study_locus</span><span class="p">,</span>
-            <span class="n">studies</span><span class="p">,</span>
-            <span class="n">colocalisation</span><span class="p">,</span>
-            <span class="s2">&quot;COLOC&quot;</span><span class="p">,</span>
-        <span class="p">)</span>
         <span class="n">coloc_clpp</span> <span class="o">=</span> <span class="n">ColocalisationFactory</span><span class="o">.</span><span class="n">_get_max_coloc_per_study_locus</span><span class="p">(</span>
             <span class="n">study_locus</span><span class="p">,</span>
             <span class="n">studies</span><span class="p">,</span>
@@ -2800,7 +3045,7 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
         <span class="p">)</span>
 
         <span class="k">return</span> <span class="n">L2GFeature</span><span class="p">(</span>
-            <span class="n">_df</span><span class="o">=</span><span class="n">coloc_llr</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">coloc_clpp</span><span class="o">.</span><span class="n">df</span><span class="p">,</span> <span class="n">allowMissingColumns</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">coloc_clpp</span><span class="o">.</span><span class="n">df</span><span class="p">,</span>
             <span class="n">_schema</span><span class="o">=</span><span class="n">L2GFeature</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
         <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
@@ -2824,64 +3069,30 @@ <h2 id="otg.method.l2g.feature_factory.ColocalisationFactory" class="doc doc-hea
 
   </div>
 
+
 </div>
 
 <div class="doc doc-object doc-class">
 
 
 
-
-<h2 id="otg.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading">
-          <code>otg.method.l2g.feature_factory.StudyLocusFactory</code>
+<h2 id="gentropy.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading">
+          <code>gentropy.method.l2g.feature_factory.StudyLocusFactory</code>
 
 
-<a href="#otg.method.l2g.feature_factory.StudyLocusFactory" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.l2g.feature_factory.StudyLocusFactory" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
           <p class="doc doc-class-bases">
-            Bases: <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code></p>
+            Bases: <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code></p>
 
   
       <p>Feature extraction in study locus.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/l2g/feature_factory.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">188</span>
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+              <summary>Source code in <code>src/gentropy/method/l2g/feature_factory.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">222</span>
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 <span class="normal">231</span>
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-<span class="normal">234</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">StudyLocusFactory</span><span class="p">(</span><span class="n">StudyLocus</span><span class="p">):</span>
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+<span class="normal">386</span>
+<span class="normal">387</span>
+<span class="normal">388</span>
+<span class="normal">389</span>
+<span class="normal">390</span>
+<span class="normal">391</span>
+<span class="normal">392</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">StudyLocusFactory</span><span class="p">(</span><span class="n">StudyLocus</span><span class="p">):</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Feature extraction in study locus.&quot;&quot;&quot;</span>
 
     <span class="nd">@staticmethod</span>
@@ -2940,6 +3309,130 @@ <h2 id="otg.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading
             <span class="p">),</span>
             <span class="n">_schema</span><span class="o">=</span><span class="n">L2GFeature</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
         <span class="p">)</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">_get_vep_features</span><span class="p">(</span>
+        <span class="n">credible_set</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
+        <span class="n">v2g</span><span class="p">:</span> <span class="n">V2G</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">L2GFeature</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Get the maximum VEP score for all variants in a locus&#39;s 95% credible set.</span>
+
+<span class="sd">        This informs about functional impact of the variants in the locus. For more information on variant consequences, see: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html</span>
+<span class="sd">        Two metrics: max VEP score per study locus and gene, and max VEP score per study locus.</span>
+
+
+<span class="sd">        Args:</span>
+<span class="sd">            credible_set (StudyLocus): Study locus dataset with the associations to be annotated</span>
+<span class="sd">            v2g (V2G): V2G dataset with the variant/gene relationships and their consequences</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            L2GFeature: Stores the features with the max VEP score.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+
+        <span class="k">def</span> <span class="nf">_aggregate_vep_feature</span><span class="p">(</span>
+            <span class="n">df</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
+            <span class="n">aggregation_expr</span><span class="p">:</span> <span class="n">Column</span><span class="p">,</span>
+            <span class="n">aggregation_cols</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+            <span class="n">feature_name</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">            </span><span class="sd">&quot;&quot;&quot;Extracts the maximum or average VEP score after grouping by the given columns. Different aggregations return different predictive annotations.</span>
+
+<span class="sd">            If the group_cols include &quot;geneId&quot;, the maximum/mean VEP score per gene is returned.</span>
+<span class="sd">            Otherwise, the maximum/mean VEP score for all genes in the neighborhood of the locus is returned.</span>
+
+<span class="sd">            Args:</span>
+<span class="sd">                df (DataFrame): DataFrame with the VEP scores for each variant in a studyLocus</span>
+<span class="sd">                aggregation_expr (Column): Aggregation expression to apply</span>
+<span class="sd">                aggregation_cols (list[str]): Columns to group by</span>
+<span class="sd">                feature_name (str): Name of the feature to be returned</span>
+
+<span class="sd">            Returns:</span>
+<span class="sd">                DataFrame: DataFrame with the maximum VEP score per locus or per locus/gene</span>
+<span class="sd">            &quot;&quot;&quot;</span>
+            <span class="k">if</span> <span class="s2">&quot;geneId&quot;</span> <span class="ow">in</span> <span class="n">aggregation_cols</span><span class="p">:</span>
+                <span class="k">return</span> <span class="n">df</span><span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="n">aggregation_cols</span><span class="p">)</span><span class="o">.</span><span class="n">agg</span><span class="p">(</span>
+                    <span class="n">aggregation_expr</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">feature_name</span><span class="p">)</span>
+                <span class="p">)</span>
+            <span class="k">return</span> <span class="p">(</span>
+                <span class="n">df</span><span class="o">.</span><span class="n">groupBy</span><span class="p">(</span><span class="n">aggregation_cols</span><span class="p">)</span>
+                <span class="o">.</span><span class="n">agg</span><span class="p">(</span>
+                    <span class="n">aggregation_expr</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="n">feature_name</span><span class="p">),</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">collect_set</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">),</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">explode</span><span class="p">(</span><span class="s2">&quot;geneId&quot;</span><span class="p">))</span>
+            <span class="p">)</span>
+
+        <span class="n">credible_set_w_variant_consequences</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">credible_set</span><span class="o">.</span><span class="n">filter_credible_set</span><span class="p">(</span><span class="n">CredibleInterval</span><span class="o">.</span><span class="n">IS95</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">withColumn</span><span class="p">(</span><span class="s2">&quot;variantInLocusId&quot;</span><span class="p">,</span> <span class="n">f</span><span class="o">.</span><span class="n">explode</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.variantId&quot;</span><span class="p">)))</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                <span class="s2">&quot;variantInLocusPosteriorProbability&quot;</span><span class="p">,</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">explode</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;locus.posteriorProbability&quot;</span><span class="p">)),</span>
+            <span class="p">)</span>
+            <span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="c1"># Join with V2G to get variant consequences</span>
+                <span class="n">v2g</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;datasourceId&quot;</span><span class="p">)</span> <span class="o">==</span> <span class="s2">&quot;variantConsequence&quot;</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">withColumnRenamed</span><span class="p">(</span><span class="s2">&quot;variantId&quot;</span><span class="p">,</span> <span class="s2">&quot;variantInLocusId&quot;</span><span class="p">),</span>
+                <span class="n">on</span><span class="o">=</span><span class="s2">&quot;variantInLocusId&quot;</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                <span class="s2">&quot;weightedScore&quot;</span><span class="p">,</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;score&quot;</span><span class="p">)</span> <span class="o">*</span> <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;variantInLocusPosteriorProbability&quot;</span><span class="p">),</span>
+            <span class="p">)</span>
+            <span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                <span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;variantId&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;studyId&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;geneId&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;score&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;weightedScore&quot;</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="o">.</span><span class="n">distinct</span><span class="p">()</span>
+            <span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">L2GFeature</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">convert_from_wide_to_long</span><span class="p">(</span>
+                <span class="n">reduce</span><span class="p">(</span>
+                    <span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">allowMissingColumns</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+                    <span class="p">[</span>
+                        <span class="c1"># Calculate overall max VEP score for all genes in the vicinity</span>
+                        <span class="n">credible_set_w_variant_consequences</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span>
+                            <span class="n">_aggregate_vep_feature</span><span class="p">,</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="s2">&quot;score&quot;</span><span class="p">),</span>
+                            <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">],</span>
+                            <span class="s2">&quot;vepMaximumNeighborhood&quot;</span><span class="p">,</span>
+                        <span class="p">),</span>
+                        <span class="c1"># Calculate overall max VEP score per gene</span>
+                        <span class="n">credible_set_w_variant_consequences</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span>
+                            <span class="n">_aggregate_vep_feature</span><span class="p">,</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="s2">&quot;score&quot;</span><span class="p">),</span>
+                            <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span>
+                            <span class="s2">&quot;vepMaximum&quot;</span><span class="p">,</span>
+                        <span class="p">),</span>
+                        <span class="c1"># Calculate mean VEP score for all genes in the vicinity</span>
+                        <span class="n">credible_set_w_variant_consequences</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span>
+                            <span class="n">_aggregate_vep_feature</span><span class="p">,</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="s2">&quot;weightedScore&quot;</span><span class="p">),</span>
+                            <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">],</span>
+                            <span class="s2">&quot;vepMeanNeighborhood&quot;</span><span class="p">,</span>
+                        <span class="p">),</span>
+                        <span class="c1"># Calculate mean VEP score per gene</span>
+                        <span class="n">credible_set_w_variant_consequences</span><span class="o">.</span><span class="n">transform</span><span class="p">(</span>
+                            <span class="n">_aggregate_vep_feature</span><span class="p">,</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="s2">&quot;weightedScore&quot;</span><span class="p">),</span>
+                            <span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span>
+                            <span class="s2">&quot;vepMean&quot;</span><span class="p">,</span>
+                        <span class="p">),</span>
+                    <span class="p">],</span>
+                <span class="p">),</span>
+                <span class="n">id_vars</span><span class="o">=</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">),</span>
+                <span class="n">var_name</span><span class="o">=</span><span class="s2">&quot;featureName&quot;</span><span class="p">,</span>
+                <span class="n">value_name</span><span class="o">=</span><span class="s2">&quot;featureValue&quot;</span><span class="p">,</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;featureValue&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">()),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="n">L2GFeature</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
             </details>
 
@@ -2961,6 +3454,7 @@ <h2 id="otg.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2984,7 +3478,7 @@ <h2 id="otg.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2995,23 +3489,7 @@ <h2 id="otg.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading
         <span class="label"> Contributors </span>
       </li>
       <li class="contributors-holder">
-        <ul class="contributors" data-bi-name="contributors"><li>
-            <a
-              href="https://github.com/d0choa"
-              title="d0choa"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/5097586?v=4" alt="d0choa"
-            /></a>
-          </li><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
-          </li></ul>
+        <ul class="contributors" data-bi-name="contributors"></ul>
       </li>
     </ul>
   </small>
@@ -3059,7 +3537,7 @@ <h2 id="otg.method.l2g.feature_factory.StudyLocusFactory" class="doc doc-heading
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/method/l2g/model/index.html b/python_api/methods/l2g/model/index.html
similarity index 87%
rename from python_api/method/l2g/model/index.html
rename to python_api/methods/l2g/model/index.html
index 213b036f1..0098fd513 100644
--- a/python_api/method/l2g/model/index.html
+++ b/python_api/methods/l2g/model/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Model - Open Targets Genetics</title>
+        <title>L2G Model - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.l2g.model.LocusToGeneModel" class="md-skip">
+        <a href="#gentropy.method.l2g.model.LocusToGeneModel" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
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+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
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+            Datasets
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     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
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@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
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     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
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     <li class="md-nav__item">
-      <a href="../../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
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     <li class="md-nav__item">
-      <a href="../../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
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-      <a href="../../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
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@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
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@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,32 +1804,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_method/" class="md-nav__link ">
+            <a href="../../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../clumping/" class="md-nav__link">
+      <a href="../../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1742,11 +1861,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../coloc/" class="md-nav__link">
+      <a href="../../clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1763,11 +1882,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ecaviar/" class="md-nav__link">
+      <a href="../../coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1903,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ld_annotator/" class="md-nav__link">
+      <a href="../../ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1924,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../pics/" class="md-nav__link">
+      <a href="../../ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1826,11 +1945,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../window_based_clumping/" class="md-nav__link">
+      <a href="../../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1858,7 +1977,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" checked>
         
           
           
@@ -1874,14 +1993,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1978,7 +2097,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel" class="md-nav__link">
     <span class="md-ellipsis">
       LocusToGeneModel
     </span>
@@ -1988,7 +2107,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.classifier" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.classifier" class="md-nav__link">
     <span class="md-ellipsis">
       classifier
     </span>
@@ -1997,7 +2116,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.feature_name_map" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.feature_name_map" class="md-nav__link">
     <span class="md-ellipsis">
       feature_name_map
     </span>
@@ -2006,90 +2125,90 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="md-nav__link">
     <span class="md-ellipsis">
-      add_pipeline_stage()
+      add_pipeline_stage
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.evaluate" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.evaluate" class="md-nav__link">
     <span class="md-ellipsis">
-      evaluate()
+      evaluate
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="md-nav__link">
     <span class="md-ellipsis">
-      features_vector_assembler()
+      features_vector_assembler
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.fit" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.fit" class="md-nav__link">
     <span class="md-ellipsis">
-      fit()
+      fit
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.get_feature_importance" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.get_feature_importance" class="md-nav__link">
     <span class="md-ellipsis">
-      get_feature_importance()
+      get_feature_importance
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.get_param_grid" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.get_param_grid" class="md-nav__link">
     <span class="md-ellipsis">
-      get_param_grid()
+      get_param_grid
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.load_from_disk" class="md-nav__link">
     <span class="md-ellipsis">
-      load_from_disk()
+      load_from_disk
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.log_to_wandb" class="md-nav__link">
     <span class="md-ellipsis">
-      log_to_wandb()
+      log_to_wandb
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.predict" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.predict" class="md-nav__link">
     <span class="md-ellipsis">
-      predict()
+      predict
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.save" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.save" class="md-nav__link">
     <span class="md-ellipsis">
-      save()
+      save
     </span>
   </a>
   
@@ -2162,32 +2281,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2198,11 +2317,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2219,11 +2338,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2240,11 +2359,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2261,11 +2380,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2282,11 +2401,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2303,11 +2422,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2324,11 +2443,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2345,11 +2464,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2366,11 +2485,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2387,11 +2506,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2408,11 +2527,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2429,11 +2548,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2450,11 +2569,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2471,11 +2590,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2525,7 +2707,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel" class="md-nav__link">
     <span class="md-ellipsis">
       LocusToGeneModel
     </span>
@@ -2535,7 +2717,7 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.classifier" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.classifier" class="md-nav__link">
     <span class="md-ellipsis">
       classifier
     </span>
@@ -2544,7 +2726,7 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.feature_name_map" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.feature_name_map" class="md-nav__link">
     <span class="md-ellipsis">
       feature_name_map
     </span>
@@ -2553,90 +2735,90 @@
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="md-nav__link">
     <span class="md-ellipsis">
-      add_pipeline_stage()
+      add_pipeline_stage
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.evaluate" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.evaluate" class="md-nav__link">
     <span class="md-ellipsis">
-      evaluate()
+      evaluate
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="md-nav__link">
     <span class="md-ellipsis">
-      features_vector_assembler()
+      features_vector_assembler
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.fit" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.fit" class="md-nav__link">
     <span class="md-ellipsis">
-      fit()
+      fit
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.get_feature_importance" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.get_feature_importance" class="md-nav__link">
     <span class="md-ellipsis">
-      get_feature_importance()
+      get_feature_importance
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.get_param_grid" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.get_param_grid" class="md-nav__link">
     <span class="md-ellipsis">
-      get_param_grid()
+      get_param_grid
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.load_from_disk" class="md-nav__link">
     <span class="md-ellipsis">
-      load_from_disk()
+      load_from_disk
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.log_to_wandb" class="md-nav__link">
     <span class="md-ellipsis">
-      log_to_wandb()
+      log_to_wandb
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.predict" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.predict" class="md-nav__link">
     <span class="md-ellipsis">
-      predict()
+      predict
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.model.LocusToGeneModel.save" class="md-nav__link">
+  <a href="#gentropy.method.l2g.model.LocusToGeneModel.save" class="md-nav__link">
     <span class="md-ellipsis">
-      save()
+      save
     </span>
   </a>
   
@@ -2671,16 +2853,15 @@ <h1>L2G Model</h1>
 
 
 
-
-<h2 id="otg.method.l2g.model.LocusToGeneModel" class="doc doc-heading">
-          <code>otg.method.l2g.model.LocusToGeneModel</code>
+<h2 id="gentropy.method.l2g.model.LocusToGeneModel" class="doc doc-heading">
+          <code>gentropy.method.l2g.model.LocusToGeneModel</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2689,9 +2870,8 @@ <h2 id="otg.method.l2g.model.LocusToGeneModel" class="doc doc-heading">
       <p>Wrapper for the Locus to Gene classifier.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 27</span>
-<span class="normal"> 28</span>
+              <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 28</span>
 <span class="normal"> 29</span>
 <span class="normal"> 30</span>
 <span class="normal"> 31</span>
@@ -2967,7 +3147,8 @@ <h2 id="otg.method.l2g.model.LocusToGeneModel" class="doc doc-heading">
 <span class="normal">301</span>
 <span class="normal">302</span>
 <span class="normal">303</span>
-<span class="normal">304</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
+<span class="normal">304</span>
+<span class="normal">305</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
 <span class="k">class</span> <span class="nc">LocusToGeneModel</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Wrapper for the Locus to Gene classifier.&quot;&quot;&quot;</span>
 
@@ -3069,7 +3250,7 @@ <h2 id="otg.method.l2g.model.LocusToGeneModel" class="doc doc-heading">
         <span class="c1">## Track feature importance</span>
         <span class="n">wandb_run</span><span class="o">.</span><span class="n">log</span><span class="p">({</span><span class="s2">&quot;importances&quot;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_feature_importance</span><span class="p">()})</span>
         <span class="c1">## Track training set</span>
-        <span class="n">training_table</span> <span class="o">=</span> <span class="n">wandb</span><span class="o">.</span><span class="n">Table</span><span class="p">(</span><span class="n">dataframe</span><span class="o">=</span><span class="n">training_data</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">toPandas</span><span class="p">())</span>
+        <span class="n">training_table</span> <span class="o">=</span> <span class="n">Table</span><span class="p">(</span><span class="n">dataframe</span><span class="o">=</span><span class="n">training_data</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">toPandas</span><span class="p">())</span>
         <span class="n">wandb_run</span><span class="o">.</span><span class="n">log</span><span class="p">({</span><span class="s2">&quot;trainingSet&quot;</span><span class="p">:</span> <span class="n">training_table</span><span class="p">})</span>
         <span class="c1"># Count number of positive and negative labels</span>
         <span class="n">gs_counts_dict</span> <span class="o">=</span> <span class="p">{</span>
@@ -3167,7 +3348,7 @@ <h2 id="otg.method.l2g.model.LocusToGeneModel" class="doc doc-heading">
         <span class="p">)</span>
 
         <span class="k">if</span> <span class="n">wandb_run_name</span> <span class="ow">and</span> <span class="n">training_data</span><span class="p">:</span>
-            <span class="n">run</span> <span class="o">=</span> <span class="n">wandb</span><span class="o">.</span><span class="n">init</span><span class="p">(</span>
+            <span class="n">run</span> <span class="o">=</span> <span class="n">wandb_init</span><span class="p">(</span>
                 <span class="n">project</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">wandb_l2g_project_name</span><span class="p">,</span>
                 <span class="n">config</span><span class="o">=</span><span class="n">hyperparameters</span><span class="p">,</span>
                 <span class="n">name</span><span class="o">=</span><span class="n">wandb_run_name</span><span class="p">,</span>
@@ -3262,8 +3443,7 @@ <h2 id="otg.method.l2g.model.LocusToGeneModel" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.classifier" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.classifier" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">classifier</span><span class="p">:</span> <span class="n">Any</span></code>
   
   <span class="doc doc-labels">
@@ -3271,7 +3451,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.classifier" class="doc doc-heading
       <small class="doc doc-label doc-label-writable"><code>writable</code></small>
   </span>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.classifier" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.classifier" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3309,15 +3489,14 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.classifier" class="doc doc-heading
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.feature_name_map" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.feature_name_map" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">feature_name_map</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-property"><code>property</code></small>
   </span>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.feature_name_map" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.feature_name_map" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3382,11 +3561,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.feature_name_map" class="doc doc-h
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">add_pipeline_stage</span><span class="p">(</span><span class="n">transformer</span><span class="p">:</span> <span class="n">Transformer</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3436,7 +3614,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="doc doc
     <tbody>
         <tr>
 <td><code>LocusToGeneModel</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.method.l2g.model.LocusToGeneModel" href="#otg.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.method.l2g.model.LocusToGeneModel" href="#gentropy.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3460,9 +3638,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="doc doc
 </code></pre></div>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">179</span>
-<span class="normal">180</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">180</span>
 <span class="normal">181</span>
 <span class="normal">182</span>
 <span class="normal">183</span>
@@ -3484,7 +3661,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="doc doc
 <span class="normal">199</span>
 <span class="normal">200</span>
 <span class="normal">201</span>
-<span class="normal">202</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">add_pipeline_stage</span><span class="p">(</span>
+<span class="normal">202</span>
+<span class="normal">203</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">add_pipeline_stage</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span> <span class="n">transformer</span><span class="p">:</span> <span class="n">Transformer</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Adds a stage to the L2G pipeline.</span>
@@ -3519,11 +3697,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage" class="doc doc
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.evaluate" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.evaluate" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">evaluate</span><span class="p">(</span><span class="n">results</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">hyperparameters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span> <span class="n">wandb_run_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">,</span> <span class="n">training_data</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.evaluate" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.evaluate" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3588,7 +3765,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.evaluate" class="doc doc-heading">
         <tr>
           <td><code>training_data</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a> | None</code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a> | None</code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3603,9 +3780,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.evaluate" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">204</span>
-<span class="normal">205</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">205</span>
 <span class="normal">206</span>
 <span class="normal">207</span>
 <span class="normal">208</span>
@@ -3636,7 +3812,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.evaluate" class="doc doc-heading">
 <span class="normal">233</span>
 <span class="normal">234</span>
 <span class="normal">235</span>
-<span class="normal">236</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">evaluate</span><span class="p">(</span>
+<span class="normal">236</span>
+<span class="normal">237</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">evaluate</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span>
     <span class="n">results</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
     <span class="n">hyperparameters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span>
@@ -3659,7 +3836,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.evaluate" class="doc doc-heading">
     <span class="p">)</span>
 
     <span class="k">if</span> <span class="n">wandb_run_name</span> <span class="ow">and</span> <span class="n">training_data</span><span class="p">:</span>
-        <span class="n">run</span> <span class="o">=</span> <span class="n">wandb</span><span class="o">.</span><span class="n">init</span><span class="p">(</span>
+        <span class="n">run</span> <span class="o">=</span> <span class="n">wandb_init</span><span class="p">(</span>
             <span class="n">project</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">wandb_l2g_project_name</span><span class="p">,</span>
             <span class="n">config</span><span class="o">=</span><span class="n">hyperparameters</span><span class="p">,</span>
             <span class="n">name</span><span class="o">=</span><span class="n">wandb_run_name</span><span class="p">,</span>
@@ -3680,15 +3857,14 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.evaluate" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">features_vector_assembler</span><span class="p">(</span><span class="n">features_cols</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">VectorAssembler</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
   </span>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3764,9 +3940,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="
 </code></pre></div>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 75</span>
-<span class="normal"> 76</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 76</span>
 <span class="normal"> 77</span>
 <span class="normal"> 78</span>
 <span class="normal"> 79</span>
@@ -3791,7 +3966,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="
 <span class="normal"> 98</span>
 <span class="normal"> 99</span>
 <span class="normal">100</span>
-<span class="normal">101</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+<span class="normal">101</span>
+<span class="normal">102</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
 <span class="k">def</span> <span class="nf">features_vector_assembler</span><span class="p">(</span><span class="n">features_cols</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">VectorAssembler</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Spark transformer to assemble the feature columns into a vector.</span>
 
@@ -3829,11 +4005,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.features_vector_assembler" class="
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.fit" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.fit" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">fit</span><span class="p">(</span><span class="n">feature_matrix</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.fit" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.fit" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3856,7 +4031,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.fit" class="doc doc-heading">
         <tr>
           <td><code>feature_matrix</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3883,7 +4058,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.fit" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>LocusToGeneModel</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.method.l2g.model.LocusToGeneModel" href="#otg.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.method.l2g.model.LocusToGeneModel" href="#gentropy.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3895,9 +4070,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.fit" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">272</span>
-<span class="normal">273</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">273</span>
 <span class="normal">274</span>
 <span class="normal">275</span>
 <span class="normal">276</span>
@@ -3909,7 +4083,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.fit" class="doc doc-heading">
 <span class="normal">282</span>
 <span class="normal">283</span>
 <span class="normal">284</span>
-<span class="normal">285</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">fit</span><span class="p">(</span>
+<span class="normal">285</span>
+<span class="normal">286</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">fit</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span>
     <span class="n">feature_matrix</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span><span class="p">:</span>
@@ -3934,11 +4109,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.fit" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.get_feature_importance" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.get_feature_importance" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_feature_importance</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">float</span><span class="p">]</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.get_feature_importance" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.get_feature_importance" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3994,9 +4168,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.get_feature_importance" class="doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">254</span>
-<span class="normal">255</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">255</span>
 <span class="normal">256</span>
 <span class="normal">257</span>
 <span class="normal">258</span>
@@ -4011,7 +4184,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.get_feature_importance" class="doc
 <span class="normal">267</span>
 <span class="normal">268</span>
 <span class="normal">269</span>
-<span class="normal">270</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_feature_importance</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">float</span><span class="p">]:</span>
+<span class="normal">270</span>
+<span class="normal">271</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_feature_importance</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">float</span><span class="p">]:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Return dictionary with relative importances of every feature in the model. Feature names are encoded and have to be mapped back to their original names.</span>
 
 <span class="sd">    Returns:</span>
@@ -4039,11 +4213,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.get_feature_importance" class="doc
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.get_param_grid" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.get_param_grid" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">get_param_grid</span><span class="p">()</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">Any</span><span class="p">]</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.get_param_grid" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.get_param_grid" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4075,9 +4248,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.get_param_grid" class="doc doc-hea
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">166</span>
-<span class="normal">167</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">167</span>
 <span class="normal">168</span>
 <span class="normal">169</span>
 <span class="normal">170</span>
@@ -4087,7 +4259,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.get_param_grid" class="doc doc-hea
 <span class="normal">174</span>
 <span class="normal">175</span>
 <span class="normal">176</span>
-<span class="normal">177</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_param_grid</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">Any</span><span class="p">]:</span>
+<span class="normal">177</span>
+<span class="normal">178</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">get_param_grid</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="nb">list</span><span class="p">[</span><span class="n">Any</span><span class="p">]:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Return the parameter grid for the model.</span>
 
 <span class="sd">    Returns:</span>
@@ -4110,15 +4283,14 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.get_param_grid" class="doc doc-hea
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.load_from_disk" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">load_from_disk</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.load_from_disk" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4182,7 +4354,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="doc doc-hea
     <tbody>
         <tr>
 <td><code>LocusToGeneModel</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.method.l2g.model.LocusToGeneModel" href="#otg.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.method.l2g.model.LocusToGeneModel" href="#gentropy.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4194,9 +4366,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="doc doc-hea
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">142</span>
-<span class="normal">143</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">143</span>
 <span class="normal">144</span>
 <span class="normal">145</span>
 <span class="normal">146</span>
@@ -4208,7 +4379,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="doc doc-hea
 <span class="normal">152</span>
 <span class="normal">153</span>
 <span class="normal">154</span>
-<span class="normal">155</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">155</span>
+<span class="normal">156</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">load_from_disk</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="n">Type</span><span class="p">[</span><span class="n">LocusToGeneModel</span><span class="p">],</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span><span class="p">:</span>
@@ -4233,11 +4405,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.load_from_disk" class="doc doc-hea
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.log_to_wandb" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">log_to_wandb</span><span class="p">(</span><span class="n">results</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span> <span class="n">training_data</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">evaluators</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="n">BinaryClassificationEvaluator</span> <span class="o">|</span> <span class="n">MulticlassClassificationEvaluator</span><span class="p">],</span> <span class="n">wandb_run</span><span class="p">:</span> <span class="n">Run</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.log_to_wandb" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4274,7 +4445,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="doc doc-headi
         <tr>
           <td><code>training_data</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4317,9 +4488,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="doc doc-headi
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">103</span>
-<span class="normal">104</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">104</span>
 <span class="normal">105</span>
 <span class="normal">106</span>
 <span class="normal">107</span>
@@ -4355,7 +4525,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="doc doc-headi
 <span class="normal">137</span>
 <span class="normal">138</span>
 <span class="normal">139</span>
-<span class="normal">140</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">log_to_wandb</span><span class="p">(</span>
+<span class="normal">140</span>
+<span class="normal">141</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">log_to_wandb</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span>
     <span class="n">results</span><span class="p">:</span> <span class="n">DataFrame</span><span class="p">,</span>
     <span class="n">training_data</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span>
@@ -4381,7 +4552,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="doc doc-headi
     <span class="c1">## Track feature importance</span>
     <span class="n">wandb_run</span><span class="o">.</span><span class="n">log</span><span class="p">({</span><span class="s2">&quot;importances&quot;</span><span class="p">:</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_feature_importance</span><span class="p">()})</span>
     <span class="c1">## Track training set</span>
-    <span class="n">training_table</span> <span class="o">=</span> <span class="n">wandb</span><span class="o">.</span><span class="n">Table</span><span class="p">(</span><span class="n">dataframe</span><span class="o">=</span><span class="n">training_data</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">toPandas</span><span class="p">())</span>
+    <span class="n">training_table</span> <span class="o">=</span> <span class="n">Table</span><span class="p">(</span><span class="n">dataframe</span><span class="o">=</span><span class="n">training_data</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">toPandas</span><span class="p">())</span>
     <span class="n">wandb_run</span><span class="o">.</span><span class="n">log</span><span class="p">({</span><span class="s2">&quot;trainingSet&quot;</span><span class="p">:</span> <span class="n">training_table</span><span class="p">})</span>
     <span class="c1"># Count number of positive and negative labels</span>
     <span class="n">gs_counts_dict</span> <span class="o">=</span> <span class="p">{</span>
@@ -4404,11 +4575,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.log_to_wandb" class="doc doc-headi
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.predict" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.predict" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">predict</span><span class="p">(</span><span class="n">feature_matrix</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.predict" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.predict" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4431,7 +4601,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.predict" class="doc doc-heading">
         <tr>
           <td><code>feature_matrix</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -4494,9 +4664,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.predict" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">287</span>
-<span class="normal">288</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">288</span>
 <span class="normal">289</span>
 <span class="normal">290</span>
 <span class="normal">291</span>
@@ -4512,7 +4681,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.predict" class="doc doc-heading">
 <span class="normal">301</span>
 <span class="normal">302</span>
 <span class="normal">303</span>
-<span class="normal">304</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">predict</span><span class="p">(</span>
+<span class="normal">304</span>
+<span class="normal">305</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">predict</span><span class="p">(</span>
     <span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span>
     <span class="n">feature_matrix</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
@@ -4541,11 +4711,10 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.predict" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">save</span><span class="p">(</span><span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
 
-<a href="#otg.method.l2g.model.LocusToGeneModel.save" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.model.LocusToGeneModel.save" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -4607,9 +4776,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/model.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">53</span>
-<span class="normal">54</span>
+            <summary>Source code in <code>src/gentropy/method/l2g/model.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">54</span>
 <span class="normal">55</span>
 <span class="normal">56</span>
 <span class="normal">57</span>
@@ -4619,7 +4787,8 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
 <span class="normal">61</span>
 <span class="normal">62</span>
 <span class="normal">63</span>
-<span class="normal">64</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">save</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="normal">64</span>
+<span class="normal">65</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="nf">save</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span> <span class="n">path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Saves fitted pipeline model to disk.</span>
 
 <span class="sd">    Args:</span>
@@ -4643,6 +4812,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -4666,7 +4836,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T15:56:05+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -4677,15 +4847,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
         <span class="label"> Contributors </span>
       </li>
       <li class="contributors-holder">
-        <ul class="contributors" data-bi-name="contributors"><li>
-            <a
-              href="https://github.com/ireneisdoomed"
-              title="ireneisdoomed"
-              data-bi-name="contributorprofile"
-              target="_blank"
-              ><img src="https://avatars.githubusercontent.com/u/45119610?v=4" alt="ireneisdoomed"
-            /></a>
-          </li></ul>
+        <ul class="contributors" data-bi-name="contributors"></ul>
       </li>
     </ul>
   </small>
@@ -4733,7 +4895,7 @@ <h3 id="otg.method.l2g.model.LocusToGeneModel.save" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/method/l2g/trainer/index.html b/python_api/methods/l2g/trainer/index.html
similarity index 86%
rename from python_api/method/l2g/trainer/index.html
rename to python_api/methods/l2g/trainer/index.html
index f95f32f2c..e6de20248 100644
--- a/python_api/method/l2g/trainer/index.html
+++ b/python_api/methods/l2g/trainer/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../model/">
       
       
-        <link rel="next" href="../../../step/_step/">
+        <link rel="next" href="../../../steps/_steps/">
       
       
       <link rel="icon" href="../../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>L2G Trainer - Open Targets Genetics</title>
+        <title>L2G Trainer - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.l2g.trainer.LocusToGeneTrainer" class="md-skip">
+        <a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../../usage/" class="md-tabs__link">
+      <a href="../../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../../installation/" class="md-nav__link">
+      <a href="../../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../../usage/" class="md-nav__link">
+      <a href="../../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../../development/_development/" class="md-nav__link ">
+            <a href="../../../../howto/_howto/" class="md-nav__link ">
               
   
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-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
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+            
+          </ul>
+        </nav>
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+      <a href="../../../../roadmap/" class="md-nav__link">
+        
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+  <span class="md-ellipsis">
+    Roadmap
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+  
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             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/intervals/" class="md-nav__link">
+      <a href="../../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_index/" class="md-nav__link">
+      <a href="../../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1685,32 +1804,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../_method/" class="md-nav__link ">
+            <a href="../../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1721,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../clumping/" class="md-nav__link">
+      <a href="../../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1742,11 +1861,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../coloc/" class="md-nav__link">
+      <a href="../../clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1763,11 +1882,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ecaviar/" class="md-nav__link">
+      <a href="../../coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1784,11 +1903,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../ld_annotator/" class="md-nav__link">
+      <a href="../../ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1805,11 +1924,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../pics/" class="md-nav__link">
+      <a href="../../ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1826,11 +1945,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../window_based_clumping/" class="md-nav__link">
+      <a href="../../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1858,7 +1977,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" checked>
         
           
           
@@ -1874,14 +1993,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1999,7 +2118,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.trainer.LocusToGeneTrainer" class="md-nav__link">
+  <a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer" class="md-nav__link">
     <span class="md-ellipsis">
       LocusToGeneTrainer
     </span>
@@ -2009,18 +2128,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="md-nav__link">
+  <a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="md-nav__link">
     <span class="md-ellipsis">
-      cross_validate()
+      cross_validate
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.trainer.LocusToGeneTrainer.train" class="md-nav__link">
+  <a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer.train" class="md-nav__link">
     <span class="md-ellipsis">
-      train()
+      train
     </span>
   </a>
   
@@ -2072,32 +2191,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../step/_step/" class="md-nav__link ">
+            <a href="../../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2108,11 +2227,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/clump/" class="md-nav__link">
+      <a href="../../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2129,11 +2248,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/colocalisation/" class="md-nav__link">
+      <a href="../../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2150,11 +2269,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2171,11 +2290,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/finngen/" class="md-nav__link">
+      <a href="../../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2192,11 +2311,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gene_index/" class="md-nav__link">
+      <a href="../../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2213,11 +2332,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2234,11 +2353,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2255,11 +2374,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/l2g/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2276,11 +2395,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ld_index/" class="md-nav__link">
+      <a href="../../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2297,11 +2416,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/pics/" class="md-nav__link">
+      <a href="../../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2318,11 +2437,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2339,11 +2458,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2360,11 +2479,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2381,11 +2500,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2435,7 +2617,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.l2g.trainer.LocusToGeneTrainer" class="md-nav__link">
+  <a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer" class="md-nav__link">
     <span class="md-ellipsis">
       LocusToGeneTrainer
     </span>
@@ -2445,18 +2627,18 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="md-nav__link">
+  <a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="md-nav__link">
     <span class="md-ellipsis">
-      cross_validate()
+      cross_validate
     </span>
   </a>
   
 </li>
         
           <li class="md-nav__item">
-  <a href="#otg.method.l2g.trainer.LocusToGeneTrainer.train" class="md-nav__link">
+  <a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer.train" class="md-nav__link">
     <span class="md-ellipsis">
-      train()
+      train
     </span>
   </a>
   
@@ -2491,16 +2673,15 @@ <h1>L2G Trainer</h1>
 
 
 
-
-<h2 id="otg.method.l2g.trainer.LocusToGeneTrainer" class="doc doc-heading">
-          <code>otg.method.l2g.trainer.LocusToGeneTrainer</code>
+<h2 id="gentropy.method.l2g.trainer.LocusToGeneTrainer" class="doc doc-heading">
+          <code>gentropy.method.l2g.trainer.LocusToGeneTrainer</code>
 
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
   </span>
 
-<a href="#otg.method.l2g.trainer.LocusToGeneTrainer" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2509,7 +2690,7 @@ <h2 id="otg.method.l2g.trainer.LocusToGeneTrainer" class="doc doc-heading">
       <p>Modelling of what is the most likely causal gene associated with a given locus.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/l2g/trainer.py</code></summary>
+              <summary>Source code in <code>src/gentropy/method/l2g/trainer.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 15</span>
 <span class="normal"> 16</span>
 <span class="normal"> 17</span>
@@ -2725,15 +2906,14 @@ <h2 id="otg.method.l2g.trainer.LocusToGeneTrainer" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">cross_validate</span><span class="p">(</span><span class="n">l2g_model</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">num_folds</span><span class="p">:</span> <span class="nb">int</span><span class="p">,</span> <span class="n">param_grid</span><span class="p">:</span> <span class="n">Optional</span><span class="p">[</span><span class="nb">list</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2758,7 +2938,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="doc doc
         <tr>
           <td><code>l2g_model</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.method.l2g.model.LocusToGeneModel" href="../model/#otg.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.method.l2g.model.LocusToGeneModel" href="../model/#gentropy.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2772,7 +2952,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="doc doc
         <tr>
           <td><code>data</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2827,7 +3007,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="doc doc
     <tbody>
         <tr>
 <td><code>LocusToGeneModel</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.method.l2g.model.LocusToGeneModel" href="../model/#otg.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.method.l2g.model.LocusToGeneModel" href="../model/#gentropy.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2873,7 +3053,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="doc doc
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/trainer.py</code></summary>
+            <summary>Source code in <code>src/gentropy/method/l2g/trainer.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 62</span>
 <span class="normal"> 63</span>
 <span class="normal"> 64</span>
@@ -2986,15 +3166,14 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate" class="doc doc
 
 
 
-
-<h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.train" class="doc doc-heading">
+<h3 id="gentropy.method.l2g.trainer.LocusToGeneTrainer.train" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">train</span><span class="p">(</span><span class="n">data</span><span class="p">:</span> <span class="n">L2GFeatureMatrix</span><span class="p">,</span> <span class="n">l2g_model</span><span class="p">:</span> <span class="n">LocusToGeneModel</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">evaluate</span><span class="p">:</span> <span class="nb">bool</span><span class="p">,</span> <span class="n">wandb_run_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="o">**</span><span class="n">hyperparams</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">])</span> <span class="o">-&gt;</span> <span class="n">LocusToGeneModel</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.l2g.trainer.LocusToGeneTrainer.train" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.l2g.trainer.LocusToGeneTrainer.train" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3017,7 +3196,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.train" class="doc doc-heading"
         <tr>
           <td><code>data</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix" href="../../../datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix">L2GFeatureMatrix</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3031,7 +3210,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.train" class="doc doc-heading"
         <tr>
           <td><code>l2g_model</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.method.l2g.model.LocusToGeneModel" href="../model/#otg.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.method.l2g.model.LocusToGeneModel" href="../model/#gentropy.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3128,7 +3307,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.train" class="doc doc-heading"
     <tbody>
         <tr>
 <td><code>LocusToGeneModel</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.method.l2g.model.LocusToGeneModel" href="../model/#otg.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.method.l2g.model.LocusToGeneModel" href="../model/#gentropy.method.l2g.model.LocusToGeneModel">LocusToGeneModel</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3140,7 +3319,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.train" class="doc doc-heading"
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/l2g/trainer.py</code></summary>
+            <summary>Source code in <code>src/gentropy/method/l2g/trainer.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">22</span>
 <span class="normal">23</span>
 <span class="normal">24</span>
@@ -3230,6 +3409,7 @@ <h3 id="otg.method.l2g.trainer.LocusToGeneTrainer.train" class="doc doc-heading"
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
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-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/method/ld_annotator/index.html b/python_api/methods/ld_annotator/index.html
similarity index 86%
rename from python_api/method/ld_annotator/index.html
rename to python_api/methods/ld_annotator/index.html
index 2d3e700f2..25e2150a3 100644
--- a/python_api/method/ld_annotator/index.html
+++ b/python_api/methods/ld_annotator/index.html
@@ -16,11 +16,11 @@
       
       
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>LDAnnotator - Open Targets Genetics</title>
+        <title>LDAnnotator - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.ld.LDAnnotator" class="md-skip">
+        <a href="#gentropy.method.ld.LDAnnotator" class="md-skip">
           Skip to content
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@@ -94,7 +94,7 @@
 
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   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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@@ -107,7 +107,7 @@
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+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
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-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
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+        
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+  Home
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+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
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+      <a href="../../../roadmap/" class="md-tabs__link">
+        
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+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
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-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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+    Home
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@@ -358,11 +392,11 @@
   
   
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+      <a href="../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +429,11 @@
           
           
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+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
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             Python API
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+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
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+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
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+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
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-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
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@@ -717,7 +868,7 @@
   
   
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+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +910,7 @@
   
   
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+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
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+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,10 +1778,20 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
   
+    
+  
   
   
     
@@ -1596,37 +1799,37 @@
     
     
     
-    <li class="md-nav__item md-nav__item--nested">
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
       
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1637,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1651,69 +1854,6 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-    
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" checked>
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1826,7 +1966,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.ld.LDAnnotator" class="md-nav__link">
+  <a href="#gentropy.method.ld.LDAnnotator" class="md-nav__link">
     <span class="md-ellipsis">
       LDAnnotator
     </span>
@@ -1836,9 +1976,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.ld.LDAnnotator.ld_annotate" class="md-nav__link">
+  <a href="#gentropy.method.ld.LDAnnotator.ld_annotate" class="md-nav__link">
     <span class="md-ellipsis">
-      ld_annotate()
+      ld_annotate
     </span>
   </a>
   
@@ -1885,27 +2025,6 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     
     
     
@@ -1916,7 +2035,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
@@ -1932,14 +2051,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2061,32 +2180,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2307,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2328,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2349,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2370,11 +2489,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2424,7 +2606,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.ld.LDAnnotator" class="md-nav__link">
+  <a href="#gentropy.method.ld.LDAnnotator" class="md-nav__link">
     <span class="md-ellipsis">
       LDAnnotator
     </span>
@@ -2434,9 +2616,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.ld.LDAnnotator.ld_annotate" class="md-nav__link">
+  <a href="#gentropy.method.ld.LDAnnotator.ld_annotate" class="md-nav__link">
     <span class="md-ellipsis">
-      ld_annotate()
+      ld_annotate
     </span>
   </a>
   
@@ -2471,12 +2653,11 @@ <h1>LDAnnotator</h1>
 
 
 
+<h2 id="gentropy.method.ld.LDAnnotator" class="doc doc-heading">
+          <code>gentropy.method.ld.LDAnnotator</code>
 
-<h2 id="otg.method.ld.LDAnnotator" class="doc doc-heading">
-          <code>otg.method.ld.LDAnnotator</code>
 
-
-<a href="#otg.method.ld.LDAnnotator" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.ld.LDAnnotator" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2485,7 +2666,7 @@ <h2 id="otg.method.ld.LDAnnotator" class="doc doc-heading">
       <p>Class to annotate linkage disequilibrium (LD) operations from GnomAD.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/ld.py</code></summary>
+              <summary>Source code in <code>src/gentropy/method/ld.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 17</span>
 <span class="normal"> 18</span>
 <span class="normal"> 19</span>
@@ -2610,7 +2791,8 @@ <h2 id="otg.method.ld.LDAnnotator" class="doc doc-heading">
 <span class="normal">138</span>
 <span class="normal">139</span>
 <span class="normal">140</span>
-<span class="normal">141</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">LDAnnotator</span><span class="p">:</span>
+<span class="normal">141</span>
+<span class="normal">142</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">LDAnnotator</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Class to annotate linkage disequilibrium (LD) operations from GnomAD.&quot;&quot;&quot;</span>
 
     <span class="nd">@staticmethod</span>
@@ -2728,7 +2910,8 @@ <h2 id="otg.method.ld.LDAnnotator" class="doc doc-heading">
                             <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">(),</span>
                             <span class="bp">cls</span><span class="o">.</span><span class="n">_calculate_weighted_r_overall</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ldSet&quot;</span><span class="p">)),</span>
                         <span class="p">),</span>
-                    <span class="p">)</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">)</span>
+                    <span class="p">)</span>
+                    <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">)</span>
                 <span class="p">),</span>
                 <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocus</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
             <span class="p">)</span>
@@ -2755,15 +2938,14 @@ <h2 id="otg.method.ld.LDAnnotator" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
+<h3 id="gentropy.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">ld_annotate</span><span class="p">(</span><span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">studies</span><span class="p">:</span> <span class="n">StudyIndex</span><span class="p">,</span> <span class="n">ld_index</span><span class="p">:</span> <span class="n">LDIndex</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.ld.LDAnnotator.ld_annotate" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.ld.LDAnnotator.ld_annotate" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -2795,7 +2977,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
         <tr>
           <td><code>associations</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2809,7 +2991,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
         <tr>
           <td><code>studies</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_index.StudyIndex" href="../../dataset/study_index/#otg.dataset.study_index.StudyIndex">StudyIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_index.StudyIndex" href="../../datasets/study_index/#gentropy.dataset.study_index.StudyIndex">StudyIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2823,7 +3005,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
         <tr>
           <td><code>ld_index</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.ld_index.LDIndex" href="../../dataset/ld_index/#otg.dataset.ld_index.LDIndex">LDIndex</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.ld_index.LDIndex" href="../../datasets/ld_index/#gentropy.dataset.ld_index.LDIndex">LDIndex</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2850,7 +3032,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2862,7 +3044,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/ld.py</code></summary>
+            <summary>Source code in <code>src/gentropy/method/ld.py</code></summary>
             <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 77</span>
 <span class="normal"> 78</span>
 <span class="normal"> 79</span>
@@ -2927,7 +3109,8 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
 <span class="normal">138</span>
 <span class="normal">139</span>
 <span class="normal">140</span>
-<span class="normal">141</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">141</span>
+<span class="normal">142</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">ld_annotate</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">LDAnnotator</span><span class="p">],</span>
     <span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span>
@@ -2985,7 +3168,8 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
                         <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">isNotNull</span><span class="p">(),</span>
                         <span class="bp">cls</span><span class="o">.</span><span class="n">_calculate_weighted_r_overall</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ldSet&quot;</span><span class="p">)),</span>
                     <span class="p">),</span>
-                <span class="p">)</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">)</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;ldPopulationStructure&quot;</span><span class="p">)</span>
             <span class="p">),</span>
             <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocus</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
         <span class="p">)</span>
@@ -3004,6 +3188,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3027,7 +3212,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
         <span class="icon twemoji">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3094,7 +3279,7 @@ <h3 id="otg.method.ld.LDAnnotator.ld_annotate" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/method/pics/index.html b/python_api/methods/pics/index.html
similarity index 83%
rename from python_api/method/pics/index.html
rename to python_api/methods/pics/index.html
index b929d2f66..9e42a0a35 100644
--- a/python_api/method/pics/index.html
+++ b/python_api/methods/pics/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../ld_annotator/">
       
       
-        <link rel="next" href="../window_based_clumping/">
+        <link rel="next" href="../l2g/_l2g/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>PICS - Open Targets Genetics</title>
+        <title>PICS - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.method.pics.PICS" class="md-skip">
+        <a href="#gentropy.method.pics.PICS" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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@@ -107,7 +107,7 @@
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-            Open Targets Genetics
+            Open Targets Gentropy
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@@ -192,13 +192,13 @@
     
     
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-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
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@@ -215,6 +215,23 @@
   
   
   
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@@ -233,7 +250,7 @@
   
   
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-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
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@@ -358,11 +392,11 @@
   
   
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@@ -395,11 +429,11 @@
           
           
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@@ -414,6 +448,123 @@
         
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+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
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+  <span class="md-ellipsis">
+    Run step in CLI
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+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
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+  <span class="md-ellipsis">
+    Run step using YAML config
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+            <a href="../../../development/_development/" class="md-nav__link ">
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
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             <span class="md-nav__icon md-icon"></span>
             Python API
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
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-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
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-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
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@@ -654,7 +805,7 @@
   
   
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-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
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-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
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-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +910,7 @@
   
   
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-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
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@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
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-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
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+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
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@@ -1005,14 +1156,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
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     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
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@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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             <span class="md-nav__icon md-icon"></span>
             Finngen
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     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
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+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
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@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
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@@ -1153,14 +1346,14 @@
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-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
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     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
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@@ -1194,7 +1387,7 @@
   
   
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+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
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@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
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@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
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@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
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@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
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@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
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@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
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             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
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@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
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@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
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@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
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@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
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             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
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             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,10 +1778,20 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
   
+    
+  
   
   
     
@@ -1596,37 +1799,37 @@
     
     
     
-    <li class="md-nav__item md-nav__item--nested">
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
       
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1637,11 +1840,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1651,69 +1854,6 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
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-        </nav>
-      
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-  
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-              
-            
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-                
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-        
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-          <div class="md-nav__link md-nav__container">
-            <a href="../_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
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-            </a>
-            
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-            Method
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-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1847,7 +1987,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.pics.PICS" class="md-nav__link">
+  <a href="#gentropy.method.pics.PICS" class="md-nav__link">
     <span class="md-ellipsis">
       PICS
     </span>
@@ -1857,9 +1997,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.pics.PICS.finemap" class="md-nav__link">
+  <a href="#gentropy.method.pics.PICS.finemap" class="md-nav__link">
     <span class="md-ellipsis">
-      finemap()
+      finemap
     </span>
   </a>
   
@@ -1885,27 +2025,6 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
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@@ -1916,7 +2035,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
@@ -1932,14 +2051,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -2061,32 +2180,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../step/_step/" class="md-nav__link ">
+            <a href="../../steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2097,11 +2216,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/clump/" class="md-nav__link">
+      <a href="../../steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2118,11 +2237,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/colocalisation/" class="md-nav__link">
+      <a href="../../steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2139,11 +2258,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../../steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2160,11 +2279,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/finngen/" class="md-nav__link">
+      <a href="../../steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2181,11 +2300,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gene_index/" class="md-nav__link">
+      <a href="../../steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2202,11 +2321,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2223,11 +2342,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2244,11 +2363,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/l2g/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2265,11 +2384,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ld_index/" class="md-nav__link">
+      <a href="../../steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2286,11 +2405,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/pics/" class="md-nav__link">
+      <a href="../../steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2307,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/ukbiobank/" class="md-nav__link">
+      <a href="../../steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2328,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_annotation_step/" class="md-nav__link">
+      <a href="../../steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2349,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_index_step/" class="md-nav__link">
+      <a href="../../steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2370,11 +2489,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../../step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../../steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2424,7 +2606,7 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.method.pics.PICS" class="md-nav__link">
+  <a href="#gentropy.method.pics.PICS" class="md-nav__link">
     <span class="md-ellipsis">
       PICS
     </span>
@@ -2434,9 +2616,9 @@
       <ul class="md-nav__list">
         
           <li class="md-nav__item">
-  <a href="#otg.method.pics.PICS.finemap" class="md-nav__link">
+  <a href="#gentropy.method.pics.PICS.finemap" class="md-nav__link">
     <span class="md-ellipsis">
-      finemap()
+      finemap
     </span>
   </a>
   
@@ -2467,16 +2649,21 @@
 
   <h1>PICS</h1>
 
-<div class="doc doc-object doc-class">
+<p><strong>PICS Overview:</strong></p>
+<p>PICS is a fine-mapping method designed to identify the most likely causal SNPs associated with a trait or disease within a genomic region. It leverages both haplotype information and the observed association patterns from genome-wide association studies (GWAS).</p>
+<p>Please refer to the original publication for in-depth details: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336207/">PICS Publication</a>.</p>
+<p>We use PICS for both GWAS clumping results and GWAS curated studies.</p>
+
 
+<div class="doc doc-object doc-class">
 
 
 
-<h2 id="otg.method.pics.PICS" class="doc doc-heading">
-          <code>otg.method.pics.PICS</code>
+<h2 id="gentropy.method.pics.PICS" class="doc doc-heading">
+          <code>gentropy.method.pics.PICS</code>
 
 
-<a href="#otg.method.pics.PICS" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.method.pics.PICS" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2485,7 +2672,7 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
       <p>Probabilistic Identification of Causal SNPs (PICS), an algorithm estimating the probability that an individual variant is causal considering the haplotype structure and observed pattern of association at the genetic locus.</p>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/method/pics.py</code></summary>
+              <summary>Source code in <code>src/gentropy/method/pics.py</code></summary>
               <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 17</span>
 <span class="normal"> 18</span>
 <span class="normal"> 19</span>
@@ -2715,7 +2902,21 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
 <span class="normal">243</span>
 <span class="normal">244</span>
 <span class="normal">245</span>
-<span class="normal">246</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">PICS</span><span class="p">:</span>
+<span class="normal">246</span>
+<span class="normal">247</span>
+<span class="normal">248</span>
+<span class="normal">249</span>
+<span class="normal">250</span>
+<span class="normal">251</span>
+<span class="normal">252</span>
+<span class="normal">253</span>
+<span class="normal">254</span>
+<span class="normal">255</span>
+<span class="normal">256</span>
+<span class="normal">257</span>
+<span class="normal">258</span>
+<span class="normal">259</span>
+<span class="normal">260</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">PICS</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Probabilistic Identification of Causal SNPs (PICS), an algorithm estimating the probability that an individual variant is causal considering the haplotype structure and observed pattern of association at the genetic locus.&quot;&quot;&quot;</span>
 
     <span class="nd">@staticmethod</span>
@@ -2828,7 +3029,7 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
 <span class="sd">            ...     Row(variantId=&quot;var2&quot;, r2Overall=None),</span>
 <span class="sd">            ... ]</span>
 <span class="sd">            &gt;&gt;&gt; PICS._finemap(ld_set_with_no_r2, lead_neglog_p=10.0, k=6.4)</span>
-<span class="sd">            [{&#39;variantId&#39;: &#39;var1&#39;, &#39;r2Overall&#39;: None}, {&#39;variantId&#39;: &#39;var2&#39;, &#39;r2Overall&#39;: None}]</span>
+<span class="sd">            []</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">ld_set</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">return</span> <span class="kc">None</span>
@@ -2846,8 +3047,7 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
                 <span class="ow">or</span> <span class="n">tag_dict</span><span class="p">[</span><span class="s2">&quot;r2Overall&quot;</span><span class="p">]</span> <span class="o">&lt;</span> <span class="mf">0.5</span>
                 <span class="ow">or</span> <span class="ow">not</span> <span class="n">lead_neglog_p</span>
             <span class="p">):</span>
-                <span class="c1"># If PICS cannot be calculated, we&#39;ll return the original credible set</span>
-                <span class="n">new_credible_set</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">tag_dict</span><span class="p">)</span>
+                <span class="c1"># If PICS cannot be calculated, we drop the variant from the credible set</span>
                 <span class="k">continue</span>
 
             <span class="n">pics_snp_mu</span> <span class="o">=</span> <span class="n">PICS</span><span class="o">.</span><span class="n">_pics_mu</span><span class="p">(</span><span class="n">lead_neglog_p</span><span class="p">,</span> <span class="n">tag_dict</span><span class="p">[</span><span class="s2">&quot;r2Overall&quot;</span><span class="p">])</span>
@@ -2887,6 +3087,7 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Run PICS on a study locus.</span>
 
 <span class="sd">        !!! info &quot;Study locus needs to be LD annotated&quot;</span>
+
 <span class="sd">            The study locus needs to be LD annotated before PICS can be calculated.</span>
 
 <span class="sd">        Args:</span>
@@ -2923,6 +3124,9 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
             <span class="k">lambda</span> <span class="n">locus</span><span class="p">,</span> <span class="n">neglog_p</span><span class="p">:</span> <span class="n">PICS</span><span class="o">.</span><span class="n">_finemap</span><span class="p">(</span><span class="n">locus</span><span class="p">,</span> <span class="n">neglog_p</span><span class="p">,</span> <span class="n">k</span><span class="p">),</span>
             <span class="n">picsed_ldset_schema</span><span class="p">,</span>
         <span class="p">)</span>
+        <span class="n">non_picsable_expr</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ldSet&quot;</span><span class="p">),</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">r2Overall</span> <span class="o">&gt;=</span> <span class="mf">0.5</span><span class="p">))</span> <span class="o">==</span> <span class="mi">0</span>
+        <span class="p">)</span>
         <span class="k">return</span> <span class="n">StudyLocus</span><span class="p">(</span>
             <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
                 <span class="n">associations</span><span class="o">.</span><span class="n">df</span>
@@ -2940,7 +3144,18 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
                         <span class="p">),</span>
                     <span class="p">),</span>
                 <span class="p">)</span>
-                <span class="c1"># Rename tagVariantId to variantId</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                    <span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span>
+                    <span class="n">StudyLocus</span><span class="o">.</span><span class="n">update_quality_flag</span><span class="p">(</span>
+                        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">),</span>
+                        <span class="n">non_picsable_expr</span><span class="p">,</span>
+                        <span class="n">StudyLocusQualityCheck</span><span class="o">.</span><span class="n">NOT_QUALIFYING_LD_BLOCK</span><span class="p">,</span>
+                    <span class="p">),</span>
+                <span class="p">)</span>
+                <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                    <span class="s2">&quot;finemappingMethod&quot;</span><span class="p">,</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;finemappingMethod&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;pics&quot;</span><span class="p">)),</span>
+                <span class="p">)</span>
                 <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;neglog_pvalue&quot;</span><span class="p">)</span>
             <span class="p">),</span>
             <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocus</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
@@ -2965,15 +3180,14 @@ <h2 id="otg.method.pics.PICS" class="doc doc-heading">
 
 
 
-
-<h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
+<h3 id="gentropy.method.pics.PICS.finemap" class="doc doc-heading">
           <code class="highlight language-python"><span class="n">finemap</span><span class="p">(</span><span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">k</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">6.4</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span></code>
   
   <span class="doc doc-labels">
       <small class="doc doc-label doc-label-classmethod"><code>classmethod</code></small>
   </span>
 
-<a href="#otg.method.pics.PICS.finemap" class="headerlink" title="Permanent link">&para;</a></h3>
+<a href="#gentropy.method.pics.PICS.finemap" class="headerlink" title="Permanent link">&para;</a></h3>
 
 
   <div class="doc doc-contents ">
@@ -3000,7 +3214,7 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
         <tr>
           <td><code>associations</code></td>
           <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3041,7 +3255,7 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
     <tbody>
         <tr>
 <td><code>StudyLocus</code></td>          <td>
-                <code><a class="autorefs autorefs-internal" title="otg.dataset.study_locus.StudyLocus" href="../../dataset/study_locus/#otg.dataset.study_locus.StudyLocus">StudyLocus</a></code>
+                <code><a class="autorefs autorefs-internal" title="gentropy.dataset.study_locus.StudyLocus" href="../../datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus">StudyLocus</a></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -3053,8 +3267,9 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
   </table>
 
           <details class="quote">
-            <summary>Source code in <code>src/otg/method/pics.py</code></summary>
-            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">182</span>
+            <summary>Source code in <code>src/gentropy/method/pics.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">181</span>
+<span class="normal">182</span>
 <span class="normal">183</span>
 <span class="normal">184</span>
 <span class="normal">185</span>
@@ -3118,13 +3333,28 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
 <span class="normal">243</span>
 <span class="normal">244</span>
 <span class="normal">245</span>
-<span class="normal">246</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
+<span class="normal">246</span>
+<span class="normal">247</span>
+<span class="normal">248</span>
+<span class="normal">249</span>
+<span class="normal">250</span>
+<span class="normal">251</span>
+<span class="normal">252</span>
+<span class="normal">253</span>
+<span class="normal">254</span>
+<span class="normal">255</span>
+<span class="normal">256</span>
+<span class="normal">257</span>
+<span class="normal">258</span>
+<span class="normal">259</span>
+<span class="normal">260</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@classmethod</span>
 <span class="k">def</span> <span class="nf">finemap</span><span class="p">(</span>
     <span class="bp">cls</span><span class="p">:</span> <span class="nb">type</span><span class="p">[</span><span class="n">PICS</span><span class="p">],</span> <span class="n">associations</span><span class="p">:</span> <span class="n">StudyLocus</span><span class="p">,</span> <span class="n">k</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">6.4</span>
 <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyLocus</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Run PICS on a study locus.</span>
 
 <span class="sd">    !!! info &quot;Study locus needs to be LD annotated&quot;</span>
+
 <span class="sd">        The study locus needs to be LD annotated before PICS can be calculated.</span>
 
 <span class="sd">    Args:</span>
@@ -3161,6 +3391,9 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
         <span class="k">lambda</span> <span class="n">locus</span><span class="p">,</span> <span class="n">neglog_p</span><span class="p">:</span> <span class="n">PICS</span><span class="o">.</span><span class="n">_finemap</span><span class="p">(</span><span class="n">locus</span><span class="p">,</span> <span class="n">neglog_p</span><span class="p">,</span> <span class="n">k</span><span class="p">),</span>
         <span class="n">picsed_ldset_schema</span><span class="p">,</span>
     <span class="p">)</span>
+    <span class="n">non_picsable_expr</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">size</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;ldSet&quot;</span><span class="p">),</span> <span class="k">lambda</span> <span class="n">x</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">r2Overall</span> <span class="o">&gt;=</span> <span class="mf">0.5</span><span class="p">))</span> <span class="o">==</span> <span class="mi">0</span>
+    <span class="p">)</span>
     <span class="k">return</span> <span class="n">StudyLocus</span><span class="p">(</span>
         <span class="n">_df</span><span class="o">=</span><span class="p">(</span>
             <span class="n">associations</span><span class="o">.</span><span class="n">df</span>
@@ -3178,7 +3411,18 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
                     <span class="p">),</span>
                 <span class="p">),</span>
             <span class="p">)</span>
-            <span class="c1"># Rename tagVariantId to variantId</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                <span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span>
+                <span class="n">StudyLocus</span><span class="o">.</span><span class="n">update_quality_flag</span><span class="p">(</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;qualityControls&quot;</span><span class="p">),</span>
+                    <span class="n">non_picsable_expr</span><span class="p">,</span>
+                    <span class="n">StudyLocusQualityCheck</span><span class="o">.</span><span class="n">NOT_QUALIFYING_LD_BLOCK</span><span class="p">,</span>
+                <span class="p">),</span>
+            <span class="p">)</span>
+            <span class="o">.</span><span class="n">withColumn</span><span class="p">(</span>
+                <span class="s2">&quot;finemappingMethod&quot;</span><span class="p">,</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;finemappingMethod&quot;</span><span class="p">),</span> <span class="n">f</span><span class="o">.</span><span class="n">lit</span><span class="p">(</span><span class="s2">&quot;pics&quot;</span><span class="p">)),</span>
+            <span class="p">)</span>
             <span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;neglog_pvalue&quot;</span><span class="p">)</span>
         <span class="p">),</span>
         <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocus</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
@@ -3195,6 +3439,7 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3218,7 +3463,7 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3285,7 +3530,7 @@ <h3 id="otg.method.pics.PICS.finemap" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/step/ukbiobank/index.html b/python_api/step/ukbiobank/index.html
deleted file mode 100644
index 281cb198f..000000000
--- a/python_api/step/ukbiobank/index.html
+++ /dev/null
@@ -1,2698 +0,0 @@
-
-<!doctype html>
-<html lang="en" class="no-js">
-  <head>
-    
-      <meta charset="utf-8">
-      <meta name="viewport" content="width=device-width,initial-scale=1">
-      
-      
-      
-      
-        <link rel="prev" href="../pics/">
-      
-      
-        <link rel="next" href="../variant_annotation_step/">
-      
-      
-      <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
-    
-    
-      
-        <title>UK Biobank - Open Targets Genetics</title>
-      
-    
-    
-      <link rel="stylesheet" href="../../../assets/stylesheets/main.50c56a3b.min.css">
-      
-        
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-  <h1>UK Biobank</h1>
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-<div class="doc doc-object doc-class">
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-<h2 id="otg.ukbiobank.UKBiobankStep" class="doc doc-heading">
-          <code>otg.ukbiobank.UKBiobankStep</code>
-
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
-
-<a href="#otg.ukbiobank.UKBiobankStep" class="headerlink" title="Permanent link">&para;</a></h2>
-
-
-  <div class="doc doc-contents first">
-
-  
-      <p>UKBiobank study table ingestion step.</p>
-
-
-
-  <p><strong>Attributes:</strong></p>
-  <table>
-    <thead>
-      <tr>
-        <th>Name</th>
-        <th>Type</th>
-        <th>Description</th>
-      </tr>
-    </thead>
-    <tbody>
-        <tr>
-          <td><code>session</code></td>
-          <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Session object.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>ukbiobank_manifest</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>UKBiobank manifest of studies.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>ukbiobank_study_index_out</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Output path for the UKBiobank study index dataset.</p>
-            </div>
-          </td>
-        </tr>
-    </tbody>
-  </table>
-
-            <details class="quote">
-              <summary>Source code in <code>src/otg/ukbiobank.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">13</span>
-<span class="normal">14</span>
-<span class="normal">15</span>
-<span class="normal">16</span>
-<span class="normal">17</span>
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-<span class="normal">40</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">UKBiobankStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;UKBiobank study table ingestion step.</span>
-
-<span class="sd">    Attributes:</span>
-<span class="sd">        session (Session): Session object.</span>
-<span class="sd">        ukbiobank_manifest (str): UKBiobank manifest of studies.</span>
-<span class="sd">        ukbiobank_study_index_out (str): Output path for the UKBiobank study index dataset.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">ukbiobank_manifest</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">ukbiobank_study_index_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">UKBiobankStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Read in the UKBiobank manifest tsv file.</span>
-        <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">ukbiobank_manifest</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span> <span class="n">inferSchema</span><span class="o">=</span><span class="kc">True</span>
-        <span class="p">)</span>
-
-        <span class="c1"># Parse the study index data.</span>
-        <span class="n">ukbiobank_study_index</span> <span class="o">=</span> <span class="n">UKBiobankStudyIndex</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">df</span><span class="p">)</span>
-
-        <span class="c1"># Write the output.</span>
-        <span class="n">ukbiobank_study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">ukbiobank_study_index_out</span>
-        <span class="p">)</span>
-</code></pre></div></td></tr></table></div>
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diff --git a/python_api/step/_step/index.html b/python_api/steps/_steps/index.html
similarity index 79%
rename from python_api/step/_step/index.html
rename to python_api/steps/_steps/index.html
index 0062e42d3..03f88080d 100644
--- a/python_api/step/_step/index.html
+++ b/python_api/steps/_steps/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../../method/l2g/trainer/">
+        <link rel="prev" href="../../methods/l2g/trainer/">
       
       
-        <link rel="next" href="../clump/">
+        <link rel="next" href="../colocalisation/">
       
       
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-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Step - Open Targets Genetics</title>
+        <title>Step - Open Targets Gentropy</title>
       
     
     
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
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+        
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+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
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+                
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+  
+  
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+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
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+    </li>
+  
+
+    
+      
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+  
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+    
+    
+    
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+      
+      
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
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+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
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-    Datasource
+    Datasources
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,7 +2120,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
@@ -2010,23 +2129,23 @@
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link md-nav__link--active" for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link md-nav__link--active" for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2146,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2167,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2188,7 +2349,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2205,11 +2366,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2226,11 +2387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2247,11 +2408,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2272,7 +2433,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2293,7 +2454,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2314,7 +2475,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2376,7 +2558,7 @@
 
 
 <h1 id="step">Step<a class="headerlink" href="#step" title="Permanent link">&para;</a></h1>
-<p>TBC</p>
+<p>This section provides description for the <code>Step</code> class. Each <code>Step</code> uses its own set of Methods and Datasets and implements the logic necessary to read a set of inputs, perform the transformation and write the outputs. All steps are available through the command line interface when running the <code>gentropy</code> command.</p>
 <hr />
 <div class="md-source-file">
   <small>
@@ -2392,14 +2574,14 @@ <h1 id="step">Step<a class="headerlink" href="#step" title="Permanent link">&par
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M14.47 15.08 11 13V7h1.5v5.25l3.08 1.83c-.41.28-.79.62-1.11 1m-1.39 4.84c-.36.05-.71.08-1.08.08-4.42 0-8-3.58-8-8s3.58-8 8-8 8 3.58 8 8c0 .37-.03.72-.08 1.08.69.1 1.33.32 1.92.64.1-.56.16-1.13.16-1.72 0-5.5-4.5-10-10-10S2 6.5 2 12s4.47 10 10 10c.59 0 1.16-.06 1.72-.16-.32-.59-.54-1.23-.64-1.92M18 15v3h-3v2h3v3h2v-3h3v-2h-3v-3h-2Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-16T08:22:37+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-16</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
        
       <li>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-10-31T12:33:26+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-10-31</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T11:17:17+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2458,7 +2640,7 @@ <h1 id="step">Step<a class="headerlink" href="#step" title="Permanent link">&par
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/step/colocalisation/index.html b/python_api/steps/colocalisation/index.html
similarity index 69%
rename from python_api/step/colocalisation/index.html
rename to python_api/steps/colocalisation/index.html
index afdb7513b..fb0eacea9 100644
--- a/python_api/step/colocalisation/index.html
+++ b/python_api/steps/colocalisation/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../clump/">
+        <link rel="prev" href="../_steps/">
       
       
         <link rel="next" href="../eqtl_catalogue/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Colocalisation - Open Targets Genetics</title>
+        <title>colocalisation - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.colocalisation.ColocalisationStep" class="md-skip">
+        <a href="#gentropy.colocalisation.ColocalisationStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Colocalisation
+              colocalisation
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
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-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,27 +2153,6 @@
                 
   
   
-  
-  
-    <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Clump
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
     
   
   
@@ -2069,7 +2167,7 @@
           
   
   <span class="md-ellipsis">
-    Colocalisation
+    colocalisation
   </span>
   
 
@@ -2080,7 +2178,7 @@
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    colocalisation
   </span>
   
 
@@ -2100,12 +2198,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.colocalisation.ColocalisationStep" class="md-nav__link">
+  <a href="#gentropy.colocalisation.ColocalisationStep" class="md-nav__link">
     <span class="md-ellipsis">
       ColocalisationStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="ColocalisationStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.colocalisation.ColocalisationStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2128,7 +2241,7 @@
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    eqtl_catalogue
   </span>
   
 
@@ -2145,11 +2258,32 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2170,7 +2304,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2191,7 +2367,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2212,7 +2388,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2233,7 +2409,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2250,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.colocalisation.ColocalisationStep" class="md-nav__link">
+  <a href="#gentropy.colocalisation.ColocalisationStep" class="md-nav__link">
     <span class="md-ellipsis">
       ColocalisationStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="ColocalisationStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.colocalisation.ColocalisationStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,116 +2647,205 @@
   
 
 
-  <h1>Colocalisation</h1>
+  <h1>colocalisation</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.colocalisation.ColocalisationStep" class="doc doc-heading">
+          <code>gentropy.colocalisation.ColocalisationStep</code>
 
-<h2 id="otg.colocalisation.ColocalisationStep" class="doc doc-heading">
-          <code>otg.colocalisation.ColocalisationStep</code>
-
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
 
-<a href="#otg.colocalisation.ColocalisationStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.colocalisation.ColocalisationStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
 
   
       <p>Colocalisation step.</p>
-<p>This workflow runs colocalization analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).</p>
+<p>This workflow runs colocalisation analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/colocalisation.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span>
+<span class="normal">32</span>
+<span class="normal">33</span>
+<span class="normal">34</span>
+<span class="normal">35</span>
+<span class="normal">36</span>
+<span class="normal">37</span>
+<span class="normal">38</span>
+<span class="normal">39</span>
+<span class="normal">40</span>
+<span class="normal">41</span>
+<span class="normal">42</span>
+<span class="normal">43</span>
+<span class="normal">44</span>
+<span class="normal">45</span>
+<span class="normal">46</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">ColocalisationStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Colocalisation step.</span>
+
+<span class="sd">    This workflow runs colocalisation analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">coloc_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run Colocalisation step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            credible_set_path (str): Input credible sets path.</span>
+<span class="sd">            study_index_path (str): Input study index path.</span>
+<span class="sd">            coloc_path (str): Output Colocalisation path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Extract</span>
+        <span class="n">credible_set</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+            <span class="n">session</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="n">si</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+            <span class="n">session</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Transform</span>
+        <span class="n">overlaps</span> <span class="o">=</span> <span class="n">credible_set</span><span class="o">.</span><span class="n">filter_credible_set</span><span class="p">(</span>
+            <span class="n">CredibleInterval</span><span class="o">.</span><span class="n">IS95</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">find_overlaps</span><span class="p">(</span><span class="n">si</span><span class="p">)</span>
+        <span class="n">ecaviar_results</span> <span class="o">=</span> <span class="n">ECaviar</span><span class="o">.</span><span class="n">colocalise</span><span class="p">(</span><span class="n">overlaps</span><span class="p">)</span>
+
+        <span class="c1"># Load</span>
+        <span class="n">ecaviar_results</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">coloc_path</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
 
 
 
-  <p><strong>Attributes:</strong></p>
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.colocalisation.ColocalisationStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">coloc_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.colocalisation.ColocalisationStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run Colocalisation step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
-        </tr>
-        <tr>
-          <td><code>study_locus_path</code></td>
-          <td>
-                <code>DictConfig</code>
-          </td>
           <td>
-            <div class="doc-md-description">
-              <p>Input Study-locus path.</p>
-            </div>
+              <em>required</em>
           </td>
         </tr>
         <tr>
-          <td><code>coloc_path</code></td>
+          <td><code>credible_set_path</code></td>
           <td>
-                <code>DictConfig</code>
+                <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output Colocalisation path.</p>
+              <p>Input credible sets path.</p>
             </div>
           </td>
-        </tr>
-        <tr>
-          <td><code>priorc1</code></td>
           <td>
-                <code>float</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Prior on variant being causal for trait 1.</p>
-            </div>
+              <em>required</em>
           </td>
         </tr>
         <tr>
-          <td><code>priorc2</code></td>
+          <td><code>study_index_path</code></td>
           <td>
-                <code>float</code>
+                <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Prior on variant being causal for trait 2.</p>
+              <p>Input study index path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
-          <td><code>priorc12</code></td>
+          <td><code>coloc_path</code></td>
           <td>
-                <code>float</code>
+                <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Prior on variant being causal for traits 1 and 2.</p>
+              <p>Output Colocalisation path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/colocalisation.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
-<span class="normal">15</span>
-<span class="normal">16</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/colocalisation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">16</span>
 <span class="normal">17</span>
 <span class="normal">18</span>
 <span class="normal">19</span>
@@ -2574,67 +2875,42 @@ <h2 id="otg.colocalisation.ColocalisationStep" class="doc doc-heading">
 <span class="normal">43</span>
 <span class="normal">44</span>
 <span class="normal">45</span>
-<span class="normal">46</span>
-<span class="normal">47</span>
-<span class="normal">48</span>
-<span class="normal">49</span>
-<span class="normal">50</span>
-<span class="normal">51</span>
-<span class="normal">52</span>
-<span class="normal">53</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">ColocalisationStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Colocalisation step.</span>
-
-<span class="sd">    This workflow runs colocalization analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">46</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">coloc_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run Colocalisation step.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        study_locus_path (DictConfig): Input Study-locus path.</span>
-<span class="sd">        coloc_path (DictConfig): Output Colocalisation path.</span>
-<span class="sd">        priorc1 (float): Prior on variant being causal for trait 1.</span>
-<span class="sd">        priorc2 (float): Prior on variant being causal for trait 2.</span>
-<span class="sd">        priorc12 (float): Prior on variant being causal for traits 1 and 2.</span>
+<span class="sd">        credible_set_path (str): Input credible sets path.</span>
+<span class="sd">        study_index_path (str): Input study index path.</span>
+<span class="sd">        coloc_path (str): Output Colocalisation path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">study_locus_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">coloc_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">priorc1</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-4</span>
-    <span class="n">priorc2</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-4</span>
-    <span class="n">priorc12</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">1e-5</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">ColocalisationStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Study-locus information</span>
-        <span class="n">sl</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">study_locus_path</span><span class="p">)</span>
-        <span class="n">si</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">study_index_path</span><span class="p">)</span>
-
-        <span class="c1"># Study-locus overlaps for 95% credible sets</span>
-        <span class="n">sl_overlaps</span> <span class="o">=</span> <span class="n">sl</span><span class="o">.</span><span class="n">filter_credible_set</span><span class="p">(</span><span class="n">CredibleInterval</span><span class="o">.</span><span class="n">IS95</span><span class="p">)</span><span class="o">.</span><span class="n">find_overlaps</span><span class="p">(</span><span class="n">si</span><span class="p">)</span>
-
-        <span class="n">coloc_results</span> <span class="o">=</span> <span class="n">Coloc</span><span class="o">.</span><span class="n">colocalise</span><span class="p">(</span>
-            <span class="n">sl_overlaps</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">priorc1</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">priorc2</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">priorc12</span>
-        <span class="p">)</span>
-        <span class="n">ecaviar_results</span> <span class="o">=</span> <span class="n">ECaviar</span><span class="o">.</span><span class="n">colocalise</span><span class="p">(</span><span class="n">sl_overlaps</span><span class="p">)</span>
-
-        <span class="n">coloc_results</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">ecaviar_results</span><span class="o">.</span><span class="n">df</span><span class="p">,</span> <span class="n">allowMissingColumns</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-
-        <span class="n">coloc_results</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">coloc_path</span><span class="p">)</span>
+    <span class="c1"># Extract</span>
+    <span class="n">credible_set</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">si</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Transform</span>
+    <span class="n">overlaps</span> <span class="o">=</span> <span class="n">credible_set</span><span class="o">.</span><span class="n">filter_credible_set</span><span class="p">(</span>
+        <span class="n">CredibleInterval</span><span class="o">.</span><span class="n">IS95</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">find_overlaps</span><span class="p">(</span><span class="n">si</span><span class="p">)</span>
+    <span class="n">ecaviar_results</span> <span class="o">=</span> <span class="n">ECaviar</span><span class="o">.</span><span class="n">colocalise</span><span class="p">(</span><span class="n">overlaps</span><span class="p">)</span>
+
+    <span class="c1"># Load</span>
+    <span class="n">ecaviar_results</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">coloc_path</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2642,6 +2918,7 @@ <h2 id="otg.colocalisation.ColocalisationStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2665,7 +2942,7 @@ <h2 id="otg.colocalisation.ColocalisationStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2724,7 +3001,7 @@ <h2 id="otg.colocalisation.ColocalisationStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/step/eqtl_catalogue/index.html b/python_api/steps/eqtl_catalogue/index.html
similarity index 67%
rename from python_api/step/eqtl_catalogue/index.html
rename to python_api/steps/eqtl_catalogue/index.html
index c04cf3ad7..2c482cdd8 100644
--- a/python_api/step/eqtl_catalogue/index.html
+++ b/python_api/steps/eqtl_catalogue/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../colocalisation/">
       
       
-        <link rel="next" href="../finngen/">
+        <link rel="next" href="../finngen_studies/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>eQTL Catalogue - Open Targets Genetics</title>
+        <title>eqtl_catalogue - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.eqtl_catalogue.EqtlCatalogueStep" class="md-skip">
+        <a href="#gentropy.eqtl_catalogue.EqtlCatalogueStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              eQTL Catalogue
+              eqtl_catalogue
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
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+  
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
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+
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+  
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@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,6 +1778,14 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
@@ -1601,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1637,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1651,67 +1852,6 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1719,7 +1859,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1740,7 +1880,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1761,7 +1901,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1782,7 +1922,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1803,7 +1943,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1823,43 +1963,22 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2036,33 +2155,12 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Clump
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     <li class="md-nav__item">
       <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    colocalisation
   </span>
   
 
@@ -2090,7 +2188,7 @@
           
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    eqtl_catalogue
   </span>
   
 
@@ -2101,7 +2199,7 @@
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    eqtl_catalogue
   </span>
   
 
@@ -2121,12 +2219,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.eqtl_catalogue.EqtlCatalogueStep" class="md-nav__link">
+  <a href="#gentropy.eqtl_catalogue.EqtlCatalogueStep" class="md-nav__link">
     <span class="md-ellipsis">
       EqtlCatalogueStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="EqtlCatalogueStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.eqtl_catalogue.EqtlCatalogueStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2145,11 +2258,32 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2170,7 +2304,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2191,7 +2367,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2212,7 +2388,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2233,7 +2409,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2250,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.eqtl_catalogue.EqtlCatalogueStep" class="md-nav__link">
+  <a href="#gentropy.eqtl_catalogue.EqtlCatalogueStep" class="md-nav__link">
     <span class="md-ellipsis">
       EqtlCatalogueStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="EqtlCatalogueStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.eqtl_catalogue.EqtlCatalogueStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>eQTL Catalogue</h1>
+  <h1>eqtl_catalogue</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
+          <code>gentropy.eqtl_catalogue.EqtlCatalogueStep</code>
 
-<h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
-          <code>otg.eqtl_catalogue.EqtlCatalogueStep</code>
 
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
-
-<a href="#otg.eqtl_catalogue.EqtlCatalogueStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.eqtl_catalogue.EqtlCatalogueStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2458,28 +2665,169 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
   
       <p>eQTL Catalogue ingestion step.</p>
 
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/eqtl_catalogue.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
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+<span class="normal">32</span>
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+<span class="normal">34</span>
+<span class="normal">35</span>
+<span class="normal">36</span>
+<span class="normal">37</span>
+<span class="normal">38</span>
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+<span class="normal">40</span>
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+<span class="normal">42</span>
+<span class="normal">43</span>
+<span class="normal">44</span>
+<span class="normal">45</span>
+<span class="normal">46</span>
+<span class="normal">47</span>
+<span class="normal">48</span>
+<span class="normal">49</span>
+<span class="normal">50</span>
+<span class="normal">51</span>
+<span class="normal">52</span>
+<span class="normal">53</span>
+<span class="normal">54</span>
+<span class="normal">55</span>
+<span class="normal">56</span>
+<span class="normal">57</span>
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+<span class="normal">59</span>
+<span class="normal">60</span>
+<span class="normal">61</span>
+<span class="normal">62</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">EqtlCatalogueStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;eQTL Catalogue ingestion step.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">eqtl_catalogue_paths_imported</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">eqtl_catalogue_study_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">eqtl_catalogue_summary_stats_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run eQTL Catalogue ingestion step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            eqtl_catalogue_paths_imported (str): Input eQTL Catalogue study index path.</span>
+<span class="sd">            eqtl_catalogue_study_index_out (str): Output eQTL Catalogue study index path.</span>
+<span class="sd">            eqtl_catalogue_summary_stats_out (str): Output eQTL Catalogue summary stats path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Fetch study index.</span>
+        <span class="n">df</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="n">eqtl_catalogue_paths_imported</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="c1"># Process partial study index.  At this point, it is not complete because we don&#39;t have the gene IDs, which we</span>
+        <span class="c1"># will only get once the summary stats are ingested.</span>
+        <span class="n">study_index_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueStudyIndex</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">df</span><span class="p">)</span><span class="o">.</span><span class="n">df</span>
+
+        <span class="c1"># Fetch summary stats.</span>
+        <span class="n">input_filenames</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="o">.</span><span class="n">summarystatsLocation</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">study_index_df</span><span class="o">.</span><span class="n">collect</span><span class="p">()]</span>
+        <span class="n">summary_stats_df</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">csv</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">repartition</span><span class="p">(</span><span class="mi">1280</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="c1"># Process summary stats.</span>
+        <span class="n">summary_stats_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueSummaryStats</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">summary_stats_df</span><span class="p">)</span><span class="o">.</span><span class="n">df</span>
+
+        <span class="c1"># Add geneId column to the study index.</span>
+        <span class="n">study_index_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueStudyIndex</span><span class="o">.</span><span class="n">add_gene_to_study_id</span><span class="p">(</span>
+            <span class="n">study_index_df</span><span class="p">,</span>
+            <span class="n">summary_stats_df</span><span class="p">,</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">df</span>
+
+        <span class="c1"># Write study index.</span>
+        <span class="n">study_index_df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
+            <span class="n">eqtl_catalogue_study_index_out</span>
+        <span class="p">)</span>
+        <span class="c1"># Write summary stats.</span>
+        <span class="p">(</span>
+            <span class="n">summary_stats_df</span><span class="o">.</span><span class="n">sortWithinPartitions</span><span class="p">(</span><span class="s2">&quot;position&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">eqtl_catalogue_summary_stats_out</span><span class="p">)</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.eqtl_catalogue.EqtlCatalogueStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">eqtl_catalogue_paths_imported</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">eqtl_catalogue_study_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">eqtl_catalogue_summary_stats_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.eqtl_catalogue.EqtlCatalogueStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run eQTL Catalogue ingestion step.</p>
+
 
 
-  <p><strong>Attributes:</strong></p>
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>eqtl_catalogue_paths_imported</code></td>
@@ -2488,9 +2836,12 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>eQTL Catalogue input files for the harmonised and imported data.</p>
+              <p>Input eQTL Catalogue study index path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>eqtl_catalogue_study_index_out</code></td>
@@ -2499,9 +2850,12 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output path for the eQTL Catalogue study index dataset.</p>
+              <p>Output eQTL Catalogue study index path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>eqtl_catalogue_summary_stats_out</code></td>
@@ -2510,16 +2864,20 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output path for the eQTL Catalogue summary stats.</p>
+              <p>Output eQTL Catalogue summary stats path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/eqtl_catalogue.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/eqtl_catalogue.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">13</span>
+<span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
 <span class="normal">17</span>
@@ -2567,79 +2925,61 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
 <span class="normal">59</span>
 <span class="normal">60</span>
 <span class="normal">61</span>
-<span class="normal">62</span>
-<span class="normal">63</span>
-<span class="normal">64</span>
-<span class="normal">65</span>
-<span class="normal">66</span>
-<span class="normal">67</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">EqtlCatalogueStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;eQTL Catalogue ingestion step.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">62</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">eqtl_catalogue_paths_imported</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">eqtl_catalogue_study_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">eqtl_catalogue_summary_stats_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run eQTL Catalogue ingestion step.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        eqtl_catalogue_paths_imported (str): eQTL Catalogue input files for the harmonised and imported data.</span>
-<span class="sd">        eqtl_catalogue_study_index_out (str): Output path for the eQTL Catalogue study index dataset.</span>
-<span class="sd">        eqtl_catalogue_summary_stats_out (str): Output path for the eQTL Catalogue summary stats.</span>
+<span class="sd">        eqtl_catalogue_paths_imported (str): Input eQTL Catalogue study index path.</span>
+<span class="sd">        eqtl_catalogue_study_index_out (str): Output eQTL Catalogue study index path.</span>
+<span class="sd">        eqtl_catalogue_summary_stats_out (str): Output eQTL Catalogue summary stats path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="n">eqtl_catalogue_paths_imported</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">eqtl_catalogue_study_index_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">eqtl_catalogue_summary_stats_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">EqtlCatalogueStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Fetch study index.</span>
-        <span class="n">df</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">eqtl_catalogue_paths_imported</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
-        <span class="p">)</span>
-        <span class="c1"># Process partial study index.  At this point, it is not complete because we don&#39;t have the gene IDs, which we</span>
-        <span class="c1"># will only get once the summary stats are ingested.</span>
-        <span class="n">study_index_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueStudyIndex</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">df</span><span class="p">)</span><span class="o">.</span><span class="n">df</span>
-
-        <span class="c1"># Fetch summary stats.</span>
-        <span class="n">input_filenames</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="o">.</span><span class="n">summarystatsLocation</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">study_index_df</span><span class="o">.</span><span class="n">collect</span><span class="p">()]</span>
-        <span class="n">summary_stats_df</span> <span class="o">=</span> <span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">csv</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">repartition</span><span class="p">(</span><span class="mi">1280</span><span class="p">)</span>
-        <span class="p">)</span>
-        <span class="c1"># Process summary stats.</span>
-        <span class="n">summary_stats_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueSummaryStats</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">summary_stats_df</span><span class="p">)</span><span class="o">.</span><span class="n">df</span>
-
-        <span class="c1"># Add geneId column to the study index.</span>
-        <span class="n">study_index_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueStudyIndex</span><span class="o">.</span><span class="n">add_gene_id_column</span><span class="p">(</span>
-            <span class="n">study_index_df</span><span class="p">,</span>
-            <span class="n">summary_stats_df</span><span class="p">,</span>
-        <span class="p">)</span><span class="o">.</span><span class="n">df</span>
-
-        <span class="c1"># Write study index.</span>
-        <span class="n">study_index_df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">eqtl_catalogue_study_index_out</span>
-        <span class="p">)</span>
-        <span class="c1"># Write summary stats.</span>
-        <span class="p">(</span>
-            <span class="n">summary_stats_df</span><span class="o">.</span><span class="n">sortWithinPartitions</span><span class="p">(</span><span class="s2">&quot;position&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">eqtl_catalogue_summary_stats_out</span><span class="p">)</span>
-        <span class="p">)</span>
+    <span class="c1"># Fetch study index.</span>
+    <span class="n">df</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="n">eqtl_catalogue_paths_imported</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="c1"># Process partial study index.  At this point, it is not complete because we don&#39;t have the gene IDs, which we</span>
+    <span class="c1"># will only get once the summary stats are ingested.</span>
+    <span class="n">study_index_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueStudyIndex</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">df</span><span class="p">)</span><span class="o">.</span><span class="n">df</span>
+
+    <span class="c1"># Fetch summary stats.</span>
+    <span class="n">input_filenames</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="o">.</span><span class="n">summarystatsLocation</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">study_index_df</span><span class="o">.</span><span class="n">collect</span><span class="p">()]</span>
+    <span class="n">summary_stats_df</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">option</span><span class="p">(</span><span class="s2">&quot;delimiter&quot;</span><span class="p">,</span> <span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">csv</span><span class="p">(</span><span class="n">input_filenames</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">repartition</span><span class="p">(</span><span class="mi">1280</span><span class="p">)</span>
+    <span class="p">)</span>
+    <span class="c1"># Process summary stats.</span>
+    <span class="n">summary_stats_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueSummaryStats</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">summary_stats_df</span><span class="p">)</span><span class="o">.</span><span class="n">df</span>
+
+    <span class="c1"># Add geneId column to the study index.</span>
+    <span class="n">study_index_df</span> <span class="o">=</span> <span class="n">EqtlCatalogueStudyIndex</span><span class="o">.</span><span class="n">add_gene_to_study_id</span><span class="p">(</span>
+        <span class="n">study_index_df</span><span class="p">,</span>
+        <span class="n">summary_stats_df</span><span class="p">,</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">df</span>
+
+    <span class="c1"># Write study index.</span>
+    <span class="n">study_index_df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
+        <span class="n">eqtl_catalogue_study_index_out</span>
+    <span class="p">)</span>
+    <span class="c1"># Write summary stats.</span>
+    <span class="p">(</span>
+        <span class="n">summary_stats_df</span><span class="o">.</span><span class="n">sortWithinPartitions</span><span class="p">(</span><span class="s2">&quot;position&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">eqtl_catalogue_summary_stats_out</span><span class="p">)</span>
+    <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2647,6 +2987,7 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2670,7 +3011,7 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2729,7 +3070,7 @@ <h2 id="otg.eqtl_catalogue.EqtlCatalogueStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/step/finngen/index.html b/python_api/steps/finngen_studies/index.html
similarity index 73%
rename from python_api/step/finngen/index.html
rename to python_api/steps/finngen_studies/index.html
index c553998e3..c3303b1fd 100644
--- a/python_api/step/finngen/index.html
+++ b/python_api/steps/finngen_studies/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../eqtl_catalogue/">
       
       
-        <link rel="next" href="../gene_index/">
+        <link rel="next" href="../finngen_sumstat_preprocess/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>FinnGen - Open Targets Genetics</title>
+        <title>finngen_studies - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.finngen.FinnGenStep" class="md-skip">
+        <a href="#gentropy.finngen_studies.FinnGenStudiesStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              FinnGen
+              finngen_studies
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
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+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
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-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2036,33 +2155,12 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Clump
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
     <li class="md-nav__item">
       <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    colocalisation
   </span>
   
 
@@ -2083,7 +2181,7 @@
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    eqtl_catalogue
   </span>
   
 
@@ -2111,7 +2209,7 @@
           
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_studies
   </span>
   
 
@@ -2122,7 +2220,7 @@
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_studies
   </span>
   
 
@@ -2142,12 +2240,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.finngen.FinnGenStep" class="md-nav__link">
+  <a href="#gentropy.finngen_studies.FinnGenStudiesStep" class="md-nav__link">
     <span class="md-ellipsis">
-      FinnGenStep
+      FinnGenStudiesStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="FinnGenStudiesStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.finngen_studies.FinnGenStudiesStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2165,12 +2278,75 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2191,7 +2367,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2212,7 +2388,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2233,7 +2409,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2250,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.finngen.FinnGenStep" class="md-nav__link">
+  <a href="#gentropy.finngen_studies.FinnGenStudiesStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      FinnGenStudiesStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="FinnGenStudiesStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.finngen_studies.FinnGenStudiesStep.__init__" class="md-nav__link">
     <span class="md-ellipsis">
-      FinnGenStep
+      __init__
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,51 +2647,109 @@
   
 
 
-  <h1>FinnGen</h1>
+  <h1>finngen_studies</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.finngen_studies.FinnGenStudiesStep" class="doc doc-heading">
+          <code>gentropy.finngen_studies.FinnGenStudiesStep</code>
+
+
+<a href="#gentropy.finngen_studies.FinnGenStudiesStep" class="headerlink" title="Permanent link">&para;</a></h2>
+
 
-<h2 id="otg.finngen.FinnGenStep" class="doc doc-heading">
-          <code>otg.finngen.FinnGenStep</code>
+  <div class="doc doc-contents first">
 
   
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
+      <p>FinnGen study index generation step.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/finngen_studies.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 9</span>
+<span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">FinnGenStudiesStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;FinnGen study index generation step.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">finngen_study_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run FinnGen study index generation step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            finngen_study_index_out (str): Output FinnGen study index path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Fetch study index.</span>
+        <span class="n">FinnGenStudyIndex</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span>
+            <span class="n">session</span><span class="o">.</span><span class="n">write_mode</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">finngen_study_index_out</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
 
-<a href="#otg.finngen.FinnGenStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
-  <div class="doc doc-contents first">
 
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.finngen_studies.FinnGenStudiesStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">finngen_study_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.finngen_studies.FinnGenStudiesStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
   
-      <p>FinnGen ingestion step.</p>
+      <p>Run FinnGen study index generation step.</p>
 
 
 
-  <p><strong>Attributes:</strong></p>
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>finngen_study_index_out</code></td>
@@ -2488,27 +2758,21 @@ <h2 id="otg.finngen.FinnGenStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output path for the FinnGen study index dataset.</p>
+              <p>Output FinnGen study index path.</p>
             </div>
           </td>
-        </tr>
-        <tr>
-          <td><code>finngen_summary_stats_out</code></td>
           <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Output path for the FinnGen summary statistics.</p>
-            </div>
+              <em>required</em>
           </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/finngen.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/finngen_studies.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
 <span class="normal">17</span>
@@ -2516,85 +2780,22 @@ <h2 id="otg.finngen.FinnGenStep" class="doc doc-heading">
 <span class="normal">19</span>
 <span class="normal">20</span>
 <span class="normal">21</span>
-<span class="normal">22</span>
-<span class="normal">23</span>
-<span class="normal">24</span>
-<span class="normal">25</span>
-<span class="normal">26</span>
-<span class="normal">27</span>
-<span class="normal">28</span>
-<span class="normal">29</span>
-<span class="normal">30</span>
-<span class="normal">31</span>
-<span class="normal">32</span>
-<span class="normal">33</span>
-<span class="normal">34</span>
-<span class="normal">35</span>
-<span class="normal">36</span>
-<span class="normal">37</span>
-<span class="normal">38</span>
-<span class="normal">39</span>
-<span class="normal">40</span>
-<span class="normal">41</span>
-<span class="normal">42</span>
-<span class="normal">43</span>
-<span class="normal">44</span>
-<span class="normal">45</span>
-<span class="normal">46</span>
-<span class="normal">47</span>
-<span class="normal">48</span>
-<span class="normal">49</span>
-<span class="normal">50</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">FinnGenStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;FinnGen ingestion step.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">22</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">finngen_study_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run FinnGen study index generation step.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        finngen_study_index_out (str): Output path for the FinnGen study index dataset.</span>
-<span class="sd">        finngen_summary_stats_out (str): Output path for the FinnGen summary statistics.</span>
+<span class="sd">        finngen_study_index_out (str): Output FinnGen study index path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">finngen_study_index_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">finngen_summary_stats_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">FinnGenStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Fetch study index.</span>
-        <span class="c1"># Process study index.</span>
-        <span class="n">study_index</span> <span class="o">=</span> <span class="n">FinnGenStudyIndex</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">)</span>
-        <span class="c1"># Write study index.</span>
-        <span class="n">study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">finngen_study_index_out</span>
-        <span class="p">)</span>
-
-        <span class="c1"># Fetch summary stats locations</span>
-        <span class="n">input_filenames</span> <span class="o">=</span> <span class="p">[</span><span class="n">row</span><span class="o">.</span><span class="n">summarystatsLocation</span> <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">collect</span><span class="p">()]</span>
-        <span class="c1"># Process summary stats.</span>
-        <span class="n">summary_stats</span> <span class="o">=</span> <span class="n">FinnGenSummaryStats</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">raw_files</span><span class="o">=</span><span class="n">input_filenames</span>
-        <span class="p">)</span>
-
-        <span class="c1"># Write summary stats.</span>
-        <span class="p">(</span>
-            <span class="n">summary_stats</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">finngen_summary_stats_out</span><span class="p">)</span>
-        <span class="p">)</span>
+    <span class="c1"># Fetch study index.</span>
+    <span class="n">FinnGenStudyIndex</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span>
+        <span class="n">session</span><span class="o">.</span><span class="n">write_mode</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">finngen_study_index_out</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2602,6 +2803,7 @@ <h2 id="otg.finngen.FinnGenStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2618,14 +2820,14 @@ <h2 id="otg.finngen.FinnGenStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M14.47 15.08 11 13V7h1.5v5.25l3.08 1.83c-.41.28-.79.62-1.11 1m-1.39 4.84c-.36.05-.71.08-1.08.08-4.42 0-8-3.58-8-8s3.58-8 8-8 8 3.58 8 8c0 .37-.03.72-.08 1.08.69.1 1.33.32 1.92.64.1-.56.16-1.13.16-1.72 0-5.5-4.5-10-10-10S2 6.5 2 12s4.47 10 10 10c.59 0 1.16-.06 1.72-.16-.32-.59-.54-1.23-.64-1.92M18 15v3h-3v2h3v3h2v-3h3v-2h-3v-3h-2Z"/></svg>
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-05-09T15:08:02+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-05-09</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-21T12:10:40+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-21</span> </span>
       </li>
        
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+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
+            <span class="md-nav__icon md-icon"></span>
+            Development
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/airflow/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Airflow configuration
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/contributing/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Contributing guidelines
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/troubleshooting/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Troubleshooting
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../development/workflows/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Pipeline workflows
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../_python_api/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Python API
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
+            <span class="md-nav__icon md-icon"></span>
+            Python API
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
+            <span class="md-nav__icon md-icon"></span>
+            Datasets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Gene Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/intervals/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Prediction
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus Overlap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant-to-gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasources
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
+            <span class="md-nav__icon md-icon"></span>
+            Datasources
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Eqtl catalogue
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
+            <span class="md-nav__icon md-icon"></span>
+            Eqtl catalogue
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Stats
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Finngen
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
+            <span class="md-nav__icon md-icon"></span>
+            Finngen
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gnomad
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/carma/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/coloc/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Coloc
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LDAnnotator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    PICS
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    L2g
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
+            <span class="md-nav__icon md-icon"></span>
+            L2g
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    W&B evaluator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Factory
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Model
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Trainer
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../_steps/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Steps
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
+            <span class="md-nav__icon md-icon"></span>
+            Steps
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_studies/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      FinnGenSumstatPreprocessStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="FinnGenSumstatPreprocessStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      FinnGenSumstatPreprocessStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="FinnGenSumstatPreprocessStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+  <h1>finngen_sumstat_preprocess</h1>
+
+<div class="doc doc-object doc-class">
+
+
+
+<h2 id="gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep" class="doc doc-heading">
+          <code>gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep</code>
+
+
+<a href="#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
+
+  
+      <p>FinnGen sumstats preprocessing.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/finngen_sumstat_preprocess.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 9</span>
+<span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">FinnGenSumstatPreprocessStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;FinnGen sumstats preprocessing.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">raw_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">out_sumstats_path</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run FinnGen summary stats preprocessing step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            raw_sumstats_path (str): Input raw summary stats path.</span>
+<span class="sd">            out_sumstats_path (str): Output summary stats path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Process summary stats.</span>
+        <span class="p">(</span>
+            <span class="n">FinnGenSummaryStats</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">raw_file</span><span class="o">=</span><span class="n">raw_sumstats_path</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">out_sumstats_path</span><span class="p">)</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">raw_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">out_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run FinnGen summary stats preprocessing step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>raw_sumstats_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input raw summary stats path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>out_sumstats_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Output summary stats path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/finngen_sumstat_preprocess.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">raw_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">out_sumstats_path</span><span class="p">:</span> <span class="nb">str</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run FinnGen summary stats preprocessing step.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        session (Session): Session object.</span>
+<span class="sd">        raw_sumstats_path (str): Input raw summary stats path.</span>
+<span class="sd">        out_sumstats_path (str): Output summary stats path.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># Process summary stats.</span>
+    <span class="p">(</span>
+        <span class="n">FinnGenSummaryStats</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">raw_file</span><span class="o">=</span><span class="n">raw_sumstats_path</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">out_sumstats_path</span><span class="p">)</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+
+  </div>
+
+  </div>
+
+
+</div>
+<hr />
+<div class="md-source-file">
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+      </li>
+      
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+      <li>
+        <span class="icon twemoji">
+          <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M12 2A10 10 0 0 0 2 12c0 4.42 2.87 8.17 6.84 9.5.5.08.66-.23.66-.5v-1.69c-2.77.6-3.36-1.34-3.36-1.34-.46-1.16-1.11-1.47-1.11-1.47-.91-.62.07-.6.07-.6 1 .07 1.53 1.03 1.53 1.03.87 1.52 2.34 1.07 2.91.83.09-.65.35-1.09.63-1.34-2.22-.25-4.55-1.11-4.55-4.92 0-1.11.38-2 1.03-2.71-.1-.25-.45-1.29.1-2.64 0 0 .84-.27 2.75 1.02.79-.22 1.65-.33 2.5-.33.85 0 1.71.11 2.5.33 1.91-1.29 2.75-1.02 2.75-1.02.55 1.35.2 2.39.1 2.64.65.71 1.03 1.6 1.03 2.71 0 3.82-2.34 4.66-4.57 4.91.36.31.69.92.69 1.85V21c0 .27.16.59.67.5C19.14 20.16 22 16.42 22 12A10 10 0 0 0 12 2Z"/></svg>
+        </span>
+        <span class="label"> Contributors </span>
+      </li>
+      <li class="contributors-holder">
+        <ul class="contributors" data-bi-name="contributors"></ul>
+      </li>
+    </ul>
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+                
+              </article>
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+          
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\ No newline at end of file
diff --git a/python_api/step/gene_index/index.html b/python_api/steps/gene_index/index.html
similarity index 72%
rename from python_api/step/gene_index/index.html
rename to python_api/steps/gene_index/index.html
index 22bef6d21..930efa035 100644
--- a/python_api/step/gene_index/index.html
+++ b/python_api/steps/gene_index/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../finngen/">
+        <link rel="prev" href="../finngen_sumstat_preprocess/">
       
       
-        <link rel="next" href="../gwas_catalog_ingestion/">
+        <link rel="next" href="../gwas_catalog_curation/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Gene Index - Open Targets Genetics</title>
+        <title>gene_index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.gene_index.GeneIndexStep" class="md-skip">
+        <a href="#gentropy.gene_index.GeneIndexStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Gene Index
+              gene_index
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
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+  
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+        
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+  
     <li class="md-tabs__item">
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
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     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
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-            Datasource
+            Datasources
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@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
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@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
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@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2132,7 +2251,7 @@
           
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2143,7 +2262,7 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2163,12 +2282,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.gene_index.GeneIndexStep" class="md-nav__link">
+  <a href="#gentropy.gene_index.GeneIndexStep" class="md-nav__link">
     <span class="md-ellipsis">
       GeneIndexStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="GeneIndexStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gene_index.GeneIndexStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2186,12 +2320,54 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2212,7 +2388,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2233,7 +2409,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2250,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.gene_index.GeneIndexStep" class="md-nav__link">
+  <a href="#gentropy.gene_index.GeneIndexStep" class="md-nav__link">
     <span class="md-ellipsis">
       GeneIndexStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="GeneIndexStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gene_index.GeneIndexStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>Gene Index</h1>
+  <h1>gene_index</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.gene_index.GeneIndexStep" class="doc doc-heading">
+          <code>gentropy.gene_index.GeneIndexStep</code>
 
-<h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
-          <code>otg.gene_index.GeneIndexStep</code>
 
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
-
-<a href="#otg.gene_index.GeneIndexStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.gene_index.GeneIndexStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2459,28 +2666,111 @@ <h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
       <p>Gene index step.</p>
 <p>This step generates a gene index dataset from an Open Targets Platform target dataset.</p>
 
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/gene_index.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 8</span>
+<span class="normal"> 9</span>
+<span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">GeneIndexStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Gene index step.</span>
+
+<span class="sd">    This step generates a gene index dataset from an Open Targets Platform target dataset.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">target_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Initialize step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            target_path (str): Input Open Targets Platform target dataset path.</span>
+<span class="sd">            gene_index_path (str): Output gene index dataset path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">platform_target</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">target_path</span><span class="p">)</span>
+        <span class="c1"># Transform</span>
+        <span class="n">gene_index</span> <span class="o">=</span> <span class="n">OpenTargetsTarget</span><span class="o">.</span><span class="n">as_gene_index</span><span class="p">(</span><span class="n">platform_target</span><span class="p">)</span>
+        <span class="c1"># Load</span>
+        <span class="n">gene_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">gene_index_path</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
 
 
-  <p><strong>Attributes:</strong></p>
+<h3 id="gentropy.gene_index.GeneIndexStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">target_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.gene_index.GeneIndexStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Initialize step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>target_path</code></td>
@@ -2489,9 +2779,12 @@ <h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Open targets Platform target dataset path.</p>
+              <p>Input Open Targets Platform target dataset path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>gene_index_path</code></td>
@@ -2500,18 +2793,19 @@ <h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output gene index path.</p>
+              <p>Output gene index dataset path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/gene_index.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">12</span>
-<span class="normal">13</span>
-<span class="normal">14</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gene_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
 <span class="normal">17</span>
@@ -2528,48 +2822,29 @@ <h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
 <span class="normal">28</span>
 <span class="normal">29</span>
 <span class="normal">30</span>
-<span class="normal">31</span>
-<span class="normal">32</span>
-<span class="normal">33</span>
-<span class="normal">34</span>
-<span class="normal">35</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">GeneIndexStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Gene index step.</span>
-
-<span class="sd">    This step generates a gene index dataset from an Open Targets Platform target dataset.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">31</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">target_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Initialize step.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        target_path (str): Open targets Platform target dataset path.</span>
-<span class="sd">        gene_index_path (str): Output gene index path.</span>
+<span class="sd">        target_path (str): Input Open Targets Platform target dataset path.</span>
+<span class="sd">        gene_index_path (str): Output gene index dataset path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">target_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">GeneIndexStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Extract</span>
-        <span class="n">platform_target</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">target_path</span><span class="p">)</span>
-        <span class="c1"># Transform</span>
-        <span class="n">gene_index</span> <span class="o">=</span> <span class="n">OpenTargetsTarget</span><span class="o">.</span><span class="n">as_gene_index</span><span class="p">(</span><span class="n">platform_target</span><span class="p">)</span>
-        <span class="c1"># Load</span>
-        <span class="n">gene_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gene_index_path</span><span class="p">)</span>
+    <span class="n">platform_target</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">target_path</span><span class="p">)</span>
+    <span class="c1"># Transform</span>
+    <span class="n">gene_index</span> <span class="o">=</span> <span class="n">OpenTargetsTarget</span><span class="o">.</span><span class="n">as_gene_index</span><span class="p">(</span><span class="n">platform_target</span><span class="p">)</span>
+    <span class="c1"># Load</span>
+    <span class="n">gene_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">gene_index_path</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2577,6 +2852,7 @@ <h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2600,7 +2876,7 @@ <h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2659,7 +2935,7 @@ <h2 id="otg.gene_index.GeneIndexStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/step/gwas_catalog_ingestion/index.html b/python_api/steps/gwas_catalog_curation/index.html
similarity index 65%
rename from python_api/step/gwas_catalog_ingestion/index.html
rename to python_api/steps/gwas_catalog_curation/index.html
index 2e41c69de..37f6ad049 100644
--- a/python_api/step/gwas_catalog_ingestion/index.html
+++ b/python_api/steps/gwas_catalog_curation/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../gene_index/">
       
       
-        <link rel="next" href="../gwas_catalog_sumstat_preprocess/">
+        <link rel="next" href="../gwas_catalog_inclusion/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>GWAS Catalog - Open Targets Genetics</title>
+        <title>gwas_catalog_study_curation - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="md-skip">
+        <a href="#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              GWAS Catalog
+              gwas_catalog_study_curation
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
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+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
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@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,7 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2153,7 +2272,7 @@
           
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2164,7 +2283,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2184,12 +2303,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="md-nav__link">
+  <a href="#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep" class="md-nav__link">
     <span class="md-ellipsis">
-      GWASCatalogIngestionStep
+      GWASCatalogStudyCurationStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="GWASCatalogStudyCurationStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2207,12 +2341,54 @@
   
   
   
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
     <li class="md-nav__item">
       <a href="../gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2233,7 +2409,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2250,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="md-nav__link">
+  <a href="#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep" class="md-nav__link">
     <span class="md-ellipsis">
-      GWASCatalogIngestionStep
+      GWASCatalogStudyCurationStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="GWASCatalogStudyCurationStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,52 +2647,177 @@
   
 
 
-  <h1>GWAS Catalog</h1>
+  <h1>gwas_catalog_study_curation</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep" class="doc doc-heading">
+          <code>gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep</code>
+
+
+<a href="#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
-<h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-heading">
-          <code>otg.gwas_catalog_ingestion.GWASCatalogIngestionStep</code>
+
+  <div class="doc doc-contents first">
 
   
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
+      <p>Annotate GWAS Catalog studies with additional curation and create a curation backlog.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/gwas_catalog_study_curation.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
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+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span>
+<span class="normal">32</span>
+<span class="normal">33</span>
+<span class="normal">34</span>
+<span class="normal">35</span>
+<span class="normal">36</span>
+<span class="normal">37</span>
+<span class="normal">38</span>
+<span class="normal">39</span>
+<span class="normal">40</span>
+<span class="normal">41</span>
+<span class="normal">42</span>
+<span class="normal">43</span>
+<span class="normal">44</span>
+<span class="normal">45</span>
+<span class="normal">46</span>
+<span class="normal">47</span>
+<span class="normal">48</span>
+<span class="normal">49</span>
+<span class="normal">50</span>
+<span class="normal">51</span>
+<span class="normal">52</span>
+<span class="normal">53</span>
+<span class="normal">54</span>
+<span class="normal">55</span>
+<span class="normal">56</span>
+<span class="normal">57</span>
+<span class="normal">58</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">GWASCatalogStudyCurationStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Annotate GWAS Catalog studies with additional curation and create a curation backlog.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">catalog_sumstats_lut</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gwas_catalog_study_curation_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step to annotate and create backlog.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
+<span class="sd">            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
+<span class="sd">            catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.</span>
+<span class="sd">            gwas_catalog_study_curation_out (str): Path for the updated curation table.</span>
+<span class="sd">            gwas_catalog_study_curation_file (str | None): Path to the original curation table. Optinal</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">catalog_studies</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">catalog_study_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="n">ancestry_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">catalog_ancestry_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="n">sumstats_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="n">catalog_sumstats_lut</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span>
+        <span class="p">)</span>
+        <span class="n">gwas_catalog_study_curation</span> <span class="o">=</span> <span class="n">read_curation_table</span><span class="p">(</span>
+            <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span> <span class="n">session</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Process GWAS Catalog studies and get list of studies for curation:</span>
+        <span class="p">(</span>
+            <span class="n">StudyIndexGWASCatalogParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
+                <span class="n">catalog_studies</span><span class="p">,</span> <span class="n">ancestry_lut</span><span class="p">,</span> <span class="n">sumstats_lut</span>
+            <span class="p">)</span>
+            <span class="c1"># Adding existing curation:</span>
+            <span class="o">.</span><span class="n">annotate_from_study_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">)</span>
+            <span class="c1"># Extract new studies for curation:</span>
+            <span class="o">.</span><span class="n">extract_studies_for_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">)</span>
+            <span class="c1"># Save table:</span>
+            <span class="o">.</span><span class="n">toPandas</span><span class="p">()</span>
+            <span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">gwas_catalog_study_curation_out</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
 
-<a href="#otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
-  <div class="doc doc-contents first">
 
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">catalog_sumstats_lut</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gwas_catalog_study_curation_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
   
-      <p>GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.</p>
-<p>!!!note This step currently only processes the GWAS Catalog curated list of top hits.</p>
+      <p>Run step to annotate and create backlog.</p>
 
 
 
-  <p><strong>Attributes:</strong></p>
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>catalog_study_files</code></td>
@@ -2492,6 +2829,9 @@ <h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-head
               <p>List of raw GWAS catalog studies file.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>catalog_ancestry_files</code></td>
@@ -2503,6 +2843,9 @@ <h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-head
               <p>List of raw ancestry annotations files from GWAS Catalog.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>catalog_sumstats_lut</code></td>
@@ -2514,68 +2857,47 @@ <h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-head
               <p>GWAS Catalog summary statistics lookup table.</p>
             </div>
           </td>
-        </tr>
-        <tr>
-          <td><code>catalog_associations_file</code></td>
-          <td>
-                <code>str</code>
-          </td>
           <td>
-            <div class="doc-md-description">
-              <p>Raw GWAS catalog associations file.</p>
-            </div>
+              <em>required</em>
           </td>
         </tr>
         <tr>
-          <td><code>variant_annotation_path</code></td>
+          <td><code>gwas_catalog_study_curation_out</code></td>
           <td>
                 <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Input variant annotation path.</p>
+              <p>Path for the updated curation table.</p>
             </div>
           </td>
-        </tr>
-        <tr>
-          <td><code>ld_populations</code></td>
           <td>
-                <code>list</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>List of populations to include.</p>
-            </div>
+              <em>required</em>
           </td>
         </tr>
         <tr>
-          <td><code>catalog_studies_out</code></td>
+          <td><code>gwas_catalog_study_curation_file</code></td>
           <td>
-                <code>str</code>
+                <code>str | None</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output GWAS catalog studies path.</p>
+              <p>Path to the original curation table. Optinal</p>
             </div>
           </td>
-        </tr>
-        <tr>
-          <td><code>catalog_associations_out</code></td>
           <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Output GWAS catalog associations path.</p>
-            </div>
+              <em>required</em>
           </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/gwas_catalog_ingestion.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">17</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gwas_catalog_study_curation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
 <span class="normal">18</span>
 <span class="normal">19</span>
 <span class="normal">20</span>
@@ -2616,96 +2938,56 @@ <h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-head
 <span class="normal">55</span>
 <span class="normal">56</span>
 <span class="normal">57</span>
-<span class="normal">58</span>
-<span class="normal">59</span>
-<span class="normal">60</span>
-<span class="normal">61</span>
-<span class="normal">62</span>
-<span class="normal">63</span>
-<span class="normal">64</span>
-<span class="normal">65</span>
-<span class="normal">66</span>
-<span class="normal">67</span>
-<span class="normal">68</span>
-<span class="normal">69</span>
-<span class="normal">70</span>
-<span class="normal">71</span>
-<span class="normal">72</span>
-<span class="normal">73</span>
-<span class="normal">74</span>
-<span class="normal">75</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">GWASCatalogIngestionStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.</span>
-
-<span class="sd">    !!!note This step currently only processes the GWAS Catalog curated list of top hits.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">58</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">catalog_sumstats_lut</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gwas_catalog_study_curation_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run step to annotate and create backlog.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
 <span class="sd">        catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
 <span class="sd">        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
 <span class="sd">        catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.</span>
-<span class="sd">        catalog_associations_file (str): Raw GWAS catalog associations file.</span>
-<span class="sd">        variant_annotation_path (str): Input variant annotation path.</span>
-<span class="sd">        ld_populations (list): List of populations to include.</span>
-<span class="sd">        catalog_studies_out (str): Output GWAS catalog studies path.</span>
-<span class="sd">        catalog_associations_out (str): Output GWAS catalog associations path.</span>
+<span class="sd">        gwas_catalog_study_curation_out (str): Path for the updated curation table.</span>
+<span class="sd">        gwas_catalog_study_curation_file (str | None): Path to the original curation table. Optinal</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">catalog_sumstats_lut</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">catalog_studies_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">catalog_associations_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">GWASCatalogIngestionStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Extract</span>
-        <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">variant_annotation_path</span><span class="p">)</span>
-        <span class="n">catalog_studies</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">catalog_study_files</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
-        <span class="p">)</span>
-        <span class="n">ancestry_lut</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">catalog_ancestry_files</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
-        <span class="p">)</span>
-        <span class="n">sumstats_lut</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">catalog_sumstats_lut</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span>
-        <span class="p">)</span>
-        <span class="n">catalog_associations</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">catalog_associations_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
-        <span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
-
-        <span class="c1"># Transform</span>
-        <span class="n">study_index</span><span class="p">,</span> <span class="n">study_locus</span> <span class="o">=</span> <span class="n">GWASCatalogStudySplitter</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
-            <span class="n">StudyIndexGWASCatalogParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
-                <span class="n">catalog_studies</span><span class="p">,</span> <span class="n">ancestry_lut</span><span class="p">,</span> <span class="n">sumstats_lut</span>
-            <span class="p">),</span>
-            <span class="n">GWASCatalogCuratedAssociationsParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">catalog_associations</span><span class="p">,</span> <span class="n">va</span><span class="p">),</span>
-        <span class="p">)</span>
-
-        <span class="c1"># Load</span>
-        <span class="n">study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">catalog_studies_out</span>
-        <span class="p">)</span>
-        <span class="n">study_locus</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">catalog_associations_out</span>
+    <span class="n">catalog_studies</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="nb">list</span><span class="p">(</span><span class="n">catalog_study_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">ancestry_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="nb">list</span><span class="p">(</span><span class="n">catalog_ancestry_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">sumstats_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="n">catalog_sumstats_lut</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span>
+    <span class="p">)</span>
+    <span class="n">gwas_catalog_study_curation</span> <span class="o">=</span> <span class="n">read_curation_table</span><span class="p">(</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span> <span class="n">session</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Process GWAS Catalog studies and get list of studies for curation:</span>
+    <span class="p">(</span>
+        <span class="n">StudyIndexGWASCatalogParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
+            <span class="n">catalog_studies</span><span class="p">,</span> <span class="n">ancestry_lut</span><span class="p">,</span> <span class="n">sumstats_lut</span>
         <span class="p">)</span>
+        <span class="c1"># Adding existing curation:</span>
+        <span class="o">.</span><span class="n">annotate_from_study_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">)</span>
+        <span class="c1"># Extract new studies for curation:</span>
+        <span class="o">.</span><span class="n">extract_studies_for_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">)</span>
+        <span class="c1"># Save table:</span>
+        <span class="o">.</span><span class="n">toPandas</span><span class="p">()</span>
+        <span class="o">.</span><span class="n">to_csv</span><span class="p">(</span><span class="n">gwas_catalog_study_curation_out</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">index</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+    <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2713,6 +2995,7 @@ <h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-head
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2729,14 +3012,14 @@ <h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-head
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M14.47 15.08 11 13V7h1.5v5.25l3.08 1.83c-.41.28-.79.62-1.11 1m-1.39 4.84c-.36.05-.71.08-1.08.08-4.42 0-8-3.58-8-8s3.58-8 8-8 8 3.58 8 8c0 .37-.03.72-.08 1.08.69.1 1.33.32 1.92.64.1-.56.16-1.13.16-1.72 0-5.5-4.5-10-10-10S2 6.5 2 12s4.47 10 10 10c.59 0 1.16-.06 1.72-.16-.32-.59-.54-1.23-.64-1.92M18 15v3h-3v2h3v3h2v-3h3v-2h-3v-3h-2Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-12T14:35:49+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-12</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-10T11:51:22+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-10</span> </span>
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         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-12T14:35:49+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-12</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2795,7 +3078,7 @@ <h2 id="otg.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-head
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/steps/gwas_catalog_inclusion/index.html b/python_api/steps/gwas_catalog_inclusion/index.html
new file mode 100644
index 000000000..491f895cc
--- /dev/null
+++ b/python_api/steps/gwas_catalog_inclusion/index.html
@@ -0,0 +1,4054 @@
+
+<!doctype html>
+<html lang="en" class="no-js">
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+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/carma/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/coloc/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Coloc
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LDAnnotator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    PICS
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    L2g
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
+            <span class="md-nav__icon md-icon"></span>
+            L2g
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    W&B evaluator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Factory
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Model
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Trainer
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../_steps/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Steps
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
+            <span class="md-nav__icon md-icon"></span>
+            Steps
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_studies/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator" class="md-nav__link">
+    <span class="md-ellipsis">
+      GWASCatalogStudyInclusionGenerator
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="GWASCatalogStudyInclusionGenerator">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.flag_eligible_studies" class="md-nav__link">
+    <span class="md-ellipsis">
+      flag_eligible_studies
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.get_gwas_catalog_study_index" class="md-nav__link">
+    <span class="md-ellipsis">
+      get_gwas_catalog_study_index
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.process_harmonised_list" class="md-nav__link">
+    <span class="md-ellipsis">
+      process_harmonised_list
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
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+        </nav>
+      
+    </li>
+  
+
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+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator" class="md-nav__link">
+    <span class="md-ellipsis">
+      GWASCatalogStudyInclusionGenerator
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="GWASCatalogStudyInclusionGenerator">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.flag_eligible_studies" class="md-nav__link">
+    <span class="md-ellipsis">
+      flag_eligible_studies
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.get_gwas_catalog_study_index" class="md-nav__link">
+    <span class="md-ellipsis">
+      get_gwas_catalog_study_index
+    </span>
+  </a>
+  
+</li>
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.process_harmonised_list" class="md-nav__link">
+    <span class="md-ellipsis">
+      process_harmonised_list
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+  <h1>gwas_catalog_study_inclusion</h1>
+
+<div class="doc doc-object doc-class">
+
+
+
+<h2 id="gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator" class="doc doc-heading">
+          <code>gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator</code>
+
+
+<a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
+
+  
+      <p>GWAS Catalog study eligibility for ingestion based on curation and the provided criteria.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code></summary>
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+<span class="normal">187</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">GWASCatalogStudyInclusionGenerator</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;GWAS Catalog study eligibility for ingestion based on curation and the provided criteria.&quot;&quot;&quot;</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">flag_eligible_studies</span><span class="p">(</span>
+        <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">criteria</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Apply filter on GWAS Catalog studies based on the provided criteria.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            study_index (StudyIndexGWASCatalog): complete study index to be filtered based on the provided filter set</span>
+<span class="sd">            criteria (str): name of the filter set to be applied.</span>
+
+<span class="sd">        Raises:</span>
+<span class="sd">            ValueError: if the provided filter set is not in the accepted values.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            DataFrame: filtered dataframe containing only eligible studies.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">filters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Column</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+            <span class="c1"># Filters applied on studies for ingesting curated associations:</span>
+            <span class="s2">&quot;curation&quot;</span><span class="p">:</span> <span class="p">(</span><span class="n">study_index</span><span class="o">.</span><span class="n">is_gwas</span><span class="p">()</span> <span class="o">&amp;</span> <span class="n">study_index</span><span class="o">.</span><span class="n">has_mapped_trait</span><span class="p">()),</span>
+            <span class="c1"># Filters applied on studies for ingesting summary statistics:</span>
+            <span class="s2">&quot;summary_stats&quot;</span><span class="p">:</span> <span class="p">(</span>
+                <span class="n">study_index</span><span class="o">.</span><span class="n">is_gwas</span><span class="p">()</span>
+                <span class="o">&amp;</span> <span class="n">study_index</span><span class="o">.</span><span class="n">has_mapped_trait</span><span class="p">()</span>
+                <span class="o">&amp;</span> <span class="p">(</span><span class="o">~</span><span class="n">study_index</span><span class="o">.</span><span class="n">is_quality_flagged</span><span class="p">())</span>
+                <span class="o">&amp;</span> <span class="n">study_index</span><span class="o">.</span><span class="n">has_summarystats</span><span class="p">()</span>
+            <span class="p">),</span>
+        <span class="p">}</span>
+
+        <span class="k">if</span> <span class="n">criteria</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">filters</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="sa">f</span><span class="s1">&#39;Wrong value as filter set (</span><span class="si">{</span><span class="n">criteria</span><span class="si">}</span><span class="s1">). Accepted: </span><span class="si">{</span><span class="s2">&quot;,&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">filters</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span><span class="si">}</span><span class="s1">&#39;</span>
+            <span class="p">)</span>
+
+        <span class="c1"># Applying the relevant filter to the study:</span>
+        <span class="k">return</span> <span class="n">study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+            <span class="s2">&quot;studyId&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;studyType&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;traitFromSource&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;traitFromSourceMappedIds&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span>
+            <span class="s2">&quot;hasSumstats&quot;</span><span class="p">,</span>
+            <span class="n">filters</span><span class="p">[</span><span class="n">criteria</span><span class="p">]</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;isEligible&quot;</span><span class="p">),</span>
+        <span class="p">)</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">process_harmonised_list</span><span class="p">(</span><span class="n">studies</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Generate spark dataframe from the provided list.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            studies (list[str]): list of path pointing to harmonised summary statistics.</span>
+<span class="sd">            session (Session): session</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            DataFrame: column name is consistent with original implementatin</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">return</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">createDataFrame</span><span class="p">([{</span><span class="s2">&quot;_c0&quot;</span><span class="p">:</span> <span class="n">path</span><span class="p">}</span> <span class="k">for</span> <span class="n">path</span> <span class="ow">in</span> <span class="n">studies</span><span class="p">])</span>
+
+    <span class="nd">@staticmethod</span>
+    <span class="k">def</span> <span class="nf">get_gwas_catalog_study_index</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">harmonised_study_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Return GWAS Catalog study index.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">            catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
+<span class="sd">            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
+<span class="sd">            harmonised_study_file (str): GWAS Catalog summary statistics lookup table.</span>
+<span class="sd">            catalog_associations_file (str): Raw GWAS catalog associations file.</span>
+<span class="sd">            gwas_catalog_study_curation_file (str): file of the curation table. Optional.</span>
+
+<span class="sd">        Returns:</span>
+<span class="sd">            StudyIndexGWASCatalog: Completely processed and fully annotated study index.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Extract</span>
+        <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+        <span class="n">catalog_studies</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">catalog_study_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="n">ancestry_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">catalog_ancestry_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="n">sumstats_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="n">harmonised_study_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span>
+        <span class="p">)</span>
+        <span class="n">catalog_associations</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="n">catalog_associations_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+        <span class="n">gwas_catalog_study_curation</span> <span class="o">=</span> <span class="n">read_curation_table</span><span class="p">(</span>
+            <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span> <span class="n">session</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Transform</span>
+        <span class="n">study_index</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">GWASCatalogStudySplitter</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+            <span class="n">StudyIndexGWASCatalogParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
+                <span class="n">catalog_studies</span><span class="p">,</span>
+                <span class="n">ancestry_lut</span><span class="p">,</span>
+                <span class="n">sumstats_lut</span><span class="p">,</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">annotate_from_study_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">),</span>
+            <span class="n">GWASCatalogCuratedAssociationsParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">catalog_associations</span><span class="p">,</span> <span class="n">va</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="k">return</span> <span class="n">study_index</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">harmonised_study_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">criteria</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">exclusion_list_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
+<span class="sd">            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
+<span class="sd">            catalog_associations_file (str): Raw GWAS catalog associations file.</span>
+<span class="sd">            gwas_catalog_study_curation_file (str): file of the curation table. Optional.</span>
+<span class="sd">            variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">            harmonised_study_file (str): GWAS Catalog summary statistics lookup table.</span>
+<span class="sd">            criteria (str): name of the filter set to be applied.</span>
+<span class="sd">            inclusion_list_path (str): Output path for the inclusion list.</span>
+<span class="sd">            exclusion_list_path (str): Output path for the exclusion list.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Create study index:</span>
+        <span class="n">study_index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_gwas_catalog_study_index</span><span class="p">(</span>
+            <span class="n">session</span><span class="p">,</span>
+            <span class="n">variant_annotation_path</span><span class="p">,</span>
+            <span class="n">catalog_study_files</span><span class="p">,</span>
+            <span class="n">catalog_ancestry_files</span><span class="p">,</span>
+            <span class="n">harmonised_study_file</span><span class="p">,</span>
+            <span class="n">catalog_associations_file</span><span class="p">,</span>
+            <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Get study indices for inclusion:</span>
+        <span class="n">flagged_studies</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">flag_eligible_studies</span><span class="p">(</span><span class="n">study_index</span><span class="p">,</span> <span class="n">criteria</span><span class="p">)</span>
+
+        <span class="c1"># Output inclusion list:</span>
+        <span class="n">eligible</span> <span class="o">=</span> <span class="p">(</span>
+            <span class="n">flagged_studies</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;isEligible&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+        <span class="p">)</span>
+        <span class="n">eligible</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">inclusion_list_path</span><span class="p">)</span>
+
+        <span class="c1"># Output exclusion list:</span>
+        <span class="n">excluded</span> <span class="o">=</span> <span class="n">flagged_studies</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">~</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;isEligible&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+        <span class="n">excluded</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">exclusion_list_path</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">harmonised_study_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">criteria</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">exclusion_list_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_study_files</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of raw GWAS catalog studies file.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_ancestry_files</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of raw ancestry annotations files from GWAS Catalog.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_associations_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Raw GWAS catalog associations file.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>gwas_catalog_study_curation_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>file of the curation table. Optional.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>variant_annotation_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input variant annotation path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>harmonised_study_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>GWAS Catalog summary statistics lookup table.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>criteria</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>name of the filter set to be applied.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>inclusion_list_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Output path for the inclusion list.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>exclusion_list_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Output path for the exclusion list.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">138</span>
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+<span class="normal">187</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">harmonised_study_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">criteria</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">exclusion_list_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run step.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        session (Session): Session object.</span>
+<span class="sd">        catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
+<span class="sd">        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
+<span class="sd">        catalog_associations_file (str): Raw GWAS catalog associations file.</span>
+<span class="sd">        gwas_catalog_study_curation_file (str): file of the curation table. Optional.</span>
+<span class="sd">        variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">        harmonised_study_file (str): GWAS Catalog summary statistics lookup table.</span>
+<span class="sd">        criteria (str): name of the filter set to be applied.</span>
+<span class="sd">        inclusion_list_path (str): Output path for the inclusion list.</span>
+<span class="sd">        exclusion_list_path (str): Output path for the exclusion list.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># Create study index:</span>
+    <span class="n">study_index</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_gwas_catalog_study_index</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">,</span>
+        <span class="n">variant_annotation_path</span><span class="p">,</span>
+        <span class="n">catalog_study_files</span><span class="p">,</span>
+        <span class="n">catalog_ancestry_files</span><span class="p">,</span>
+        <span class="n">harmonised_study_file</span><span class="p">,</span>
+        <span class="n">catalog_associations_file</span><span class="p">,</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Get study indices for inclusion:</span>
+    <span class="n">flagged_studies</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">flag_eligible_studies</span><span class="p">(</span><span class="n">study_index</span><span class="p">,</span> <span class="n">criteria</span><span class="p">)</span>
+
+    <span class="c1"># Output inclusion list:</span>
+    <span class="n">eligible</span> <span class="o">=</span> <span class="p">(</span>
+        <span class="n">flagged_studies</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;isEligible&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="s2">&quot;studyId&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+    <span class="p">)</span>
+    <span class="n">eligible</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">inclusion_list_path</span><span class="p">)</span>
+
+    <span class="c1"># Output exclusion list:</span>
+    <span class="n">excluded</span> <span class="o">=</span> <span class="n">flagged_studies</span><span class="o">.</span><span class="n">filter</span><span class="p">(</span><span class="o">~</span><span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;isEligible&quot;</span><span class="p">))</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+    <span class="n">excluded</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">exclusion_list_path</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.flag_eligible_studies" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">flag_eligible_studies</span><span class="p">(</span><span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">criteria</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
+  </span>
+
+<a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.flag_eligible_studies" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Apply filter on GWAS Catalog studies based on the provided criteria.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>study_index</code></td>
+          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="../../datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>complete study index to be filtered based on the provided filter set</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>criteria</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>name of the filter set to be applied.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Raises:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td>
+                <code>ValueError</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>if the provided filter set is not in the accepted values.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>DataFrame</code></td>          <td>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>filtered dataframe containing only eligible studies.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">27</span>
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+<span class="normal">69</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+<span class="k">def</span> <span class="nf">flag_eligible_studies</span><span class="p">(</span>
+    <span class="n">study_index</span><span class="p">:</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">,</span> <span class="n">criteria</span><span class="p">:</span> <span class="nb">str</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Apply filter on GWAS Catalog studies based on the provided criteria.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        study_index (StudyIndexGWASCatalog): complete study index to be filtered based on the provided filter set</span>
+<span class="sd">        criteria (str): name of the filter set to be applied.</span>
+
+<span class="sd">    Raises:</span>
+<span class="sd">        ValueError: if the provided filter set is not in the accepted values.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        DataFrame: filtered dataframe containing only eligible studies.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="n">filters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Column</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+        <span class="c1"># Filters applied on studies for ingesting curated associations:</span>
+        <span class="s2">&quot;curation&quot;</span><span class="p">:</span> <span class="p">(</span><span class="n">study_index</span><span class="o">.</span><span class="n">is_gwas</span><span class="p">()</span> <span class="o">&amp;</span> <span class="n">study_index</span><span class="o">.</span><span class="n">has_mapped_trait</span><span class="p">()),</span>
+        <span class="c1"># Filters applied on studies for ingesting summary statistics:</span>
+        <span class="s2">&quot;summary_stats&quot;</span><span class="p">:</span> <span class="p">(</span>
+            <span class="n">study_index</span><span class="o">.</span><span class="n">is_gwas</span><span class="p">()</span>
+            <span class="o">&amp;</span> <span class="n">study_index</span><span class="o">.</span><span class="n">has_mapped_trait</span><span class="p">()</span>
+            <span class="o">&amp;</span> <span class="p">(</span><span class="o">~</span><span class="n">study_index</span><span class="o">.</span><span class="n">is_quality_flagged</span><span class="p">())</span>
+            <span class="o">&amp;</span> <span class="n">study_index</span><span class="o">.</span><span class="n">has_summarystats</span><span class="p">()</span>
+        <span class="p">),</span>
+    <span class="p">}</span>
+
+    <span class="k">if</span> <span class="n">criteria</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">filters</span><span class="p">:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="sa">f</span><span class="s1">&#39;Wrong value as filter set (</span><span class="si">{</span><span class="n">criteria</span><span class="si">}</span><span class="s1">). Accepted: </span><span class="si">{</span><span class="s2">&quot;,&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">filters</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span><span class="si">}</span><span class="s1">&#39;</span>
+        <span class="p">)</span>
+
+    <span class="c1"># Applying the relevant filter to the study:</span>
+    <span class="k">return</span> <span class="n">study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+        <span class="s2">&quot;studyId&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;studyType&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;traitFromSource&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;traitFromSourceMappedIds&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;qualityControls&quot;</span><span class="p">,</span>
+        <span class="s2">&quot;hasSumstats&quot;</span><span class="p">,</span>
+        <span class="n">filters</span><span class="p">[</span><span class="n">criteria</span><span class="p">]</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;isEligible&quot;</span><span class="p">),</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.get_gwas_catalog_study_index" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">get_gwas_catalog_study_index</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">harmonised_study_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span></code>
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
+  </span>
+
+<a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.get_gwas_catalog_study_index" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Return GWAS Catalog study index.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>variant_annotation_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input variant annotation path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_study_files</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of raw GWAS catalog studies file.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_ancestry_files</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of raw ancestry annotations files from GWAS Catalog.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>harmonised_study_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>GWAS Catalog summary statistics lookup table.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_associations_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Raw GWAS catalog associations file.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>gwas_catalog_study_curation_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>file of the curation table. Optional.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>StudyIndexGWASCatalog</code></td>          <td>
+                <code><a class="autorefs autorefs-internal" title="gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog" href="../../datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog">StudyIndexGWASCatalog</a></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Completely processed and fully annotated study index.</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 84</span>
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+<span class="normal">136</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+<span class="k">def</span> <span class="nf">get_gwas_catalog_study_index</span><span class="p">(</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">harmonised_study_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="n">StudyIndexGWASCatalog</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Return GWAS Catalog study index.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        session (Session): Session object.</span>
+<span class="sd">        variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">        catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
+<span class="sd">        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
+<span class="sd">        harmonised_study_file (str): GWAS Catalog summary statistics lookup table.</span>
+<span class="sd">        catalog_associations_file (str): Raw GWAS catalog associations file.</span>
+<span class="sd">        gwas_catalog_study_curation_file (str): file of the curation table. Optional.</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        StudyIndexGWASCatalog: Completely processed and fully annotated study index.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># Extract</span>
+    <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+    <span class="n">catalog_studies</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="nb">list</span><span class="p">(</span><span class="n">catalog_study_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">ancestry_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="nb">list</span><span class="p">(</span><span class="n">catalog_ancestry_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">sumstats_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="n">harmonised_study_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span>
+    <span class="p">)</span>
+    <span class="n">catalog_associations</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="n">catalog_associations_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+    <span class="n">gwas_catalog_study_curation</span> <span class="o">=</span> <span class="n">read_curation_table</span><span class="p">(</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span> <span class="n">session</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Transform</span>
+    <span class="n">study_index</span><span class="p">,</span> <span class="n">_</span> <span class="o">=</span> <span class="n">GWASCatalogStudySplitter</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+        <span class="n">StudyIndexGWASCatalogParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
+            <span class="n">catalog_studies</span><span class="p">,</span>
+            <span class="n">ancestry_lut</span><span class="p">,</span>
+            <span class="n">sumstats_lut</span><span class="p">,</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">annotate_from_study_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">),</span>
+        <span class="n">GWASCatalogCuratedAssociationsParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">catalog_associations</span><span class="p">,</span> <span class="n">va</span><span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="k">return</span> <span class="n">study_index</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.process_harmonised_list" class="doc doc-heading">
+          <code class="highlight language-python"><span class="n">process_harmonised_list</span><span class="p">(</span><span class="n">studies</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span></code>
+  
+  <span class="doc doc-labels">
+      <small class="doc doc-label doc-label-staticmethod"><code>staticmethod</code></small>
+  </span>
+
+<a href="#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.process_harmonised_list" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Generate spark dataframe from the provided list.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>studies</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>list of path pointing to harmonised summary statistics.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>session</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Returns:</strong></p>
+  <table>
+    <thead>
+      <tr>
+<th>Name</th>        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+<td><code>DataFrame</code></td>          <td>
+                <code><span title="pyspark.sql.DataFrame">DataFrame</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>column name is consistent with original implementatin</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">71</span>
+<span class="normal">72</span>
+<span class="normal">73</span>
+<span class="normal">74</span>
+<span class="normal">75</span>
+<span class="normal">76</span>
+<span class="normal">77</span>
+<span class="normal">78</span>
+<span class="normal">79</span>
+<span class="normal">80</span>
+<span class="normal">81</span>
+<span class="normal">82</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@staticmethod</span>
+<span class="k">def</span> <span class="nf">process_harmonised_list</span><span class="p">(</span><span class="n">studies</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">DataFrame</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Generate spark dataframe from the provided list.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        studies (list[str]): list of path pointing to harmonised summary statistics.</span>
+<span class="sd">        session (Session): session</span>
+
+<span class="sd">    Returns:</span>
+<span class="sd">        DataFrame: column name is consistent with original implementatin</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="k">return</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">createDataFrame</span><span class="p">([{</span><span class="s2">&quot;_c0&quot;</span><span class="p">:</span> <span class="n">path</span><span class="p">}</span> <span class="k">for</span> <span class="n">path</span> <span class="ow">in</span> <span class="n">studies</span><span class="p">])</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
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+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Locus Overlap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variant-to-gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasources
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
+            <span class="md-nav__icon md-icon"></span>
+            Datasources
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Eqtl catalogue
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
+            <span class="md-nav__icon md-icon"></span>
+            Eqtl catalogue
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Stats
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Finngen
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
+            <span class="md-nav__icon md-icon"></span>
+            Finngen
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gnomad
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/carma/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/coloc/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Coloc
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LDAnnotator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    PICS
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    L2g
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
+            <span class="md-nav__icon md-icon"></span>
+            L2g
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    W&B evaluator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Factory
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Model
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Trainer
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../_steps/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Steps
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
+            <span class="md-nav__icon md-icon"></span>
+            Steps
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_studies/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      GWASCatalogIngestionStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="GWASCatalogIngestionStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      GWASCatalogIngestionStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="GWASCatalogIngestionStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+  <h1>gwas_catalog_ingestion</h1>
+
+<div class="doc doc-object doc-class">
+
+
+
+<h2 id="gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="doc doc-heading">
+          <code>gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep</code>
+
+
+<a href="#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
+
+  
+      <p>GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.</p>
+<p>!!! note This step currently only processes the GWAS Catalog curated list of top hits.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/gwas_catalog_ingestion.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">16</span>
+<span class="normal">17</span>
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+<span class="normal">86</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">GWASCatalogIngestionStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.</span>
+
+<span class="sd">    !!! note This step currently only processes the GWAS Catalog curated list of top hits.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">catalog_sumstats_lut</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">catalog_studies_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">catalog_associations_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
+<span class="sd">            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
+<span class="sd">            catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.</span>
+<span class="sd">            catalog_associations_file (str): Raw GWAS catalog associations file.</span>
+<span class="sd">            variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">            catalog_studies_out (str): Output GWAS catalog studies path.</span>
+<span class="sd">            catalog_associations_out (str): Output GWAS catalog associations path.</span>
+<span class="sd">            gwas_catalog_study_curation_file (str | None): file of the curation table. Optional.</span>
+<span class="sd">            inclusion_list_path (str | None): optional inclusion list (parquet)</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Extract</span>
+        <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+        <span class="n">catalog_studies</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">catalog_study_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="n">ancestry_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">catalog_ancestry_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+        <span class="n">sumstats_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="n">catalog_sumstats_lut</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span>
+        <span class="p">)</span>
+        <span class="n">catalog_associations</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="n">catalog_associations_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+        <span class="n">gwas_catalog_study_curation</span> <span class="o">=</span> <span class="n">read_curation_table</span><span class="p">(</span>
+            <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span> <span class="n">session</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Transform</span>
+        <span class="n">study_index</span><span class="p">,</span> <span class="n">study_locus</span> <span class="o">=</span> <span class="n">GWASCatalogStudySplitter</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+            <span class="n">StudyIndexGWASCatalogParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
+                <span class="n">catalog_studies</span><span class="p">,</span> <span class="n">ancestry_lut</span><span class="p">,</span> <span class="n">sumstats_lut</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">annotate_from_study_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">),</span>
+            <span class="n">GWASCatalogCuratedAssociationsParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">catalog_associations</span><span class="p">,</span> <span class="n">va</span><span class="p">),</span>
+        <span class="p">)</span>
+
+        <span class="c1"># if inclusion list is provided apply filter:</span>
+        <span class="k">if</span> <span class="n">inclusion_list_path</span><span class="p">:</span>
+            <span class="n">inclusion_list</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
+                <span class="n">inclusion_list_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+            <span class="p">)</span>
+
+            <span class="n">study_index</span> <span class="o">=</span> <span class="n">study_index</span><span class="o">.</span><span class="n">apply_inclusion_list</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">)</span>
+            <span class="n">study_locus</span> <span class="o">=</span> <span class="n">study_locus</span><span class="o">.</span><span class="n">apply_inclusion_list</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">)</span>
+
+        <span class="c1"># Load</span>
+        <span class="n">study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">catalog_studies_out</span><span class="p">)</span>
+        <span class="n">study_locus</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">catalog_associations_out</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">catalog_sumstats_lut</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">catalog_studies_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">catalog_associations_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_study_files</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of raw GWAS catalog studies file.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_ancestry_files</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of raw ancestry annotations files from GWAS Catalog.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_sumstats_lut</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>GWAS Catalog summary statistics lookup table.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_associations_file</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Raw GWAS catalog associations file.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>variant_annotation_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input variant annotation path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_studies_out</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Output GWAS catalog studies path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>catalog_associations_out</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Output GWAS catalog associations path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>gwas_catalog_study_curation_file</code></td>
+          <td>
+                <code>str | None</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>file of the curation table. Optional.</p>
+            </div>
+          </td>
+          <td>
+                <code>None</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>inclusion_list_path</code></td>
+          <td>
+                <code>str | None</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>optional inclusion list (parquet)</p>
+            </div>
+          </td>
+          <td>
+                <code>None</code>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gwas_catalog_ingestion.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">22</span>
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+<span class="normal">86</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">catalog_study_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">catalog_ancestry_files</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">catalog_sumstats_lut</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">catalog_associations_file</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">catalog_studies_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">catalog_associations_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gwas_catalog_study_curation_file</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run step.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        session (Session): Session object.</span>
+<span class="sd">        catalog_study_files (list[str]): List of raw GWAS catalog studies file.</span>
+<span class="sd">        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.</span>
+<span class="sd">        catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.</span>
+<span class="sd">        catalog_associations_file (str): Raw GWAS catalog associations file.</span>
+<span class="sd">        variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">        catalog_studies_out (str): Output GWAS catalog studies path.</span>
+<span class="sd">        catalog_associations_out (str): Output GWAS catalog associations path.</span>
+<span class="sd">        gwas_catalog_study_curation_file (str | None): file of the curation table. Optional.</span>
+<span class="sd">        inclusion_list_path (str | None): optional inclusion list (parquet)</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># Extract</span>
+    <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+    <span class="n">catalog_studies</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="nb">list</span><span class="p">(</span><span class="n">catalog_study_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">ancestry_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="nb">list</span><span class="p">(</span><span class="n">catalog_ancestry_files</span><span class="p">),</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">sumstats_lut</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="n">catalog_sumstats_lut</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">False</span>
+    <span class="p">)</span>
+    <span class="n">catalog_associations</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="n">catalog_associations_file</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+    <span class="n">gwas_catalog_study_curation</span> <span class="o">=</span> <span class="n">read_curation_table</span><span class="p">(</span>
+        <span class="n">gwas_catalog_study_curation_file</span><span class="p">,</span> <span class="n">session</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Transform</span>
+    <span class="n">study_index</span><span class="p">,</span> <span class="n">study_locus</span> <span class="o">=</span> <span class="n">GWASCatalogStudySplitter</span><span class="o">.</span><span class="n">split</span><span class="p">(</span>
+        <span class="n">StudyIndexGWASCatalogParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
+            <span class="n">catalog_studies</span><span class="p">,</span> <span class="n">ancestry_lut</span><span class="p">,</span> <span class="n">sumstats_lut</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">annotate_from_study_curation</span><span class="p">(</span><span class="n">gwas_catalog_study_curation</span><span class="p">),</span>
+        <span class="n">GWASCatalogCuratedAssociationsParser</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span><span class="n">catalog_associations</span><span class="p">,</span> <span class="n">va</span><span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="c1"># if inclusion list is provided apply filter:</span>
+    <span class="k">if</span> <span class="n">inclusion_list_path</span><span class="p">:</span>
+        <span class="n">inclusion_list</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
+            <span class="n">inclusion_list_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+
+        <span class="n">study_index</span> <span class="o">=</span> <span class="n">study_index</span><span class="o">.</span><span class="n">apply_inclusion_list</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">)</span>
+        <span class="n">study_locus</span> <span class="o">=</span> <span class="n">study_locus</span><span class="o">.</span><span class="n">apply_inclusion_list</span><span class="p">(</span><span class="n">inclusion_list</span><span class="p">)</span>
+
+    <span class="c1"># Load</span>
+    <span class="n">study_index</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">catalog_studies_out</span><span class="p">)</span>
+    <span class="n">study_locus</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">catalog_associations_out</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+
+  </div>
+
+  </div>
+
+
+</div>
+<hr />
+<div class="md-source-file">
+  <small>
+    <ul
+      class="metadata page-metadata"
+      data-bi-name="page info"
+      lang="en-us"
+      dir="ltr"
+    >
+      <!-- mkdocs-git-revision-date-plugin -->
+      
+      <li>
+        <span class="icon twemoji">
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+        </span>
+        <span class="label"> Contributors </span>
+      </li>
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+            </div>
+          
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+<script>var target=document.getElementById(location.hash.slice(1));target&&target.name&&(target.checked=target.name.startsWith("__tabbed_"))</script>
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+  
+  <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M13 20h-2V8l-5.5 5.5-1.42-1.42L12 4.16l7.92 7.92-1.42 1.42L13 8v12Z"/></svg>
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\ No newline at end of file
diff --git a/python_api/step/gwas_catalog_sumstat_preprocess/index.html b/python_api/steps/gwas_catalog_sumstat_preprocess/index.html
similarity index 71%
rename from python_api/step/gwas_catalog_sumstat_preprocess/index.html
rename to python_api/steps/gwas_catalog_sumstat_preprocess/index.html
index 416aed174..3a534e604 100644
--- a/python_api/step/gwas_catalog_sumstat_preprocess/index.html
+++ b/python_api/steps/gwas_catalog_sumstat_preprocess/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>GWAS Catalog sumstat preprocess - Open Targets Genetics</title>
+        <title>gwas_catalog_sumstat_preprocess - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="md-skip">
+        <a href="#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              GWAS Catalog sumstat preprocess
+              gwas_catalog_sumstat_preprocess
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
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+  
+  Home
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+        
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
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+      
+        
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+  
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@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
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@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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+      <a href="../../../installation/" class="md-nav__link">
         
   
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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@@ -414,6 +448,123 @@
         
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+            <span class="md-nav__icon md-icon"></span>
+            How-to
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+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
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+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
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+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
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+            
+          </ul>
+        </nav>
+      
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+  
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+  
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+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+    </li>
+  
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+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
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-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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@@ -612,7 +763,7 @@
   
   
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-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2146,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2174,7 +2335,7 @@
           
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2185,7 +2346,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2205,12 +2366,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="md-nav__link">
+  <a href="#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogSumstatsPreprocessStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="GWASCatalogSumstatsPreprocessStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2233,7 +2409,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2250,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="md-nav__link">
+  <a href="#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="md-nav__link">
     <span class="md-ellipsis">
       GWASCatalogSumstatsPreprocessStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="GWASCatalogSumstatsPreprocessStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>GWAS Catalog sumstat preprocess</h1>
+  <h1>gwas_catalog_sumstat_preprocess</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="doc doc-heading">
+          <code>gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep</code>
 
-<h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="doc doc-heading">
-          <code>otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep</code>
 
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
-
-<a href="#otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2458,28 +2665,99 @@ <h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" c
   
       <p>Step to preprocess GWAS Catalog harmonised summary stats.</p>
 
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/gwas_catalog_sumstat_preprocess.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">GWASCatalogSumstatsPreprocessStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Step to preprocess GWAS Catalog harmonised summary stats.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">raw_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">out_sumstats_path</span><span class="p">:</span> <span class="nb">str</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step to preprocess GWAS Catalog harmonised summary stats and produce SummaryStatistics dataset.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            raw_sumstats_path (str): Input GWAS Catalog harmonised summary stats path.</span>
+<span class="sd">            out_sumstats_path (str): Output SummaryStatistics dataset path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Processing dataset:</span>
+        <span class="n">GWASCatalogSummaryStatistics</span><span class="o">.</span><span class="n">from_gwas_harmonized_summary_stats</span><span class="p">(</span>
+            <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">raw_sumstats_path</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">out_sumstats_path</span><span class="p">)</span>
+        <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Processing dataset successfully completed.&quot;</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
 
 
-  <p><strong>Attributes:</strong></p>
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">raw_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">out_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run step to preprocess GWAS Catalog harmonised summary stats and produce SummaryStatistics dataset.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>raw_sumstats_path</code></td>
@@ -2488,9 +2766,12 @@ <h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" c
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Input raw GWAS Catalog summary statistics path.</p>
+              <p>Input GWAS Catalog harmonised summary stats path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>out_sumstats_path</code></td>
@@ -2499,17 +2780,19 @@ <h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" c
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output GWAS Catalog summary statistics path.</p>
+              <p>Output SummaryStatistics dataset path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/gwas_catalog_sumstat_preprocess.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">12</span>
-<span class="normal">13</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/gwas_catalog_sumstat_preprocess.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">13</span>
 <span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
@@ -2523,54 +2806,26 @@ <h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" c
 <span class="normal">24</span>
 <span class="normal">25</span>
 <span class="normal">26</span>
-<span class="normal">27</span>
-<span class="normal">28</span>
-<span class="normal">29</span>
-<span class="normal">30</span>
-<span class="normal">31</span>
-<span class="normal">32</span>
-<span class="normal">33</span>
-<span class="normal">34</span>
-<span class="normal">35</span>
-<span class="normal">36</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">GWASCatalogSumstatsPreprocessStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Step to preprocess GWAS Catalog harmonised summary stats.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">27</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">raw_sumstats_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">out_sumstats_path</span><span class="p">:</span> <span class="nb">str</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run step to preprocess GWAS Catalog harmonised summary stats and produce SummaryStatistics dataset.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        raw_sumstats_path (str): Input raw GWAS Catalog summary statistics path.</span>
-<span class="sd">        out_sumstats_path (str): Output GWAS Catalog summary statistics path.</span>
+<span class="sd">        raw_sumstats_path (str): Input GWAS Catalog harmonised summary stats path.</span>
+<span class="sd">        out_sumstats_path (str): Output SummaryStatistics dataset path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">raw_sumstats_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">out_sumstats_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">GWASCatalogSumstatsPreprocessStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Extract</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">raw_sumstats_path</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">out_sumstats_path</span><span class="p">)</span>
-
-        <span class="c1"># Processing dataset:</span>
-        <span class="n">GWASCatalogSummaryStatistics</span><span class="o">.</span><span class="n">from_gwas_harmonized_summary_stats</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">raw_sumstats_path</span>
-        <span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">out_sumstats_path</span><span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Processing dataset successfully completed.&quot;</span><span class="p">)</span>
+    <span class="c1"># Processing dataset:</span>
+    <span class="n">GWASCatalogSummaryStatistics</span><span class="o">.</span><span class="n">from_gwas_harmonized_summary_stats</span><span class="p">(</span>
+        <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">raw_sumstats_path</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">out_sumstats_path</span><span class="p">)</span>
+    <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Processing dataset successfully completed.&quot;</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2578,6 +2833,7 @@ <h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" c
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2601,7 +2857,7 @@ <h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" c
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2660,7 +2916,7 @@ <h2 id="otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep" c
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/step/l2g/index.html b/python_api/steps/l2g/index.html
similarity index 56%
rename from python_api/step/l2g/index.html
rename to python_api/steps/l2g/index.html
index 9b4ea666b..bbf07f38e 100644
--- a/python_api/step/l2g/index.html
+++ b/python_api/steps/l2g/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../gwas_catalog_sumstat_preprocess/">
       
       
-        <link rel="next" href="../ld_index/">
+        <link rel="next" href="../ld_clump/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Locus-to-gene (L2G) - Open Targets Genetics</title>
+        <title>locus_to_gene - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.l2g.LocusToGeneStep" class="md-skip">
+        <a href="#gentropy.l2g.LocusToGeneStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Locus-to-gene (L2G)
+              locus_to_gene
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,6 +1778,14 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
@@ -1601,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1637,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1651,67 +1852,6 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
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-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
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-    
-    
-    
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-      
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-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
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-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
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-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
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-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1719,7 +1859,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1740,7 +1880,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1761,7 +1901,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1782,7 +1922,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1803,7 +1943,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1823,43 +1963,22 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
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-
-              
-            
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-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2146,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2167,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2195,7 +2356,7 @@
           
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2206,7 +2367,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2226,12 +2387,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.l2g.LocusToGeneStep" class="md-nav__link">
+  <a href="#gentropy.l2g.LocusToGeneStep" class="md-nav__link">
     <span class="md-ellipsis">
       LocusToGeneStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="LocusToGeneStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.l2g.LocusToGeneStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2250,11 +2426,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.l2g.LocusToGeneStep" class="md-nav__link">
+  <a href="#gentropy.l2g.LocusToGeneStep" class="md-nav__link">
     <span class="md-ellipsis">
       LocusToGeneStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="LocusToGeneStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.l2g.LocusToGeneStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>Locus-to-gene (L2G)</h1>
+  <h1>locus_to_gene</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.l2g.LocusToGeneStep" class="doc doc-heading">
+          <code>gentropy.l2g.LocusToGeneStep</code>
 
-<h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
-          <code>otg.l2g.LocusToGeneStep</code>
-
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
 
-<a href="#otg.l2g.LocusToGeneStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.l2g.LocusToGeneStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2458,200 +2665,13 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
   
       <p>Locus to gene step.</p>
 
-
-
-  <p><strong>Attributes:</strong></p>
-  <table>
-    <thead>
-      <tr>
-        <th>Name</th>
-        <th>Type</th>
-        <th>Description</th>
-      </tr>
-    </thead>
-    <tbody>
-        <tr>
-          <td><code>session</code></td>
-          <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Session object.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>extended_spark_conf</code></td>
-          <td>
-                <code>dict[str, str] | None</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Extended Spark configuration.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>run_mode</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>One of "train" or "predict".</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>wandb_run_name</code></td>
-          <td>
-                <code>str | None</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Name of the run to be tracked on W&amp;B.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>perform_cross_validation</code></td>
-          <td>
-                <code>bool</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Whether to perform cross validation.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>model_path</code></td>
-          <td>
-                <code>str | None</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to save the model.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>predictions_path</code></td>
-          <td>
-                <code>str | None</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to save the predictions.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>credible_set_path</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to credible set Parquet files.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>variant_gene_path</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to variant to gene Parquet files.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>colocalisation_path</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to colocalisation Parquet files.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>study_index_path</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to study index Parquet files.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>study_locus_overlap_path</code></td>
-          <td>
-                <code>str</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to study locus overlap Parquet files.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>gold_standard_curation_path</code></td>
-          <td>
-                <code>str | None</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to gold standard curation JSON files.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>gene_interactions_path</code></td>
-          <td>
-                <code>str | None</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Path to gene interactions Parquet files.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>features_list</code></td>
-          <td>
-                <code>list[str]</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>List of features to use.</p>
-            </div>
-          </td>
-        </tr>
-        <tr>
-          <td><code>hyperparameters</code></td>
-          <td>
-                <code>dict</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>Hyperparameters for the model.</p>
-            </div>
-          </td>
-        </tr>
-    </tbody>
-  </table>
-
             <details class="quote">
-              <summary>Source code in <code>src/otg/l2g.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 26</span>
+              <summary>Source code in <code>src/gentropy/l2g.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 22</span>
+<span class="normal"> 23</span>
+<span class="normal"> 24</span>
+<span class="normal"> 25</span>
+<span class="normal"> 26</span>
 <span class="normal"> 27</span>
 <span class="normal"> 28</span>
 <span class="normal"> 29</span>
@@ -2801,141 +2821,103 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
 <span class="normal">173</span>
 <span class="normal">174</span>
 <span class="normal">175</span>
-<span class="normal">176</span>
-<span class="normal">177</span>
-<span class="normal">178</span>
-<span class="normal">179</span>
-<span class="normal">180</span>
-<span class="normal">181</span>
-<span class="normal">182</span>
-<span class="normal">183</span>
-<span class="normal">184</span>
-<span class="normal">185</span>
-<span class="normal">186</span>
-<span class="normal">187</span>
-<span class="normal">188</span>
-<span class="normal">189</span>
-<span class="normal">190</span>
-<span class="normal">191</span>
-<span class="normal">192</span>
-<span class="normal">193</span>
-<span class="normal">194</span>
-<span class="normal">195</span>
-<span class="normal">196</span>
-<span class="normal">197</span>
-<span class="normal">198</span>
-<span class="normal">199</span>
-<span class="normal">200</span>
-<span class="normal">201</span>
-<span class="normal">202</span>
-<span class="normal">203</span>
-<span class="normal">204</span>
-<span class="normal">205</span>
-<span class="normal">206</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">LocusToGeneStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Locus to gene step.</span>
-
-<span class="sd">    Attributes:</span>
-<span class="sd">        session (Session): Session object.</span>
-<span class="sd">        extended_spark_conf (dict[str, str] | None): Extended Spark configuration.</span>
-<span class="sd">        run_mode (str): One of &quot;train&quot; or &quot;predict&quot;.</span>
-<span class="sd">        wandb_run_name (str | None): Name of the run to be tracked on W&amp;B.</span>
-<span class="sd">        perform_cross_validation (bool): Whether to perform cross validation.</span>
-<span class="sd">        model_path (str | None): Path to save the model.</span>
-<span class="sd">        predictions_path (str | None): Path to save the predictions.</span>
-<span class="sd">        credible_set_path (str): Path to credible set Parquet files.</span>
-<span class="sd">        variant_gene_path (str): Path to variant to gene Parquet files.</span>
-<span class="sd">        colocalisation_path (str): Path to colocalisation Parquet files.</span>
-<span class="sd">        study_index_path (str): Path to study index Parquet files.</span>
-<span class="sd">        study_locus_overlap_path (str): Path to study locus overlap Parquet files.</span>
-<span class="sd">        gold_standard_curation_path (str | None): Path to gold standard curation JSON files.</span>
-<span class="sd">        gene_interactions_path (str | None): Path to gene interactions Parquet files.</span>
-<span class="sd">        features_list (list[str]): List of features to use.</span>
-<span class="sd">        hyperparameters (dict): Hyperparameters for the model.</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">extended_spark_conf</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">run_mode</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">wandb_run_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span>
-    <span class="n">perform_cross_validation</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span>
-    <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">predictions_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">variant_gene_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">colocalisation_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">study_locus_overlap_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">gold_standard_curation_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">gene_interactions_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span>
-        <span class="n">default_factory</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="p">[</span>
-            <span class="c1"># average distance of all tagging variants to gene TSS</span>
-            <span class="s2">&quot;distanceTssMean&quot;</span><span class="p">,</span>
-            <span class="c1"># # minimum distance of all tagging variants to gene TSS</span>
-            <span class="c1"># &quot;distanceTssMinimum&quot;,</span>
-            <span class="c1"># # max clpp for each (study, locus, gene) aggregating over all eQTLs</span>
-            <span class="c1"># &quot;eqtlColocClppLocalMaximum&quot;,</span>
-            <span class="c1"># # max clpp for each (study, locus) aggregating over all eQTLs</span>
-            <span class="c1"># &quot;eqtlColocClppNeighborhoodMaximum&quot;,</span>
-            <span class="c1"># # max log-likelihood ratio value for each (study, locus, gene) aggregating over all eQTLs</span>
-            <span class="c1"># &quot;eqtlColocLlrLocalMaximum&quot;,</span>
-            <span class="c1"># # max log-likelihood ratio value for each (study, locus) aggregating over all eQTLs</span>
-            <span class="c1"># &quot;eqtlColocLlrNeighborhoodMaximum&quot;,</span>
-            <span class="c1"># # max clpp for each (study, locus, gene) aggregating over all pQTLs</span>
-            <span class="c1"># &quot;pqtlColocClppLocalMaximum&quot;,</span>
-            <span class="c1"># # max clpp for each (study, locus) aggregating over all pQTLs</span>
-            <span class="c1"># &quot;pqtlColocClppNeighborhoodMaximum&quot;,</span>
-            <span class="c1"># # max log-likelihood ratio value for each (study, locus, gene) aggregating over all pQTLs</span>
-            <span class="c1"># &quot;pqtlColocLlrLocalMaximum&quot;,</span>
-            <span class="c1"># # max log-likelihood ratio value for each (study, locus) aggregating over all pQTLs</span>
-            <span class="c1"># &quot;pqtlColocLlrNeighborhoodMaximum&quot;,</span>
-            <span class="c1"># # max clpp for each (study, locus, gene) aggregating over all sQTLs</span>
-            <span class="c1"># &quot;sqtlColocClppLocalMaximum&quot;,</span>
-            <span class="c1"># # max clpp for each (study, locus) aggregating over all sQTLs</span>
-            <span class="c1"># &quot;sqtlColocClppNeighborhoodMaximum&quot;,</span>
-            <span class="c1"># # max log-likelihood ratio value for each (study, locus, gene) aggregating over all sQTLs</span>
-            <span class="c1"># &quot;sqtlColocLlrLocalMaximum&quot;,</span>
-            <span class="c1"># # max log-likelihood ratio value for each (study, locus) aggregating over all sQTLs</span>
-            <span class="c1"># &quot;sqtlColocLlrNeighborhoodMaximum&quot;,</span>
-        <span class="p">]</span>
-    <span class="p">)</span>
-    <span class="n">hyperparameters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span>
-        <span class="n">default_factory</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="p">{</span>
-            <span class="s2">&quot;max_depth&quot;</span><span class="p">:</span> <span class="mi">5</span><span class="p">,</span>
-            <span class="s2">&quot;loss_function&quot;</span><span class="p">:</span> <span class="s2">&quot;binary:logistic&quot;</span><span class="p">,</span>
-        <span class="p">}</span>
-    <span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LocusToGeneStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="normal">176</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">LocusToGeneStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Locus to gene step.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">run_mode</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">predictions_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">variant_gene_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">colocalisation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gold_standard_curation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gene_interactions_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">hyperparameters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span>
+        <span class="n">wandb_run_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">perform_cross_validation</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.</span>
 
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            run_mode (str): One of &quot;train&quot; or &quot;predict&quot;.</span>
+<span class="sd">            model_path (str): Path to save the model.</span>
+<span class="sd">            predictions_path (str): Path to save the predictions.</span>
+<span class="sd">            credible_set_path (str): Path to credible set Parquet files.</span>
+<span class="sd">            variant_gene_path (str): Path to variant to gene Parquet files.</span>
+<span class="sd">            colocalisation_path (str): Path to colocalisation Parquet files.</span>
+<span class="sd">            study_index_path (str): Path to study index Parquet files.</span>
+<span class="sd">            gold_standard_curation_path (str): Path to gold standard curation JSON files.</span>
+<span class="sd">            gene_interactions_path (str): Path to gene interactions Parquet files.</span>
+<span class="sd">            features_list (list[str]): List of features to use.</span>
+<span class="sd">            hyperparameters (dict[str, Any]): Hyperparameters for the model.</span>
+<span class="sd">            wandb_run_name (str | None): Name of the run to be tracked on W&amp;B.</span>
+<span class="sd">            perform_cross_validation (bool): Whether to perform cross validation.</span>
+
 <span class="sd">        Raises:</span>
 <span class="sd">            ValueError: if run_mode is not one of &quot;train&quot; or &quot;predict&quot;.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Sci-kit learn version: &quot;</span><span class="p">,</span> <span class="n">sklearn</span><span class="o">.</span><span class="n">__version__</span><span class="p">)</span>  <span class="c1"># noqa: T201</span>
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">run_mode</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;train&quot;</span><span class="p">,</span> <span class="s2">&quot;predict&quot;</span><span class="p">]:</span>
+        <span class="k">if</span> <span class="n">run_mode</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;train&quot;</span><span class="p">,</span> <span class="s2">&quot;predict&quot;</span><span class="p">]:</span>
             <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                <span class="sa">f</span><span class="s2">&quot;run_mode must be one of &#39;train&#39; or &#39;predict&#39;, got </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">run_mode</span><span class="si">}</span><span class="s2">&quot;</span>
+                <span class="sa">f</span><span class="s2">&quot;run_mode must be one of &#39;train&#39; or &#39;predict&#39;, got </span><span class="si">{</span><span class="n">run_mode</span><span class="si">}</span><span class="s2">&quot;</span>
             <span class="p">)</span>
         <span class="c1"># Load common inputs</span>
         <span class="n">credible_set</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+            <span class="n">session</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
         <span class="p">)</span>
         <span class="n">studies</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">study_index_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+            <span class="n">session</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
         <span class="p">)</span>
-        <span class="n">v2g</span> <span class="o">=</span> <span class="n">V2G</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">variant_gene_path</span><span class="p">)</span>
-        <span class="c1"># coloc = Colocalisation.from_parquet(self.session, self.colocalisation_path) # TODO: run step</span>
+        <span class="n">v2g</span> <span class="o">=</span> <span class="n">V2G</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_gene_path</span><span class="p">)</span>
+        <span class="n">coloc</span> <span class="o">=</span> <span class="n">Colocalisation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">colocalisation_path</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">run_mode</span> <span class="o">==</span> <span class="s2">&quot;train&quot;</span><span class="p">:</span>
-            <span class="c1"># Process gold standard and L2G features</span>
-            <span class="n">study_locus_overlap</span> <span class="o">=</span> <span class="n">StudyLocusOverlap</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">study_locus_overlap_path</span>
+        <span class="k">if</span> <span class="n">run_mode</span> <span class="o">==</span> <span class="s2">&quot;predict&quot;</span><span class="p">:</span>
+            <span class="k">if</span> <span class="ow">not</span> <span class="n">model_path</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">predictions_path</span><span class="p">:</span>
+                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                    <span class="s2">&quot;model_path and predictions_path must be set for predict mode.&quot;</span>
+                <span class="p">)</span>
+            <span class="n">predictions</span> <span class="o">=</span> <span class="n">L2GPrediction</span><span class="o">.</span><span class="n">from_credible_set</span><span class="p">(</span>
+                <span class="n">model_path</span><span class="p">,</span> <span class="nb">list</span><span class="p">(</span><span class="n">features_list</span><span class="p">),</span> <span class="n">credible_set</span><span class="p">,</span> <span class="n">studies</span><span class="p">,</span> <span class="n">v2g</span><span class="p">,</span> <span class="n">coloc</span>
             <span class="p">)</span>
-            <span class="n">gs_curation</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">json</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gold_standard_curation_path</span><span class="p">)</span>
-            <span class="n">interactions</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">gene_interactions_path</span><span class="p">)</span>
+            <span class="n">predictions</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">predictions_path</span><span class="p">)</span>
+            <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">predictions_path</span><span class="p">)</span>
+        <span class="k">elif</span> <span class="p">(</span>
+            <span class="n">run_mode</span> <span class="o">==</span> <span class="s2">&quot;train&quot;</span>
+            <span class="ow">and</span> <span class="n">gold_standard_curation_path</span>
+            <span class="ow">and</span> <span class="n">gene_interactions_path</span>
+        <span class="p">):</span>
+            <span class="c1"># Process gold standard and L2G features</span>
+            <span class="n">gs_curation</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">json</span><span class="p">(</span><span class="n">gold_standard_curation_path</span><span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+            <span class="n">interactions</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">gene_interactions_path</span><span class="p">)</span>
+            <span class="n">study_locus_overlap</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="p">(</span>
+                <span class="c1"># We just extract overlaps of associations in the gold standard. This parsing is a duplication of the one in the gold standard curation,</span>
+                <span class="c1"># but we need to do it here to be able to parse gold standards later</span>
+                <span class="n">_df</span><span class="o">=</span><span class="n">credible_set</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                    <span class="n">f</span><span class="o">.</span><span class="n">broadcast</span><span class="p">(</span>
+                        <span class="n">gs_curation</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                            <span class="n">StudyLocus</span><span class="o">.</span><span class="n">assign_study_locus_id</span><span class="p">(</span>
+                                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;association_info.otg_id&quot;</span><span class="p">),</span>  <span class="c1"># studyId</span>
+                                <span class="n">f</span><span class="o">.</span><span class="n">concat_ws</span><span class="p">(</span>  <span class="c1"># variantId</span>
+                                    <span class="s2">&quot;_&quot;</span><span class="p">,</span>
+                                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.locus_GRCh38.chromosome&quot;</span><span class="p">),</span>
+                                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.locus_GRCh38.position&quot;</span><span class="p">),</span>
+                                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.alleles.reference&quot;</span><span class="p">),</span>
+                                    <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.alleles.alternative&quot;</span><span class="p">),</span>
+                                <span class="p">),</span>
+                            <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">),</span>
+                        <span class="p">)</span>
+                    <span class="p">),</span>
+                    <span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
+                    <span class="s2">&quot;inner&quot;</span><span class="p">,</span>
+                <span class="p">),</span>
+                <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocus</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+            <span class="p">)</span><span class="o">.</span><span class="n">find_overlaps</span><span class="p">(</span><span class="n">studies</span><span class="p">)</span>
 
             <span class="n">gold_standards</span> <span class="o">=</span> <span class="n">L2GGoldStandard</span><span class="o">.</span><span class="n">from_otg_curation</span><span class="p">(</span>
                 <span class="n">gold_standard_curation</span><span class="o">=</span><span class="n">gs_curation</span><span class="p">,</span>
@@ -2945,11 +2927,11 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
             <span class="p">)</span>
 
             <span class="n">fm</span> <span class="o">=</span> <span class="n">L2GFeatureMatrix</span><span class="o">.</span><span class="n">generate_features</span><span class="p">(</span>
-                <span class="n">features_list</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">features_list</span><span class="p">,</span>
+                <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
                 <span class="n">study_locus</span><span class="o">=</span><span class="n">credible_set</span><span class="p">,</span>
                 <span class="n">study_index</span><span class="o">=</span><span class="n">studies</span><span class="p">,</span>
                 <span class="n">variant_gene</span><span class="o">=</span><span class="n">v2g</span><span class="p">,</span>
-                <span class="c1"># colocalisation=coloc,</span>
+                <span class="n">colocalisation</span><span class="o">=</span><span class="n">coloc</span><span class="p">,</span>
             <span class="p">)</span>
 
             <span class="c1"># Join and fill null values with 0</span>
@@ -2972,11 +2954,11 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
                 <span class="n">max_depth</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span>
             <span class="p">)</span>
             <span class="n">l2g_model</span> <span class="o">=</span> <span class="n">LocusToGeneModel</span><span class="p">(</span>
-                <span class="n">features_list</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">features_list</span><span class="p">),</span> <span class="n">estimator</span><span class="o">=</span><span class="n">estimator</span>
+                <span class="n">features_list</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">features_list</span><span class="p">),</span> <span class="n">estimator</span><span class="o">=</span><span class="n">estimator</span>
             <span class="p">)</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">perform_cross_validation</span><span class="p">:</span>
+            <span class="k">if</span> <span class="n">perform_cross_validation</span><span class="p">:</span>
                 <span class="c1"># Perform cross validation to extract what are the best hyperparameters</span>
-                <span class="n">cv_folds</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">hyperparameters</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;cross_validation_folds&quot;</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
+                <span class="n">cv_folds</span> <span class="o">=</span> <span class="n">hyperparameters</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;cross_validation_folds&quot;</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
                 <span class="n">LocusToGeneTrainer</span><span class="o">.</span><span class="n">cross_validate</span><span class="p">(</span>
                     <span class="n">l2g_model</span><span class="o">=</span><span class="n">l2g_model</span><span class="p">,</span>
                     <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span>
@@ -2987,31 +2969,13 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
                 <span class="n">LocusToGeneTrainer</span><span class="o">.</span><span class="n">train</span><span class="p">(</span>
                     <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span>
                     <span class="n">l2g_model</span><span class="o">=</span><span class="n">l2g_model</span><span class="p">,</span>
-                    <span class="n">features_list</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">features_list</span><span class="p">),</span>
-                    <span class="n">model_path</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">model_path</span><span class="p">,</span>
+                    <span class="n">features_list</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">features_list</span><span class="p">),</span>
+                    <span class="n">model_path</span><span class="o">=</span><span class="n">model_path</span><span class="p">,</span>
                     <span class="n">evaluate</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
-                    <span class="n">wandb_run_name</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">wandb_run_name</span><span class="p">,</span>
-                    <span class="o">**</span><span class="bp">self</span><span class="o">.</span><span class="n">hyperparameters</span><span class="p">,</span>
-                <span class="p">)</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">model_path</span><span class="p">)</span>
-
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">run_mode</span> <span class="o">==</span> <span class="s2">&quot;predict&quot;</span><span class="p">:</span>
-            <span class="k">if</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">model_path</span> <span class="ow">or</span> <span class="ow">not</span> <span class="bp">self</span><span class="o">.</span><span class="n">predictions_path</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                    <span class="s2">&quot;model_path and predictions_path must be set for predict mode.&quot;</span>
+                    <span class="n">wandb_run_name</span><span class="o">=</span><span class="n">wandb_run_name</span><span class="p">,</span>
+                    <span class="o">**</span><span class="n">hyperparameters</span><span class="p">,</span>
                 <span class="p">)</span>
-            <span class="n">predictions</span> <span class="o">=</span> <span class="n">L2GPrediction</span><span class="o">.</span><span class="n">from_credible_set</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">model_path</span><span class="p">,</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">features_list</span><span class="p">,</span>
-                <span class="n">credible_set</span><span class="p">,</span>
-                <span class="n">studies</span><span class="p">,</span>
-                <span class="n">v2g</span><span class="p">,</span>
-                <span class="c1"># coloc</span>
-            <span class="p">)</span>
-            <span class="n">predictions</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">predictions_path</span>
-            <span class="p">)</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">predictions_path</span><span class="p">)</span>
+                <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">model_path</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
             </details>
 
@@ -3028,11 +2992,574 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
 
 
 
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.l2g.LocusToGeneStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">run_mode</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">predictions_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">variant_gene_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">colocalisation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gold_standard_curation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gene_interactions_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">hyperparameters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span> <span class="n">wandb_run_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">perform_cross_validation</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.l2g.LocusToGeneStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>run_mode</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>One of "train" or "predict".</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>model_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to save the model.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>predictions_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to save the predictions.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>credible_set_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to credible set Parquet files.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>variant_gene_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to variant to gene Parquet files.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>colocalisation_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to colocalisation Parquet files.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>study_index_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to study index Parquet files.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>gold_standard_curation_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to gold standard curation JSON files.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>gene_interactions_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to gene interactions Parquet files.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>features_list</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of features to use.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>hyperparameters</code></td>
+          <td>
+                <code>dict[str, <span title="typing.Any">Any</span>]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Hyperparameters for the model.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>wandb_run_name</code></td>
+          <td>
+                <code>str | None</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Name of the run to be tracked on W&amp;B.</p>
+            </div>
+          </td>
+          <td>
+                <code>None</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>perform_cross_validation</code></td>
+          <td>
+                <code>bool</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Whether to perform cross validation.</p>
+            </div>
+          </td>
+          <td>
+                <code>False</code>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+
+
+  <p><strong>Raises:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Type</th>
+        <th>Description</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td>
+                <code>ValueError</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>if run_mode is not one of "train" or "predict".</p>
+            </div>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/l2g.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 25</span>
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+<span class="normal">176</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">run_mode</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">model_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">predictions_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">variant_gene_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">colocalisation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gold_standard_curation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gene_interactions_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">features_list</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">hyperparameters</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="n">Any</span><span class="p">],</span>
+    <span class="n">wandb_run_name</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">perform_cross_validation</span><span class="p">:</span> <span class="nb">bool</span> <span class="o">=</span> <span class="kc">False</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run step.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        session (Session): Session object.</span>
+<span class="sd">        run_mode (str): One of &quot;train&quot; or &quot;predict&quot;.</span>
+<span class="sd">        model_path (str): Path to save the model.</span>
+<span class="sd">        predictions_path (str): Path to save the predictions.</span>
+<span class="sd">        credible_set_path (str): Path to credible set Parquet files.</span>
+<span class="sd">        variant_gene_path (str): Path to variant to gene Parquet files.</span>
+<span class="sd">        colocalisation_path (str): Path to colocalisation Parquet files.</span>
+<span class="sd">        study_index_path (str): Path to study index Parquet files.</span>
+<span class="sd">        gold_standard_curation_path (str): Path to gold standard curation JSON files.</span>
+<span class="sd">        gene_interactions_path (str): Path to gene interactions Parquet files.</span>
+<span class="sd">        features_list (list[str]): List of features to use.</span>
+<span class="sd">        hyperparameters (dict[str, Any]): Hyperparameters for the model.</span>
+<span class="sd">        wandb_run_name (str | None): Name of the run to be tracked on W&amp;B.</span>
+<span class="sd">        perform_cross_validation (bool): Whether to perform cross validation.</span>
+
+<span class="sd">    Raises:</span>
+<span class="sd">        ValueError: if run_mode is not one of &quot;train&quot; or &quot;predict&quot;.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Sci-kit learn version: &quot;</span><span class="p">,</span> <span class="n">sklearn</span><span class="o">.</span><span class="n">__version__</span><span class="p">)</span>  <span class="c1"># noqa: T201</span>
+    <span class="k">if</span> <span class="n">run_mode</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;train&quot;</span><span class="p">,</span> <span class="s2">&quot;predict&quot;</span><span class="p">]:</span>
+        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+            <span class="sa">f</span><span class="s2">&quot;run_mode must be one of &#39;train&#39; or &#39;predict&#39;, got </span><span class="si">{</span><span class="n">run_mode</span><span class="si">}</span><span class="s2">&quot;</span>
+        <span class="p">)</span>
+    <span class="c1"># Load common inputs</span>
+    <span class="n">credible_set</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">studies</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+    <span class="n">v2g</span> <span class="o">=</span> <span class="n">V2G</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_gene_path</span><span class="p">)</span>
+    <span class="n">coloc</span> <span class="o">=</span> <span class="n">Colocalisation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">colocalisation_path</span><span class="p">)</span>
+
+    <span class="k">if</span> <span class="n">run_mode</span> <span class="o">==</span> <span class="s2">&quot;predict&quot;</span><span class="p">:</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">model_path</span> <span class="ow">or</span> <span class="ow">not</span> <span class="n">predictions_path</span><span class="p">:</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
+                <span class="s2">&quot;model_path and predictions_path must be set for predict mode.&quot;</span>
+            <span class="p">)</span>
+        <span class="n">predictions</span> <span class="o">=</span> <span class="n">L2GPrediction</span><span class="o">.</span><span class="n">from_credible_set</span><span class="p">(</span>
+            <span class="n">model_path</span><span class="p">,</span> <span class="nb">list</span><span class="p">(</span><span class="n">features_list</span><span class="p">),</span> <span class="n">credible_set</span><span class="p">,</span> <span class="n">studies</span><span class="p">,</span> <span class="n">v2g</span><span class="p">,</span> <span class="n">coloc</span>
+        <span class="p">)</span>
+        <span class="n">predictions</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">predictions_path</span><span class="p">)</span>
+        <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">predictions_path</span><span class="p">)</span>
+    <span class="k">elif</span> <span class="p">(</span>
+        <span class="n">run_mode</span> <span class="o">==</span> <span class="s2">&quot;train&quot;</span>
+        <span class="ow">and</span> <span class="n">gold_standard_curation_path</span>
+        <span class="ow">and</span> <span class="n">gene_interactions_path</span>
+    <span class="p">):</span>
+        <span class="c1"># Process gold standard and L2G features</span>
+        <span class="n">gs_curation</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">json</span><span class="p">(</span><span class="n">gold_standard_curation_path</span><span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+        <span class="n">interactions</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">gene_interactions_path</span><span class="p">)</span>
+        <span class="n">study_locus_overlap</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="p">(</span>
+            <span class="c1"># We just extract overlaps of associations in the gold standard. This parsing is a duplication of the one in the gold standard curation,</span>
+            <span class="c1"># but we need to do it here to be able to parse gold standards later</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">credible_set</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">broadcast</span><span class="p">(</span>
+                    <span class="n">gs_curation</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+                        <span class="n">StudyLocus</span><span class="o">.</span><span class="n">assign_study_locus_id</span><span class="p">(</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;association_info.otg_id&quot;</span><span class="p">),</span>  <span class="c1"># studyId</span>
+                            <span class="n">f</span><span class="o">.</span><span class="n">concat_ws</span><span class="p">(</span>  <span class="c1"># variantId</span>
+                                <span class="s2">&quot;_&quot;</span><span class="p">,</span>
+                                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.locus_GRCh38.chromosome&quot;</span><span class="p">),</span>
+                                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.locus_GRCh38.position&quot;</span><span class="p">),</span>
+                                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.alleles.reference&quot;</span><span class="p">),</span>
+                                <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;sentinel_variant.alleles.alternative&quot;</span><span class="p">),</span>
+                            <span class="p">),</span>
+                        <span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">),</span>
+                    <span class="p">)</span>
+                <span class="p">),</span>
+                <span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;inner&quot;</span><span class="p">,</span>
+            <span class="p">),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="n">StudyLocus</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">find_overlaps</span><span class="p">(</span><span class="n">studies</span><span class="p">)</span>
+
+        <span class="n">gold_standards</span> <span class="o">=</span> <span class="n">L2GGoldStandard</span><span class="o">.</span><span class="n">from_otg_curation</span><span class="p">(</span>
+            <span class="n">gold_standard_curation</span><span class="o">=</span><span class="n">gs_curation</span><span class="p">,</span>
+            <span class="n">v2g</span><span class="o">=</span><span class="n">v2g</span><span class="p">,</span>
+            <span class="n">study_locus_overlap</span><span class="o">=</span><span class="n">study_locus_overlap</span><span class="p">,</span>
+            <span class="n">interactions</span><span class="o">=</span><span class="n">interactions</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="n">fm</span> <span class="o">=</span> <span class="n">L2GFeatureMatrix</span><span class="o">.</span><span class="n">generate_features</span><span class="p">(</span>
+            <span class="n">features_list</span><span class="o">=</span><span class="n">features_list</span><span class="p">,</span>
+            <span class="n">study_locus</span><span class="o">=</span><span class="n">credible_set</span><span class="p">,</span>
+            <span class="n">study_index</span><span class="o">=</span><span class="n">studies</span><span class="p">,</span>
+            <span class="n">variant_gene</span><span class="o">=</span><span class="n">v2g</span><span class="p">,</span>
+            <span class="n">colocalisation</span><span class="o">=</span><span class="n">coloc</span><span class="p">,</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Join and fill null values with 0</span>
+        <span class="n">data</span> <span class="o">=</span> <span class="n">L2GFeatureMatrix</span><span class="p">(</span>
+            <span class="n">_df</span><span class="o">=</span><span class="n">fm</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">join</span><span class="p">(</span>
+                <span class="n">f</span><span class="o">.</span><span class="n">broadcast</span><span class="p">(</span>
+                    <span class="n">gold_standards</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">drop</span><span class="p">(</span><span class="s2">&quot;variantId&quot;</span><span class="p">,</span> <span class="s2">&quot;studyId&quot;</span><span class="p">,</span> <span class="s2">&quot;sources&quot;</span><span class="p">)</span>
+                <span class="p">),</span>
+                <span class="n">on</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;studyLocusId&quot;</span><span class="p">,</span> <span class="s2">&quot;geneId&quot;</span><span class="p">],</span>
+                <span class="n">how</span><span class="o">=</span><span class="s2">&quot;inner&quot;</span><span class="p">,</span>
+            <span class="p">),</span>
+            <span class="n">_schema</span><span class="o">=</span><span class="n">L2GFeatureMatrix</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">fill_na</span><span class="p">()</span>
+
+        <span class="c1"># Instantiate classifier</span>
+        <span class="n">estimator</span> <span class="o">=</span> <span class="n">SparkXGBClassifier</span><span class="p">(</span>
+            <span class="n">eval_metric</span><span class="o">=</span><span class="s2">&quot;logloss&quot;</span><span class="p">,</span>
+            <span class="n">features_col</span><span class="o">=</span><span class="s2">&quot;features&quot;</span><span class="p">,</span>
+            <span class="n">label_col</span><span class="o">=</span><span class="s2">&quot;label&quot;</span><span class="p">,</span>
+            <span class="n">max_depth</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="n">l2g_model</span> <span class="o">=</span> <span class="n">LocusToGeneModel</span><span class="p">(</span>
+            <span class="n">features_list</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">features_list</span><span class="p">),</span> <span class="n">estimator</span><span class="o">=</span><span class="n">estimator</span>
+        <span class="p">)</span>
+        <span class="k">if</span> <span class="n">perform_cross_validation</span><span class="p">:</span>
+            <span class="c1"># Perform cross validation to extract what are the best hyperparameters</span>
+            <span class="n">cv_folds</span> <span class="o">=</span> <span class="n">hyperparameters</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s2">&quot;cross_validation_folds&quot;</span><span class="p">,</span> <span class="mi">5</span><span class="p">)</span>
+            <span class="n">LocusToGeneTrainer</span><span class="o">.</span><span class="n">cross_validate</span><span class="p">(</span>
+                <span class="n">l2g_model</span><span class="o">=</span><span class="n">l2g_model</span><span class="p">,</span>
+                <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span>
+                <span class="n">num_folds</span><span class="o">=</span><span class="n">cv_folds</span><span class="p">,</span>
+            <span class="p">)</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="c1"># Train model</span>
+            <span class="n">LocusToGeneTrainer</span><span class="o">.</span><span class="n">train</span><span class="p">(</span>
+                <span class="n">data</span><span class="o">=</span><span class="n">data</span><span class="p">,</span>
+                <span class="n">l2g_model</span><span class="o">=</span><span class="n">l2g_model</span><span class="p">,</span>
+                <span class="n">features_list</span><span class="o">=</span><span class="nb">list</span><span class="p">(</span><span class="n">features_list</span><span class="p">),</span>
+                <span class="n">model_path</span><span class="o">=</span><span class="n">model_path</span><span class="p">,</span>
+                <span class="n">evaluate</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+                <span class="n">wandb_run_name</span><span class="o">=</span><span class="n">wandb_run_name</span><span class="p">,</span>
+                <span class="o">**</span><span class="n">hyperparameters</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">model_path</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
 
   </div>
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -3056,7 +3583,7 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
         <span class="icon twemoji">
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-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -3115,7 +3642,7 @@ <h2 id="otg.l2g.LocusToGeneStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/step/clump/index.html b/python_api/steps/ld_clump/index.html
similarity index 67%
rename from python_api/step/clump/index.html
rename to python_api/steps/ld_clump/index.html
index 586b9d8d6..63d0e5bab 100644
--- a/python_api/step/clump/index.html
+++ b/python_api/steps/ld_clump/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../_step/">
+        <link rel="prev" href="../l2g/">
       
       
-        <link rel="next" href="../colocalisation/">
+        <link rel="next" href="../ld_index/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Clump - Open Targets Genetics</title>
+        <title>ld_based_clumping - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.clump.ClumpStep" class="md-skip">
+        <a href="#gentropy.ld_based_clumping.LDBasedClumpingStep" class="md-skip">
           Skip to content
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@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Clump
+              ld_based_clumping
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
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+  Home
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     <li class="md-tabs__item">
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
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+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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-    How-to
+    Installation
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@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
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+    </li>
+  
+
+    
+      
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+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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               </label>
             
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,6 +1778,14 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
@@ -1601,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1637,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1651,67 +1852,6 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1719,7 +1859,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1740,7 +1880,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1761,7 +1901,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1782,7 +1922,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1803,7 +1943,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1823,43 +1963,22 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
         
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
         
         
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2034,63 +2153,60 @@
                 
   
   
-    
-  
   
   
-    <li class="md-nav__item md-nav__item--active">
-      
-      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
-      
-      
-      
-        <label class="md-nav__link md-nav__link--active" for="__toc">
-          
+    <li class="md-nav__item">
+      <a href="../colocalisation/" class="md-nav__link">
+        
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
-          <span class="md-nav__icon md-icon"></span>
-        </label>
-      
-      <a href="./" class="md-nav__link md-nav__link--active">
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    eqtl_catalogue
   </span>
   
 
       </a>
-      
-        
+    </li>
+  
 
-<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+              
+            
+              
+                
   
   
   
   
-    <label class="md-nav__title" for="__toc">
-      <span class="md-nav__icon md-icon"></span>
-      Table of contents
-    </label>
-    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
-      
-        <li class="md-nav__item">
-  <a href="#otg.clump.ClumpStep" class="md-nav__link">
-    <span class="md-ellipsis">
-      ClumpStep
-    </span>
-  </a>
+    <li class="md-nav__item">
+      <a href="../finngen_studies/" class="md-nav__link">
+        
   
-</li>
-      
-    </ul>
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
   
-</nav>
-      
+
+      </a>
     </li>
   
 
@@ -2103,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2124,11 +2240,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    gene_index
   </span>
   
 
@@ -2145,11 +2261,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2166,11 +2282,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../gene_index/" class="md-nav__link">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2191,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2212,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2233,7 +2349,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2247,18 +2363,78 @@
                 
   
   
+    
   
   
-    <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
       </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.ld_based_clumping.LDBasedClumpingStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      LDBasedClumpingStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="LDBasedClumpingStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.ld_based_clumping.LDBasedClumpingStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
     </li>
   
 
@@ -2271,11 +2447,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2292,11 +2468,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2317,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.clump.ClumpStep" class="md-nav__link">
+  <a href="#gentropy.ld_based_clumping.LDBasedClumpingStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      LDBasedClumpingStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="LDBasedClumpingStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.ld_based_clumping.LDBasedClumpingStep.__init__" class="md-nav__link">
     <span class="md-ellipsis">
-      ClumpStep
+      __init__
     </span>
   </a>
   
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,66 +2647,177 @@
   
 
 
-  <h1>Clump</h1>
+  <h1>ld_based_clumping</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.ld_based_clumping.LDBasedClumpingStep" class="doc doc-heading">
+          <code>gentropy.ld_based_clumping.LDBasedClumpingStep</code>
+
 
-<h2 id="otg.clump.ClumpStep" class="doc doc-heading">
-          <code>otg.clump.ClumpStep</code>
+<a href="#gentropy.ld_based_clumping.LDBasedClumpingStep" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
 
   
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
+      <p>Step to perform LD-based clumping on study locus dataset.</p>
+<p>As a first step, study locus is enriched with population specific linked-variants.
+That's why the study index and the ld index is required for this step. Study loci are flaggged
+in the resulting dataset, which can be explained by a more significant association
+from the same study.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/ld_based_clumping.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span>
+<span class="normal">32</span>
+<span class="normal">33</span>
+<span class="normal">34</span>
+<span class="normal">35</span>
+<span class="normal">36</span>
+<span class="normal">37</span>
+<span class="normal">38</span>
+<span class="normal">39</span>
+<span class="normal">40</span>
+<span class="normal">41</span>
+<span class="normal">42</span>
+<span class="normal">43</span>
+<span class="normal">44</span>
+<span class="normal">45</span>
+<span class="normal">46</span>
+<span class="normal">47</span>
+<span class="normal">48</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">LDBasedClumpingStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Step to perform LD-based clumping on study locus dataset.</span>
+
+<span class="sd">    As a first step, study locus is enriched with population specific linked-variants.</span>
+<span class="sd">    That&#39;s why the study index and the ld index is required for this step. Study loci are flaggged</span>
+<span class="sd">    in the resulting dataset, which can be explained by a more significant association</span>
+<span class="sd">    from the same study.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">study_locus_input_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">ld_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">clumped_study_locus_output_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run LD-based clumping step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            study_locus_input_path (str): Path to the input study locus.</span>
+<span class="sd">            study_index_path (str): Path to the study index.</span>
+<span class="sd">            ld_index_path (str): Path to the LD index.</span>
+<span class="sd">            clumped_study_locus_output_path (str): path of the resulting, clumped study-locus dataset.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">study_locus</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">study_locus_input_path</span><span class="p">)</span>
+        <span class="n">ld_index</span> <span class="o">=</span> <span class="n">LDIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">ld_index_path</span><span class="p">)</span>
+        <span class="n">study_index</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">)</span>
+
+        <span class="p">(</span>
+            <span class="n">study_locus</span>
+            <span class="c1"># Annotating study locus with LD information:</span>
+            <span class="o">.</span><span class="n">annotate_ld</span><span class="p">(</span><span class="n">study_index</span><span class="p">,</span> <span class="n">ld_index</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">clump</span><span class="p">()</span>
+            <span class="c1"># Save result:</span>
+            <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">clumped_study_locus_output_path</span><span class="p">)</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
 
-<a href="#otg.clump.ClumpStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
-  <div class="doc doc-contents first">
 
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.ld_based_clumping.LDBasedClumpingStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">study_locus_input_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">ld_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">clumped_study_locus_output_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.ld_based_clumping.LDBasedClumpingStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
   
-      <p>Perform clumping of an association dataset to identify independent signals.</p>
-<p>Two types of clumping are supported and are applied based on the input dataset:
-- Clumping of summary statistics based on a window-based approach.
-- Clumping of study locus based on LD.</p>
-<p>Both approaches yield a StudyLocus dataset.</p>
+      <p>Run LD-based clumping step.</p>
 
 
 
-  <p><strong>Attributes:</strong></p>
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
-          <td><code>input_path</code></td>
+          <td><code>study_locus_input_path</code></td>
           <td>
                 <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Input path for the study locus or summary statistics files.</p>
+              <p>Path to the input study locus.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>study_index_path</code></td>
@@ -2503,9 +2826,12 @@ <h2 id="otg.clump.ClumpStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Path to study index.</p>
+              <p>Path to the study index.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>ld_index_path</code></td>
@@ -2514,42 +2840,33 @@ <h2 id="otg.clump.ClumpStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Path to LD index.</p>
+              <p>Path to the LD index.</p>
             </div>
           </td>
-        </tr>
-        <tr>
-          <td><code>locus_collect_distance</code></td>
           <td>
-                <code>int | None</code>
-          </td>
-          <td>
-            <div class="doc-md-description">
-              <p>The distance to collect locus around semi-indices.</p>
-            </div>
+              <em>required</em>
           </td>
         </tr>
         <tr>
-          <td><code>clumped_study_locus_path</code></td>
+          <td><code>clumped_study_locus_output_path</code></td>
           <td>
                 <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output path for the clumped study locus dataset.</p>
+              <p>path of the resulting, clumped study-locus dataset.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/clump.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">15</span>
-<span class="normal">16</span>
-<span class="normal">17</span>
-<span class="normal">18</span>
-<span class="normal">19</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/ld_based_clumping.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">19</span>
 <span class="normal">20</span>
 <span class="normal">21</span>
 <span class="normal">22</span>
@@ -2578,104 +2895,41 @@ <h2 id="otg.clump.ClumpStep" class="doc doc-heading">
 <span class="normal">45</span>
 <span class="normal">46</span>
 <span class="normal">47</span>
-<span class="normal">48</span>
-<span class="normal">49</span>
-<span class="normal">50</span>
-<span class="normal">51</span>
-<span class="normal">52</span>
-<span class="normal">53</span>
-<span class="normal">54</span>
-<span class="normal">55</span>
-<span class="normal">56</span>
-<span class="normal">57</span>
-<span class="normal">58</span>
-<span class="normal">59</span>
-<span class="normal">60</span>
-<span class="normal">61</span>
-<span class="normal">62</span>
-<span class="normal">63</span>
-<span class="normal">64</span>
-<span class="normal">65</span>
-<span class="normal">66</span>
-<span class="normal">67</span>
-<span class="normal">68</span>
-<span class="normal">69</span>
-<span class="normal">70</span>
-<span class="normal">71</span>
-<span class="normal">72</span>
-<span class="normal">73</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">ClumpStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Perform clumping of an association dataset to identify independent signals.</span>
-
-<span class="sd">    Two types of clumping are supported and are applied based on the input dataset:</span>
-<span class="sd">    - Clumping of summary statistics based on a window-based approach.</span>
-<span class="sd">    - Clumping of study locus based on LD.</span>
-
-<span class="sd">    Both approaches yield a StudyLocus dataset.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">48</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">study_locus_input_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">ld_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">clumped_study_locus_output_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run LD-based clumping step.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        input_path (str): Input path for the study locus or summary statistics files.</span>
-<span class="sd">        study_index_path (str): Path to study index.</span>
-<span class="sd">        ld_index_path (str): Path to LD index.</span>
-<span class="sd">        locus_collect_distance (int | None): The distance to collect locus around semi-indices.</span>
-<span class="sd">        clumped_study_locus_path (str): Output path for the clumped study locus dataset.</span>
+<span class="sd">        study_locus_input_path (str): Path to the input study locus.</span>
+<span class="sd">        study_index_path (str): Path to the study index.</span>
+<span class="sd">        ld_index_path (str): Path to the LD index.</span>
+<span class="sd">        clumped_study_locus_output_path (str): path of the resulting, clumped study-locus dataset.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">input_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">clumped_study_locus_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">study_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-    <span class="n">ld_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-
-    <span class="n">locus_collect_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default</span><span class="o">=</span><span class="kc">None</span><span class="p">)</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">ClumpStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run the clumping step.</span>
-
-<span class="sd">        Raises:</span>
-<span class="sd">            ValueError: If study index and LD index paths are not provided for study locus.</span>
-<span class="sd">        &quot;&quot;&quot;</span>
-        <span class="n">input_cols</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">input_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
-        <span class="p">)</span><span class="o">.</span><span class="n">columns</span>
-        <span class="k">if</span> <span class="s2">&quot;studyLocusId&quot;</span> <span class="ow">in</span> <span class="n">input_cols</span><span class="p">:</span>
-            <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">study_index_path</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="bp">self</span><span class="o">.</span><span class="n">ld_index_path</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-                    <span class="s2">&quot;Study index and LD index paths are required for clumping study locus.&quot;</span>
-                <span class="p">)</span>
-            <span class="n">study_locus</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_path</span><span class="p">)</span>
-            <span class="n">ld_index</span> <span class="o">=</span> <span class="n">LDIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">ld_index_path</span><span class="p">)</span>
-            <span class="n">study_index</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">study_index_path</span><span class="p">)</span>
-
-            <span class="n">clumped_study_locus</span> <span class="o">=</span> <span class="n">study_locus</span><span class="o">.</span><span class="n">annotate_ld</span><span class="p">(</span>
-                <span class="n">study_index</span><span class="o">=</span><span class="n">study_index</span><span class="p">,</span> <span class="n">ld_index</span><span class="o">=</span><span class="n">ld_index</span>
-            <span class="p">)</span><span class="o">.</span><span class="n">clump</span><span class="p">()</span>
-        <span class="k">else</span><span class="p">:</span>
-            <span class="n">sumstats</span> <span class="o">=</span> <span class="n">SummaryStatistics</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">input_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
-            <span class="p">)</span><span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="mi">4000</span><span class="p">)</span>
-            <span class="n">clumped_study_locus</span> <span class="o">=</span> <span class="n">sumstats</span><span class="o">.</span><span class="n">window_based_clumping</span><span class="p">(</span>
-                <span class="n">locus_collect_distance</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">locus_collect_distance</span>
-            <span class="p">)</span>
-
-        <span class="n">clumped_study_locus</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">clumped_study_locus_path</span>
-        <span class="p">)</span>
+    <span class="n">study_locus</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">study_locus_input_path</span><span class="p">)</span>
+    <span class="n">ld_index</span> <span class="o">=</span> <span class="n">LDIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">ld_index_path</span><span class="p">)</span>
+    <span class="n">study_index</span> <span class="o">=</span> <span class="n">StudyIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">study_index_path</span><span class="p">)</span>
+
+    <span class="p">(</span>
+        <span class="n">study_locus</span>
+        <span class="c1"># Annotating study locus with LD information:</span>
+        <span class="o">.</span><span class="n">annotate_ld</span><span class="p">(</span><span class="n">study_index</span><span class="p">,</span> <span class="n">ld_index</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">clump</span><span class="p">()</span>
+        <span class="c1"># Save result:</span>
+        <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">clumped_study_locus_output_path</span><span class="p">)</span>
+    <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2683,6 +2937,7 @@ <h2 id="otg.clump.ClumpStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2699,14 +2954,14 @@ <h2 id="otg.clump.ClumpStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M14.47 15.08 11 13V7h1.5v5.25l3.08 1.83c-.41.28-.79.62-1.11 1m-1.39 4.84c-.36.05-.71.08-1.08.08-4.42 0-8-3.58-8-8s3.58-8 8-8 8 3.58 8 8c0 .37-.03.72-.08 1.08.69.1 1.33.32 1.92.64.1-.56.16-1.13.16-1.72 0-5.5-4.5-10-10-10S2 6.5 2 12s4.47 10 10 10c.59 0 1.16-.06 1.72-.16-.32-.59-.54-1.23-.64-1.92M18 15v3h-3v2h3v3h2v-3h3v-2h-3v-3h-2Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-11-30T15:56:35+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-11-30</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-10T11:51:22+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-10</span> </span>
       </li>
        
       <li>
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2765,7 +3020,7 @@ <h2 id="otg.clump.ClumpStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/step/ld_index/index.html b/python_api/steps/ld_index/index.html
similarity index 72%
rename from python_api/step/ld_index/index.html
rename to python_api/steps/ld_index/index.html
index e699f6e98..efb1e7823 100644
--- a/python_api/step/ld_index/index.html
+++ b/python_api/steps/ld_index/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../l2g/">
+        <link rel="prev" href="../ld_clump/">
       
       
         <link rel="next" href="../pics/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>LD Index - Open Targets Genetics</title>
+        <title>ld_index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.ld_index.LDIndexStep" class="md-skip">
+        <a href="#gentropy.ld_index.LDIndexStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              LD Index
+              ld_index
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
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-            Dataset
+            Datasets
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@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
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@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
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@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
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               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
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               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
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-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
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-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
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-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2146,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2167,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2188,7 +2349,28 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
   </span>
   
 
@@ -2216,7 +2398,7 @@
           
   
   <span class="md-ellipsis">
-    LD Index
+    ld_index
   </span>
   
 
@@ -2227,7 +2409,7 @@
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_index
   </span>
   
 
@@ -2247,12 +2429,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.ld_index.LDIndexStep" class="md-nav__link">
+  <a href="#gentropy.ld_index.LDIndexStep" class="md-nav__link">
     <span class="md-ellipsis">
       LDIndexStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="LDIndexStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.ld_index.LDIndexStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2275,7 +2472,7 @@
         
   
   <span class="md-ellipsis">
-    PICS
+    pics
   </span>
   
 
@@ -2292,11 +2489,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    variant_annotation
   </span>
   
 
@@ -2313,11 +2510,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../variant_annotation_step/" class="md-nav__link">
+      <a href="../variant_index_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_index
   </span>
   
 
@@ -2334,11 +2531,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../variant_index_step/" class="md-nav__link">
+      <a href="../variant_to_gene_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_to_gene
   </span>
   
 
@@ -2355,11 +2552,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../variant_to_gene_step/" class="md-nav__link">
+      <a href="../window_based_clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.ld_index.LDIndexStep" class="md-nav__link">
+  <a href="#gentropy.ld_index.LDIndexStep" class="md-nav__link">
     <span class="md-ellipsis">
       LDIndexStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="LDIndexStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.ld_index.LDIndexStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>LD Index</h1>
+  <h1>ld_index</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.ld_index.LDIndexStep" class="doc doc-heading">
+          <code>gentropy.ld_index.LDIndexStep</code>
 
-<h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
-          <code>otg.ld_index.LDIndexStep</code>
-
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
 
-<a href="#otg.ld_index.LDIndexStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.ld_index.LDIndexStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2462,28 +2669,113 @@ <h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
 <p>Suggested params: high memory machine, 5TB of boot disk, no SSDs.</p>
 </div>
 
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/ld_index.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span>
+<span class="normal">32</span>
+<span class="normal">33</span>
+<span class="normal">34</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">LDIndexStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;LD index step.</span>
+
+<span class="sd">    !!! warning &quot;This step is resource intensive&quot;</span>
+
+<span class="sd">        Suggested params: high memory machine, 5TB of boot disk, no SSDs.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">min_r2</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">ld_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            min_r2 (float): Minimum r2 to consider when considering variants within a window.</span>
+<span class="sd">            ld_index_out (str): Output LD index path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="n">hl</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">sc</span><span class="o">=</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">sparkContext</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="s2">&quot;/dev/null&quot;</span><span class="p">)</span>
+        <span class="p">(</span>
+            <span class="n">GnomADLDMatrix</span><span class="p">()</span>
+            <span class="o">.</span><span class="n">as_ld_index</span><span class="p">(</span><span class="n">min_r2</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">ld_index_out</span><span class="p">)</span>
+        <span class="p">)</span>
+        <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">ld_index_out</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
 
 
-  <p><strong>Attributes:</strong></p>
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.ld_index.LDIndexStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">min_r2</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">ld_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.ld_index.LDIndexStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>min_r2</code></td>
@@ -2495,6 +2787,9 @@ <h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
               <p>Minimum r2 to consider when considering variants within a window.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>ld_index_out</code></td>
@@ -2506,18 +2801,16 @@ <h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
               <p>Output LD index path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/ld_index.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">13</span>
-<span class="normal">14</span>
-<span class="normal">15</span>
-<span class="normal">16</span>
-<span class="normal">17</span>
-<span class="normal">18</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/ld_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">18</span>
 <span class="normal">19</span>
 <span class="normal">20</span>
 <span class="normal">21</span>
@@ -2533,56 +2826,28 @@ <h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
 <span class="normal">31</span>
 <span class="normal">32</span>
 <span class="normal">33</span>
-<span class="normal">34</span>
-<span class="normal">35</span>
-<span class="normal">36</span>
-<span class="normal">37</span>
-<span class="normal">38</span>
-<span class="normal">39</span>
-<span class="normal">40</span>
-<span class="normal">41</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">LDIndexStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;LD index step.</span>
+<span class="normal">34</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">min_r2</span><span class="p">:</span> <span class="nb">float</span><span class="p">,</span> <span class="n">ld_index_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run step.</span>
 
-<span class="sd">    !!! warning &quot;This step is resource intensive&quot;</span>
-<span class="sd">        Suggested params: high memory machine, 5TB of boot disk, no SSDs.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
 <span class="sd">        min_r2 (float): Minimum r2 to consider when considering variants within a window.</span>
 <span class="sd">        ld_index_out (str): Output LD index path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="n">min_r2</span><span class="p">:</span> <span class="nb">float</span> <span class="o">=</span> <span class="mf">0.5</span>
-    <span class="n">ld_index_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">LDIndexStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="n">hl</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">sc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">sparkContext</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="s2">&quot;/dev/null&quot;</span><span class="p">)</span>
-        <span class="p">(</span>
-            <span class="n">GnomADLDMatrix</span><span class="p">()</span>
-            <span class="o">.</span><span class="n">as_ld_index</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">min_r2</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ld_index_out</span><span class="p">)</span>
-        <span class="p">)</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ld_index_out</span><span class="p">)</span>
+    <span class="n">hl</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">sc</span><span class="o">=</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">sparkContext</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="s2">&quot;/dev/null&quot;</span><span class="p">)</span>
+    <span class="p">(</span>
+        <span class="n">GnomADLDMatrix</span><span class="p">()</span>
+        <span class="o">.</span><span class="n">as_ld_index</span><span class="p">(</span><span class="n">min_r2</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">ld_index_out</span><span class="p">)</span>
+    <span class="p">)</span>
+    <span class="n">session</span><span class="o">.</span><span class="n">logger</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="n">ld_index_out</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2590,6 +2855,7 @@ <h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2613,7 +2879,7 @@ <h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2672,7 +2938,7 @@ <h2 id="otg.ld_index.LDIndexStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/step/pics/index.html b/python_api/steps/pics/index.html
similarity index 72%
rename from python_api/step/pics/index.html
rename to python_api/steps/pics/index.html
index 4e0dd4a6d..ffe207041 100644
--- a/python_api/step/pics/index.html
+++ b/python_api/steps/pics/index.html
@@ -12,15 +12,15 @@
         <link rel="prev" href="../ld_index/">
       
       
-        <link rel="next" href="../ukbiobank/">
+        <link rel="next" href="../variant_annotation_step/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>PICS - Open Targets Genetics</title>
+        <title>pics - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.pics.PICSStep" class="md-skip">
+        <a href="#gentropy.pics.PICSStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              PICS
+              pics
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
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+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
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           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
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@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
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-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2146,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2167,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2188,7 +2349,28 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
   </span>
   
 
@@ -2209,7 +2391,7 @@
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_index
   </span>
   
 
@@ -2237,7 +2419,7 @@
           
   
   <span class="md-ellipsis">
-    PICS
+    pics
   </span>
   
 
@@ -2248,7 +2430,7 @@
         
   
   <span class="md-ellipsis">
-    PICS
+    pics
   </span>
   
 
@@ -2268,12 +2450,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.pics.PICSStep" class="md-nav__link">
+  <a href="#gentropy.pics.PICSStep" class="md-nav__link">
     <span class="md-ellipsis">
       PICSStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="PICSStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.pics.PICSStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2292,11 +2489,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    variant_annotation
   </span>
   
 
@@ -2313,11 +2510,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../variant_annotation_step/" class="md-nav__link">
+      <a href="../variant_index_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_index
   </span>
   
 
@@ -2334,11 +2531,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../variant_index_step/" class="md-nav__link">
+      <a href="../variant_to_gene_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_to_gene
   </span>
   
 
@@ -2355,11 +2552,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../variant_to_gene_step/" class="md-nav__link">
+      <a href="../window_based_clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.pics.PICSStep" class="md-nav__link">
+  <a href="#gentropy.pics.PICSStep" class="md-nav__link">
     <span class="md-ellipsis">
       PICSStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="PICSStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.pics.PICSStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>PICS</h1>
+  <h1>pics</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.pics.PICSStep" class="doc doc-heading">
+          <code>gentropy.pics.PICSStep</code>
 
-<h2 id="otg.pics.PICSStep" class="doc doc-heading">
-          <code>otg.pics.PICSStep</code>
-
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
 
-<a href="#otg.pics.PICSStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.pics.PICSStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2458,28 +2665,111 @@ <h2 id="otg.pics.PICSStep" class="doc doc-heading">
   
       <p>PICS finemapping of LD-annotated StudyLocus.</p>
 
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/pics.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span>
+<span class="normal">32</span>
+<span class="normal">33</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">PICSStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;PICS finemapping of LD-annotated StudyLocus.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">study_locus_ld_annotated_in</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">picsed_study_locus_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run PICS on LD annotated study-locus.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            study_locus_ld_annotated_in (str): Input LD annotated study-locus path.</span>
+<span class="sd">            picsed_study_locus_out (str): Output PICSed study-locus path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Extract</span>
+        <span class="n">study_locus_ld_annotated</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+            <span class="n">session</span><span class="p">,</span> <span class="n">study_locus_ld_annotated_in</span>
+        <span class="p">)</span>
+        <span class="c1"># PICS</span>
+        <span class="n">picsed_sl</span> <span class="o">=</span> <span class="n">PICS</span><span class="o">.</span><span class="n">finemap</span><span class="p">(</span><span class="n">study_locus_ld_annotated</span><span class="p">)</span><span class="o">.</span><span class="n">annotate_credible_sets</span><span class="p">()</span>
+        <span class="c1"># Write</span>
+        <span class="n">picsed_sl</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">picsed_study_locus_out</span><span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
 
 
-  <p><strong>Attributes:</strong></p>
+
+<h3 id="gentropy.pics.PICSStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">study_locus_ld_annotated_in</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">picsed_study_locus_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.pics.PICSStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run PICS on LD annotated study-locus.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>study_locus_ld_annotated_in</code></td>
@@ -2488,9 +2778,12 @@ <h2 id="otg.pics.PICSStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Path to Study Locus with the LD information annotated</p>
+              <p>Input LD annotated study-locus path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>picsed_study_locus_out</code></td>
@@ -2499,16 +2792,20 @@ <h2 id="otg.pics.PICSStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Path to Study Locus after running PICS</p>
+              <p>Output PICSed study-locus path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/pics.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/pics.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">13</span>
+<span class="normal">14</span>
 <span class="normal">15</span>
 <span class="normal">16</span>
 <span class="normal">17</span>
@@ -2527,54 +2824,32 @@ <h2 id="otg.pics.PICSStep" class="doc doc-heading">
 <span class="normal">30</span>
 <span class="normal">31</span>
 <span class="normal">32</span>
-<span class="normal">33</span>
-<span class="normal">34</span>
-<span class="normal">35</span>
-<span class="normal">36</span>
-<span class="normal">37</span>
-<span class="normal">38</span>
-<span class="normal">39</span>
-<span class="normal">40</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">PICSStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;PICS finemapping of LD-annotated StudyLocus.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">33</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">study_locus_ld_annotated_in</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">picsed_study_locus_out</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run PICS on LD annotated study-locus.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-
-<span class="sd">        study_locus_ld_annotated_in (str): Path to Study Locus with the LD information annotated</span>
-<span class="sd">        picsed_study_locus_out (str): Path to Study Locus after running PICS</span>
+<span class="sd">        study_locus_ld_annotated_in (str): Input LD annotated study-locus path.</span>
+<span class="sd">        picsed_study_locus_out (str): Output PICSed study-locus path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">study_locus_ld_annotated_in</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">picsed_study_locus_out</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">PICSStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Extract</span>
-        <span class="n">study_locus_ld_annotated</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">study_locus_ld_annotated_in</span>
-        <span class="p">)</span>
-        <span class="c1"># PICS</span>
-        <span class="n">picsed_sl</span> <span class="o">=</span> <span class="n">PICS</span><span class="o">.</span><span class="n">finemap</span><span class="p">(</span><span class="n">study_locus_ld_annotated</span><span class="p">)</span><span class="o">.</span><span class="n">annotate_credible_sets</span><span class="p">()</span>
-        <span class="c1"># Write</span>
-        <span class="n">picsed_sl</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">picsed_study_locus_out</span>
-        <span class="p">)</span>
+    <span class="c1"># Extract</span>
+    <span class="n">study_locus_ld_annotated</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">,</span> <span class="n">study_locus_ld_annotated_in</span>
+    <span class="p">)</span>
+    <span class="c1"># PICS</span>
+    <span class="n">picsed_sl</span> <span class="o">=</span> <span class="n">PICS</span><span class="o">.</span><span class="n">finemap</span><span class="p">(</span><span class="n">study_locus_ld_annotated</span><span class="p">)</span><span class="o">.</span><span class="n">annotate_credible_sets</span><span class="p">()</span>
+    <span class="c1"># Write</span>
+    <span class="n">picsed_sl</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">picsed_study_locus_out</span><span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2582,6 +2857,7 @@ <h2 id="otg.pics.PICSStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2605,7 +2881,7 @@ <h2 id="otg.pics.PICSStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2664,7 +2940,7 @@ <h2 id="otg.pics.PICSStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
     </a>
   
diff --git a/python_api/step/variant_annotation_step/index.html b/python_api/steps/variant_annotation_step/index.html
similarity index 73%
rename from python_api/step/variant_annotation_step/index.html
rename to python_api/steps/variant_annotation_step/index.html
index 65d5d4791..75e9ec3d2 100644
--- a/python_api/step/variant_annotation_step/index.html
+++ b/python_api/steps/variant_annotation_step/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../ukbiobank/">
+        <link rel="prev" href="../pics/">
       
       
         <link rel="next" href="../variant_index_step/">
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Variant Annotation - Open Targets Genetics</title>
+        <title>variant_annotation - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.variant_annotation.VariantAnnotationStep" class="md-skip">
+        <a href="#gentropy.variant_annotation.VariantAnnotationStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Variant Annotation
+              variant_annotation
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +392,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +429,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
   </span>
   
 
@@ -414,6 +448,123 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
+    
+    
+    
+      
+      
+    
+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -531,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -547,14 +698,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -576,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -612,7 +763,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -633,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -696,7 +847,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -717,7 +868,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -738,7 +889,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -759,7 +910,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -780,7 +931,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -822,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -843,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -864,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -885,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -906,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2146,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2167,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2188,7 +2349,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2205,11 +2366,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2226,11 +2387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2247,11 +2408,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2279,7 +2440,7 @@
           
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2290,7 +2451,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2310,12 +2471,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.variant_annotation.VariantAnnotationStep" class="md-nav__link">
+  <a href="#gentropy.variant_annotation.VariantAnnotationStep" class="md-nav__link">
     <span class="md-ellipsis">
       VariantAnnotationStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="VariantAnnotationStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.variant_annotation.VariantAnnotationStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2338,7 +2514,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.variant_annotation.VariantAnnotationStep" class="md-nav__link">
+  <a href="#gentropy.variant_annotation.VariantAnnotationStep" class="md-nav__link">
     <span class="md-ellipsis">
       VariantAnnotationStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="VariantAnnotationStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.variant_annotation.VariantAnnotationStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>Variant Annotation</h1>
+  <h1>variant_annotation</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.variant_annotation.VariantAnnotationStep" class="doc doc-heading">
+          <code>gentropy.variant_annotation.VariantAnnotationStep</code>
 
-<h2 id="otg.variant_annotation.VariantAnnotationStep" class="doc doc-heading">
-          <code>otg.variant_annotation.VariantAnnotationStep</code>
 
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
-
-<a href="#otg.variant_annotation.VariantAnnotationStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.variant_annotation.VariantAnnotationStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2459,28 +2666,109 @@ <h2 id="otg.variant_annotation.VariantAnnotationStep" class="doc doc-heading">
       <p>Variant annotation step.</p>
 <p>Variant annotation step produces a dataset of the type <code>VariantAnnotation</code> derived from gnomADs <code>gnomad.genomes.vX.X.X.sites.ht</code> Hail's table. This dataset is used to validate variants and as a source of annotation.</p>
 
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/variant_annotation.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span>
+<span class="normal">32</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">VariantAnnotationStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Variant annotation step.</span>
+
+<span class="sd">    Variant annotation step produces a dataset of the type `VariantAnnotation` derived from gnomADs `gnomad.genomes.vX.X.X.sites.ht` Hail&#39;s table. This dataset is used to validate variants and as a source of annotation.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
 
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run Variant Annotation step.</span>
 
-  <p><strong>Attributes:</strong></p>
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            variant_annotation_path (str): Variant annotation dataset path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Initialise hail session.</span>
+        <span class="n">hl</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">sc</span><span class="o">=</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">sparkContext</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="s2">&quot;/dev/null&quot;</span><span class="p">)</span>
+        <span class="c1"># Run variant annotation.</span>
+        <span class="n">variant_annotation</span> <span class="o">=</span> <span class="n">GnomADVariants</span><span class="p">()</span><span class="o">.</span><span class="n">as_variant_annotation</span><span class="p">()</span>
+        <span class="c1"># Write data partitioned by chromosome and position.</span>
+        <span class="p">(</span>
+            <span class="n">variant_annotation</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
+                <span class="n">variant_annotation_path</span>
+            <span class="p">)</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.variant_annotation.VariantAnnotationStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.variant_annotation.VariantAnnotationStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run Variant Annotation step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>variant_annotation_path</code></td>
@@ -2489,19 +2777,19 @@ <h2 id="otg.variant_annotation.VariantAnnotationStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output variant annotation path.</p>
+              <p>Variant annotation dataset path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/variant_annotation.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">13</span>
-<span class="normal">14</span>
-<span class="normal">15</span>
-<span class="normal">16</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/variant_annotation.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">16</span>
 <span class="normal">17</span>
 <span class="normal">18</span>
 <span class="normal">19</span>
@@ -2517,52 +2805,28 @@ <h2 id="otg.variant_annotation.VariantAnnotationStep" class="doc doc-heading">
 <span class="normal">29</span>
 <span class="normal">30</span>
 <span class="normal">31</span>
-<span class="normal">32</span>
-<span class="normal">33</span>
-<span class="normal">34</span>
-<span class="normal">35</span>
-<span class="normal">36</span>
-<span class="normal">37</span>
-<span class="normal">38</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">VariantAnnotationStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Variant annotation step.</span>
-
-<span class="sd">    Variant annotation step produces a dataset of the type `VariantAnnotation` derived from gnomADs `gnomad.genomes.vX.X.X.sites.ht` Hail&#39;s table. This dataset is used to validate variants and as a source of annotation.</span>
+<span class="normal">32</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run Variant Annotation step.</span>
 
-<span class="sd">    Attributes:</span>
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        variant_annotation_path (str): Output variant annotation path.</span>
+<span class="sd">        variant_annotation_path (str): Variant annotation dataset path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">VariantAnnotationStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Initialise hail session.</span>
-        <span class="n">hl</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">sc</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">sparkContext</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="s2">&quot;/dev/null&quot;</span><span class="p">)</span>
-        <span class="c1"># Run variant annotation.</span>
-        <span class="n">variant_annotation</span> <span class="o">=</span> <span class="n">GnomADVariants</span><span class="p">()</span><span class="o">.</span><span class="n">as_variant_annotation</span><span class="p">()</span>
-        <span class="c1"># Write data partitioned by chromosome and position.</span>
-        <span class="p">(</span>
-            <span class="n">variant_annotation</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
-                <span class="bp">self</span><span class="o">.</span><span class="n">variant_annotation_path</span>
-            <span class="p">)</span>
+    <span class="c1"># Initialise hail session.</span>
+    <span class="n">hl</span><span class="o">.</span><span class="n">init</span><span class="p">(</span><span class="n">sc</span><span class="o">=</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">sparkContext</span><span class="p">,</span> <span class="n">log</span><span class="o">=</span><span class="s2">&quot;/dev/null&quot;</span><span class="p">)</span>
+    <span class="c1"># Run variant annotation.</span>
+    <span class="n">variant_annotation</span> <span class="o">=</span> <span class="n">GnomADVariants</span><span class="p">()</span><span class="o">.</span><span class="n">as_variant_annotation</span><span class="p">()</span>
+    <span class="c1"># Write data partitioned by chromosome and position.</span>
+    <span class="p">(</span>
+        <span class="n">variant_annotation</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span>
+            <span class="n">variant_annotation_path</span>
         <span class="p">)</span>
+    <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2570,6 +2834,7 @@ <h2 id="otg.variant_annotation.VariantAnnotationStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2593,7 +2858,7 @@ <h2 id="otg.variant_annotation.VariantAnnotationStep" class="doc doc-heading">
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+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
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-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/python_api/step/variant_index_step/index.html b/python_api/steps/variant_index_step/index.html
similarity index 71%
rename from python_api/step/variant_index_step/index.html
rename to python_api/steps/variant_index_step/index.html
index 838da4564..55e128b5d 100644
--- a/python_api/step/variant_index_step/index.html
+++ b/python_api/steps/variant_index_step/index.html
@@ -16,11 +16,11 @@
       
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Variant Index - Open Targets Genetics</title>
+        <title>variant_index - Open Targets Gentropy</title>
       
     
     
@@ -78,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.variant_index.VariantIndexStep" class="md-skip">
+        <a href="#gentropy.variant_index.VariantIndexStep" class="md-skip">
           Skip to content
         </a>
       
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Variant Index
+              variant_index
             
           </span>
         </div>
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
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+  
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+      
+        
+  
+  
+  
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@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -249,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
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       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -309,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
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-    opentargets/genetics_etl_python
+    opentargets/gentropy
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 </a>
     </div>
@@ -338,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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-    Installation
+    Home
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@@ -358,11 +392,11 @@
   
   
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+      <a href="../../../installation/" class="md-nav__link">
         
   
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+    Installation
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@@ -395,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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@@ -414,6 +448,123 @@
         
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
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+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+  
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+      
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
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+            
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+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
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+    Datasets
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+            Datasets
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+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
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@@ -633,7 +784,7 @@
   
   
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+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -654,7 +805,7 @@
   
   
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+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
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@@ -675,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
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-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -717,7 +868,7 @@
   
   
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+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -738,7 +889,7 @@
   
   
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-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -759,7 +910,7 @@
   
   
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-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
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@@ -780,7 +931,7 @@
   
   
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-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -801,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
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@@ -822,7 +973,7 @@
   
   
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-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
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@@ -843,7 +994,7 @@
   
   
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+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
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@@ -864,7 +1015,7 @@
   
   
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+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
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@@ -885,7 +1036,7 @@
   
   
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-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
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@@ -906,7 +1057,7 @@
   
   
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-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
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@@ -944,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -989,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1005,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1025,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1063,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1079,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1099,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1137,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1153,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1173,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1194,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1232,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1248,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1268,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1289,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1310,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1331,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1369,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1385,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1405,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1426,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1447,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1468,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1506,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1522,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1542,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1563,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1585,80 +1778,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
-          </div>
-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1683,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1719,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1740,11 +1859,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1761,11 +1880,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1782,11 +1901,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1803,11 +1922,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1824,11 +1943,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1854,12 +1973,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1870,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1890,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1911,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1932,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1953,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -2001,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2037,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2058,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2079,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2100,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2125,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2146,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2167,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2188,7 +2349,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2205,11 +2366,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2226,11 +2387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2247,11 +2408,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2272,7 +2433,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2300,7 +2461,7 @@
           
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2311,7 +2472,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2331,12 +2492,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.variant_index.VariantIndexStep" class="md-nav__link">
+  <a href="#gentropy.variant_index.VariantIndexStep" class="md-nav__link">
     <span class="md-ellipsis">
       VariantIndexStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="VariantIndexStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.variant_index.VariantIndexStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2359,7 +2535,28 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2409,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.variant_index.VariantIndexStep" class="md-nav__link">
+  <a href="#gentropy.variant_index.VariantIndexStep" class="md-nav__link">
     <span class="md-ellipsis">
       VariantIndexStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="VariantIndexStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.variant_index.VariantIndexStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2435,22 +2647,17 @@
   
 
 
-  <h1>Variant Index</h1>
+  <h1>variant_index</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.variant_index.VariantIndexStep" class="doc doc-heading">
+          <code>gentropy.variant_index.VariantIndexStep</code>
 
-<h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
-          <code>otg.variant_index.VariantIndexStep</code>
-
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
 
-<a href="#otg.variant_index.VariantIndexStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.variant_index.VariantIndexStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2459,28 +2666,133 @@ <h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
       <p>Run variant index step to only variants in study-locus sets.</p>
 <p>Using a <code>VariantAnnotation</code> dataset as a reference, this step creates and writes a dataset of the type <code>VariantIndex</code> that includes only variants that have disease-association data with a reduced set of annotations.</p>
 
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/variant_index.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">10</span>
+<span class="normal">11</span>
+<span class="normal">12</span>
+<span class="normal">13</span>
+<span class="normal">14</span>
+<span class="normal">15</span>
+<span class="normal">16</span>
+<span class="normal">17</span>
+<span class="normal">18</span>
+<span class="normal">19</span>
+<span class="normal">20</span>
+<span class="normal">21</span>
+<span class="normal">22</span>
+<span class="normal">23</span>
+<span class="normal">24</span>
+<span class="normal">25</span>
+<span class="normal">26</span>
+<span class="normal">27</span>
+<span class="normal">28</span>
+<span class="normal">29</span>
+<span class="normal">30</span>
+<span class="normal">31</span>
+<span class="normal">32</span>
+<span class="normal">33</span>
+<span class="normal">34</span>
+<span class="normal">35</span>
+<span class="normal">36</span>
+<span class="normal">37</span>
+<span class="normal">38</span>
+<span class="normal">39</span>
+<span class="normal">40</span>
+<span class="normal">41</span>
+<span class="normal">42</span>
+<span class="normal">43</span>
+<span class="normal">44</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">VariantIndexStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run variant index step to only variants in study-locus sets.</span>
+
+<span class="sd">    Using a `VariantAnnotation` dataset as a reference, this step creates and writes a dataset of the type `VariantIndex` that includes only variants that have disease-association data with a reduced set of annotations.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">:</span> <span class="n">VariantIndexStep</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run VariantIndex step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            variant_annotation_path (str): Variant annotation dataset path.</span>
+<span class="sd">            credible_set_path (str): Credible set dataset path.</span>
+<span class="sd">            variant_index_path (str): Variant index dataset path.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># Extract</span>
+        <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+        <span class="n">credible_set</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+            <span class="n">session</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+        <span class="p">)</span>
+
+        <span class="c1"># Transform</span>
+        <span class="n">vi</span> <span class="o">=</span> <span class="n">VariantIndex</span><span class="o">.</span><span class="n">from_variant_annotation</span><span class="p">(</span><span class="n">va</span><span class="p">,</span> <span class="n">credible_set</span><span class="p">)</span>
+
+        <span class="p">(</span>
+            <span class="n">vi</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">variant_index_path</span><span class="p">)</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
 
 
-  <p><strong>Attributes:</strong></p>
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.variant_index.VariantIndexStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.variant_index.VariantIndexStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run VariantIndex step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
   <table>
     <thead>
       <tr>
         <th>Name</th>
         <th>Type</th>
         <th>Description</th>
+        <th>Default</th>
       </tr>
     </thead>
     <tbody>
         <tr>
           <td><code>session</code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
               <p>Session object.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>variant_annotation_path</code></td>
@@ -2489,20 +2801,26 @@ <h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Input variant annotation path.</p>
+              <p>Variant annotation dataset path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
-          <td><code>study_locus_path</code></td>
+          <td><code>credible_set_path</code></td>
           <td>
                 <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Input study-locus path.</p>
+              <p>Credible set dataset path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
         <tr>
           <td><code>variant_index_path</code></td>
@@ -2511,18 +2829,19 @@ <h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
           </td>
           <td>
             <div class="doc-md-description">
-              <p>Output variant index path.</p>
+              <p>Variant index dataset path.</p>
             </div>
           </td>
+          <td>
+              <em>required</em>
+          </td>
         </tr>
     </tbody>
   </table>
 
-            <details class="quote">
-              <summary>Source code in <code>src/otg/variant_index.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">14</span>
-<span class="normal">15</span>
-<span class="normal">16</span>
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/variant_index.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">16</span>
 <span class="normal">17</span>
 <span class="normal">18</span>
 <span class="normal">19</span>
@@ -2550,57 +2869,40 @@ <h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
 <span class="normal">41</span>
 <span class="normal">42</span>
 <span class="normal">43</span>
-<span class="normal">44</span>
-<span class="normal">45</span>
-<span class="normal">46</span>
-<span class="normal">47</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">VariantIndexStep</span><span class="p">:</span>
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run variant index step to only variants in study-locus sets.</span>
-
-<span class="sd">    Using a `VariantAnnotation` dataset as a reference, this step creates and writes a dataset of the type `VariantIndex` that includes only variants that have disease-association data with a reduced set of annotations.</span>
-
-<span class="sd">    Attributes:</span>
+<span class="normal">44</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">:</span> <span class="n">VariantIndexStep</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run VariantIndex step.</span>
+
+<span class="sd">    Args:</span>
 <span class="sd">        session (Session): Session object.</span>
-<span class="sd">        variant_annotation_path (str): Input variant annotation path.</span>
-<span class="sd">        study_locus_path (str): Input study-locus path.</span>
-<span class="sd">        variant_index_path (str): Output variant index path.</span>
+<span class="sd">        variant_annotation_path (str): Variant annotation dataset path.</span>
+<span class="sd">        credible_set_path (str): Credible set dataset path.</span>
+<span class="sd">        variant_index_path (str): Variant index dataset path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">credible_set_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">VariantIndexStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
-        <span class="c1"># Extract</span>
-        <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">variant_annotation_path</span><span class="p">)</span>
-        <span class="n">credible_set</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
-        <span class="p">)</span>
-
-        <span class="c1"># Transform</span>
-        <span class="n">vi</span> <span class="o">=</span> <span class="n">VariantIndex</span><span class="o">.</span><span class="n">from_variant_annotation</span><span class="p">(</span><span class="n">va</span><span class="p">,</span> <span class="n">credible_set</span><span class="p">)</span>
-
-        <span class="p">(</span>
-            <span class="n">vi</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">variant_index_path</span><span class="p">)</span>
-        <span class="p">)</span>
+    <span class="c1"># Extract</span>
+    <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+    <span class="n">credible_set</span> <span class="o">=</span> <span class="n">StudyLocus</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+        <span class="n">session</span><span class="p">,</span> <span class="n">credible_set_path</span><span class="p">,</span> <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Transform</span>
+    <span class="n">vi</span> <span class="o">=</span> <span class="n">VariantIndex</span><span class="o">.</span><span class="n">from_variant_annotation</span><span class="p">(</span><span class="n">va</span><span class="p">,</span> <span class="n">credible_set</span><span class="p">)</span>
+
+    <span class="p">(</span>
+        <span class="n">vi</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">variant_index_path</span><span class="p">)</span>
+    <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
-            </details>
-
-  
-
-  <div class="doc doc-children">
-
-
-
-
-
-
-
+          </details>
+  </div>
 
+</div>
 
 
 
@@ -2608,6 +2910,7 @@ <h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
@@ -2631,7 +2934,7 @@ <h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
         <span class="icon twemoji">
           <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1-2.1-2M12.5 7v5.2l4 2.4-1 1L11 13V7h1.5M11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2v1.8Z"/></svg>
         </span>
-        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2023-12-05T12:06:58+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2023-12-05</span> </span>
+        <span class="label"> <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-timeago"><span class="timeago" datetime="2024-01-18T13:35:25+00:00" locale="en"></span></span><span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-01-18</span> </span>
       </li>
       
 
@@ -2690,7 +2993,7 @@ <h2 id="otg.variant_index.VariantIndexStep" class="doc doc-heading">
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 496 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M165.9 397.4c0 2-2.3 3.6-5.2 3.6-3.3.3-5.6-1.3-5.6-3.6 0-2 2.3-3.6 5.2-3.6 3-.3 5.6 1.3 5.6 3.6zm-31.1-4.5c-.7 2 1.3 4.3 4.3 4.9 2.6 1 5.6 0 6.2-2s-1.3-4.3-4.3-5.2c-2.6-.7-5.5.3-6.2 2.3zm44.2-1.7c-2.9.7-4.9 2.6-4.6 4.9.3 2 2.9 3.3 5.9 2.6 2.9-.7 4.9-2.6 4.6-4.6-.3-1.9-3-3.2-5.9-2.9zM244.8 8C106.1 8 0 113.3 0 252c0 110.9 69.8 205.8 169.5 239.2 12.8 2.3 17.3-5.6 17.3-12.1 0-6.2-.3-40.4-.3-61.4 0 0-70 15-84.7-29.8 0 0-11.4-29.1-27.8-36.6 0 0-22.9-15.7 1.6-15.4 0 0 24.9 2 38.6 25.8 21.9 38.6 58.6 27.5 72.9 20.9 2.3-16 8.8-27.1 16-33.7-55.9-6.2-112.3-14.3-112.3-110.5 0-27.5 7.6-41.3 23.6-58.9-2.6-6.5-11.1-33.3 2.6-67.9 20.9-6.5 69 27 69 27 20-5.6 41.5-8.5 62.8-8.5s42.8 2.9 62.8 8.5c0 0 48.1-33.6 69-27 13.7 34.7 5.2 61.4 2.6 67.9 16 17.7 25.8 31.5 25.8 58.9 0 96.5-58.9 104.2-114.8 110.5 9.2 7.9 17 22.9 17 46.4 0 33.7-.3 75.4-.3 83.6 0 6.5 4.6 14.4 17.3 12.1C428.2 457.8 496 362.9 496 252 496 113.3 383.5 8 244.8 8zM97.2 352.9c-1.3 1-1 3.3.7 5.2 1.6 1.6 3.9 2.3 5.2 1 1.3-1 1-3.3-.7-5.2-1.6-1.6-3.9-2.3-5.2-1zm-10.8-8.1c-.7 1.3.3 2.9 2.3 3.9 1.6 1 3.6.7 4.3-.7.7-1.3-.3-2.9-2.3-3.9-2-.6-3.6-.3-4.3.7zm32.4 35.6c-1.6 1.3-1 4.3 1.3 6.2 2.3 2.3 5.2 2.6 6.5 1 1.3-1.3.7-4.3-1.3-6.2-2.2-2.3-5.2-2.6-6.5-1zm-11.4-14.7c-1.6 1-1.6 3.6 0 5.9 1.6 2.3 4.3 3.3 5.6 2.3 1.6-1.3 1.6-3.9 0-6.2-1.4-2.3-4-3.3-5.6-2z"/></svg>
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diff --git a/python_api/step/variant_to_gene_step/index.html b/python_api/steps/variant_to_gene_step/index.html
similarity index 61%
rename from python_api/step/variant_to_gene_step/index.html
rename to python_api/steps/variant_to_gene_step/index.html
index 7da1c5ea2..7fd297fdc 100644
--- a/python_api/step/variant_to_gene_step/index.html
+++ b/python_api/steps/variant_to_gene_step/index.html
@@ -12,13 +12,15 @@
         <link rel="prev" href="../variant_index_step/">
       
       
+        <link rel="next" href="../window_based_clumping/">
+      
       
       <link rel="icon" href="../../../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Variant-to-gene - Open Targets Genetics</title>
+        <title>variant_to_gene - Open Targets Gentropy</title>
       
     
     
@@ -76,7 +78,7 @@
     <div data-md-component="skip">
       
         
-        <a href="#otg.v2g.V2GStep" class="md-skip">
+        <a href="#gentropy.v2g.V2GStep" class="md-skip">
           Skip to content
         </a>
       
@@ -92,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href="../../.." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../../../assets/imgs/otlogo.png" alt="logo">
 
@@ -105,13 +107,13 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
           <span class="md-ellipsis">
             
-              Variant-to-gene
+              variant_to_gene
             
           </span>
         </div>
@@ -190,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -213,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../.." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
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+      
+        
+  
+  
+  
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       <a href="../../../installation/" class="md-tabs__link">
         
@@ -231,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../../../usage/" class="md-tabs__link">
+      <a href="../../../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -247,6 +266,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href="../../../roadmap/" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
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       <a href="../../../development/_development/" class="md-tabs__link">
         
@@ -307,22 +343,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href="../../.." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href="../../.." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
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-    Open Targets Genetics
+    Open Targets Gentropy
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-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -336,11 +372,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../../installation/" class="md-nav__link">
+      <a href="../../.." class="md-nav__link">
         
   
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-    Installation
+    Home
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@@ -356,11 +392,11 @@
   
   
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-      <a href="../../../usage/" class="md-nav__link">
+      <a href="../../../installation/" class="md-nav__link">
         
   
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+    Installation
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@@ -393,11 +429,11 @@
           
           
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-            <a href="../../../development/_development/" class="md-nav__link ">
+            <a href="../../../howto/_howto/" class="md-nav__link ">
               
   
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+    How-to
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@@ -412,6 +448,123 @@
         
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           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
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+  
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+    <li class="md-nav__item">
+      <a href="../../../roadmap/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
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+  
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+      
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+    
+    
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
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+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
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+            <a href="../../../development/_development/" class="md-nav__link ">
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+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
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@@ -529,7 +682,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" checked>
         
           
           
@@ -545,14 +698,14 @@
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-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
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-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -574,32 +727,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
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-            <a href="../../dataset/_dataset/" class="md-nav__link ">
+            <a href="../../datasets/_datasets/" class="md-nav__link ">
               
   
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-    Dataset
+    Datasets
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+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
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@@ -610,7 +763,7 @@
   
   
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-      <a href="../../dataset/colocalisation/" class="md-nav__link">
+      <a href="../../datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -631,7 +784,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/gene_index/" class="md-nav__link">
+      <a href="../../datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -652,7 +805,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/intervals/" class="md-nav__link">
+      <a href="../../datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -673,7 +826,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/l2g_feature/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -694,7 +847,7 @@
   
   
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-      <a href="../../dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../../datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
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@@ -715,7 +868,7 @@
   
   
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-      <a href="../../dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasets/l2g_gold_standard/" class="md-nav__link">
         
   
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@@ -736,7 +889,7 @@
   
   
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-      <a href="../../dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../../datasets/l2g_prediction/" class="md-nav__link">
         
   
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@@ -757,7 +910,7 @@
   
   
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-      <a href="../../dataset/ld_index/" class="md-nav__link">
+      <a href="../../datasets/ld_index/" class="md-nav__link">
         
   
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@@ -778,7 +931,7 @@
   
   
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-      <a href="../../dataset/study_index/" class="md-nav__link">
+      <a href="../../datasets/study_index/" class="md-nav__link">
         
   
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@@ -799,7 +952,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus/" class="md-nav__link">
+      <a href="../../datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -820,7 +973,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../../datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -841,7 +994,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/summary_statistics/" class="md-nav__link">
+      <a href="../../datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -862,7 +1015,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_annotation/" class="md-nav__link">
+      <a href="../../datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -883,7 +1036,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_index/" class="md-nav__link">
+      <a href="../../datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -904,7 +1057,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../../datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -942,32 +1095,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/_datasource/" class="md-nav__link ">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -987,12 +1140,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1003,14 +1156,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1023,7 +1176,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1061,12 +1235,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1077,14 +1251,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1097,7 +1271,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1135,12 +1330,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1151,14 +1346,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1171,7 +1366,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1192,7 +1387,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1230,12 +1425,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1246,14 +1441,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1266,7 +1461,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1287,7 +1482,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1308,7 +1503,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1329,7 +1524,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1367,12 +1562,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1383,14 +1578,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1403,7 +1598,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1424,7 +1619,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1445,7 +1640,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/jung/" class="md-nav__link">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1466,7 +1661,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1504,12 +1699,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1520,14 +1715,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1540,7 +1735,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1561,7 +1756,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/open_targets/target/" class="md-nav__link">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1583,6 +1778,14 @@
 
               
             
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
               
                 
   
@@ -1599,32 +1802,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
+            <a href="../../methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Ukbiobank
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1635,11 +1838,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../../datasource/ukbiobank/study_index/" class="md-nav__link">
+      <a href="../../methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Study Index
+    CARMA
   </span>
   
 
@@ -1649,67 +1852,6 @@
 
               
             
-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
-          </ul>
-        </nav>
-      
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-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
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-      
-        
-        
-        
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
-        
-          
-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../../method/_method/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Method
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
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-        
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
-            <span class="md-nav__icon md-icon"></span>
-            Method
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
               
                 
   
@@ -1717,7 +1859,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/clumping/" class="md-nav__link">
+      <a href="../../methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1738,7 +1880,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/coloc/" class="md-nav__link">
+      <a href="../../methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1759,7 +1901,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ecaviar/" class="md-nav__link">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1780,7 +1922,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/ld_annotator/" class="md-nav__link">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1801,7 +1943,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/pics/" class="md-nav__link">
+      <a href="../../methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1821,43 +1963,22 @@
   
   
   
-    <li class="md-nav__item">
-      <a href="../../method/window_based_clumping/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Window-based clumping
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
-            
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
-      
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../../method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1868,14 +1989,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1888,7 +2009,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/evaluator/" class="md-nav__link">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1909,7 +2030,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1930,7 +2051,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/model/" class="md-nav__link">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1951,7 +2072,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../../method/l2g/trainer/" class="md-nav__link">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1999,32 +2120,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" checked>
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../_step/" class="md-nav__link ">
+            <a href="../_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="true">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2035,11 +2156,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../clump/" class="md-nav__link">
+      <a href="../colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2056,11 +2177,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../colocalisation/" class="md-nav__link">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2077,11 +2198,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../eqtl_catalogue/" class="md-nav__link">
+      <a href="../finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2098,11 +2219,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../finngen/" class="md-nav__link">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2123,7 +2244,49 @@
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2144,7 +2307,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2165,7 +2328,7 @@
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2186,7 +2349,7 @@
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    locus_to_gene
   </span>
   
 
@@ -2203,11 +2366,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ld_index/" class="md-nav__link">
+      <a href="../ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    ld_based_clumping
   </span>
   
 
@@ -2224,11 +2387,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../pics/" class="md-nav__link">
+      <a href="../ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    ld_index
   </span>
   
 
@@ -2245,11 +2408,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../ukbiobank/" class="md-nav__link">
+      <a href="../pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    pics
   </span>
   
 
@@ -2270,7 +2433,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    variant_annotation
   </span>
   
 
@@ -2291,7 +2454,7 @@
         
   
   <span class="md-ellipsis">
-    Variant Index
+    variant_index
   </span>
   
 
@@ -2319,7 +2482,7 @@
           
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
   </span>
   
 
@@ -2330,7 +2493,7 @@
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_to_gene
   </span>
   
 
@@ -2350,12 +2513,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.v2g.V2GStep" class="md-nav__link">
+  <a href="#gentropy.v2g.V2GStep" class="md-nav__link">
     <span class="md-ellipsis">
       V2GStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="V2GStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.v2g.V2GStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2367,6 +2545,27 @@
 
               
             
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
           </ul>
         </nav>
       
@@ -2407,12 +2606,27 @@
     <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
       
         <li class="md-nav__item">
-  <a href="#otg.v2g.V2GStep" class="md-nav__link">
+  <a href="#gentropy.v2g.V2GStep" class="md-nav__link">
     <span class="md-ellipsis">
       V2GStep
     </span>
   </a>
   
+    <nav class="md-nav" aria-label="V2GStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.v2g.V2GStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
 </li>
       
     </ul>
@@ -2433,22 +2647,17 @@
   
 
 
-  <h1>Variant-to-gene</h1>
+  <h1>variant_to_gene</h1>
 
 <div class="doc doc-object doc-class">
 
 
 
+<h2 id="gentropy.v2g.V2GStep" class="doc doc-heading">
+          <code>gentropy.v2g.V2GStep</code>
 
-<h2 id="otg.v2g.V2GStep" class="doc doc-heading">
-          <code>otg.v2g.V2GStep</code>
-
-  
-  <span class="doc doc-labels">
-      <small class="doc doc-label doc-label-dataclass"><code>dataclass</code></small>
-  </span>
 
-<a href="#otg.v2g.V2GStep" class="headerlink" title="Permanent link">&para;</a></h2>
+<a href="#gentropy.v2g.V2GStep" class="headerlink" title="Permanent link">&para;</a></h2>
 
 
   <div class="doc doc-contents first">
@@ -2475,9 +2684,9 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
     </thead>
     <tbody>
         <tr>
-          <td><code>session</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.session">session</span></code></td>
           <td>
-                <code><span title="otg.common.session.Session">Session</span></code>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2486,7 +2695,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>variant_index_path</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.variant_index_path">variant_index_path</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2497,7 +2706,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>variant_annotation_path</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.variant_annotation_path">variant_annotation_path</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2508,7 +2717,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>gene_index_path</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.gene_index_path">gene_index_path</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2519,7 +2728,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>vep_consequences_path</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.vep_consequences_path">vep_consequences_path</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2530,7 +2739,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>liftover_chain_file_path</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.liftover_chain_file_path">liftover_chain_file_path</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2541,9 +2750,9 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>liftover_max_length_difference</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.liftover_max_length_difference">liftover_max_length_difference</span></code></td>
           <td>
-                <code>int</code>
+                <code>str</code>
           </td>
           <td>
             <div class="doc-md-description">
@@ -2552,7 +2761,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>max_distance</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.max_distance">max_distance</span></code></td>
           <td>
                 <code>int</code>
           </td>
@@ -2563,7 +2772,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>approved_biotypes</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.approved_biotypes">approved_biotypes</span></code></td>
           <td>
                 <code>list[str]</code>
           </td>
@@ -2574,7 +2783,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>intervals</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.intervals">intervals</span></code></td>
           <td>
                 <code>dict</code>
           </td>
@@ -2585,7 +2794,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
           </td>
         </tr>
         <tr>
-          <td><code>v2g_path</code></td>
+          <td><code><span title="gentropy.v2g.V2GStep.v2g_path">v2g_path</span></code></td>
           <td>
                 <code>str</code>
           </td>
@@ -2599,8 +2808,11 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
   </table>
 
             <details class="quote">
-              <summary>Source code in <code>src/otg/v2g.py</code></summary>
-              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 20</span>
+              <summary>Source code in <code>src/gentropy/v2g.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 17</span>
+<span class="normal"> 18</span>
+<span class="normal"> 19</span>
+<span class="normal"> 20</span>
 <span class="normal"> 21</span>
 <span class="normal"> 22</span>
 <span class="normal"> 23</span>
@@ -2709,13 +2921,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
 <span class="normal">126</span>
 <span class="normal">127</span>
 <span class="normal">128</span>
-<span class="normal">129</span>
-<span class="normal">130</span>
-<span class="normal">131</span>
-<span class="normal">132</span>
-<span class="normal">133</span>
-<span class="normal">134</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="nd">@dataclass</span>
-<span class="k">class</span> <span class="nc">V2GStep</span><span class="p">:</span>
+<span class="normal">129</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">V2GStep</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;Variant-to-gene (V2G) step.</span>
 
 <span class="sd">    This step aims to generate a dataset that contains multiple pieces of evidence supporting the functional association of specific variants with genes. Some of the evidence types include:</span>
@@ -2738,42 +2944,41 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
 <span class="sd">        v2g_path (str): Output V2G path.</span>
 <span class="sd">    &quot;&quot;&quot;</span>
 
-    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">vep_consequences_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">liftover_chain_file_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-    <span class="n">liftover_max_length_difference</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">100</span>
-    <span class="n">max_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">500_000</span>
-    <span class="n">approved_biotypes</span><span class="p">:</span> <span class="n">List</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span>
-        <span class="n">default_factory</span><span class="o">=</span><span class="k">lambda</span><span class="p">:</span> <span class="p">[</span>
-            <span class="s2">&quot;protein_coding&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;3prime_overlapping_ncRNA&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;antisense&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;bidirectional_promoter_lncRNA&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;IG_C_gene&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;IG_D_gene&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;IG_J_gene&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;IG_V_gene&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;lincRNA&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;macro_lncRNA&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;non_coding&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;sense_intronic&quot;</span><span class="p">,</span>
-            <span class="s2">&quot;sense_overlapping&quot;</span><span class="p">,</span>
-        <span class="p">]</span>
-    <span class="p">)</span>
-    <span class="n">intervals</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="n">field</span><span class="p">(</span><span class="n">default_factory</span><span class="o">=</span><span class="nb">dict</span><span class="p">)</span>
-    <span class="n">v2g_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="n">MISSING</span>
-
-    <span class="k">def</span> <span class="nf">__post_init__</span><span class="p">(</span><span class="bp">self</span><span class="p">:</span> <span class="n">V2GStep</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
-<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run step.&quot;&quot;&quot;</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">vep_consequences_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">liftover_chain_file_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">approved_biotypes</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+        <span class="n">interval_sources</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">],</span>
+        <span class="n">v2g_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">max_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">500_000</span><span class="p">,</span>
+        <span class="n">liftover_max_length_difference</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run Variant-to-gene (V2G) step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            variant_index_path (str): Input variant index path.</span>
+<span class="sd">            variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">            gene_index_path (str): Input gene index path.</span>
+<span class="sd">            vep_consequences_path (str): Input VEP consequences path.</span>
+<span class="sd">            liftover_chain_file_path (str): Path to GRCh37 to GRCh38 chain file.</span>
+<span class="sd">            approved_biotypes (list[str]): List of approved biotypes.</span>
+<span class="sd">            interval_sources (dict[str, str]): Dictionary of interval sources.</span>
+<span class="sd">            v2g_path (str): Output V2G path.</span>
+<span class="sd">            max_distance (int): Maximum distance to consider.</span>
+<span class="sd">            liftover_max_length_difference (int): Maximum length difference for liftover.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
         <span class="c1"># Read</span>
-        <span class="n">gene_index</span> <span class="o">=</span> <span class="n">GeneIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">gene_index_path</span><span class="p">)</span>
-        <span class="n">vi</span> <span class="o">=</span> <span class="n">VariantIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">variant_index_path</span><span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
-        <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">variant_annotation_path</span><span class="p">)</span>
-        <span class="n">vep_consequences</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">vep_consequences_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+        <span class="n">gene_index</span> <span class="o">=</span> <span class="n">GeneIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">gene_index_path</span><span class="p">)</span>
+        <span class="n">vi</span> <span class="o">=</span> <span class="n">VariantIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_index_path</span><span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+        <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+        <span class="n">vep_consequences</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+            <span class="n">vep_consequences_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
         <span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
             <span class="n">f</span><span class="o">.</span><span class="n">element_at</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;Accession&quot;</span><span class="p">,</span> <span class="sa">r</span><span class="s2">&quot;/&quot;</span><span class="p">),</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
                 <span class="s2">&quot;variantFunctionalConsequenceId&quot;</span>
@@ -2785,12 +2990,12 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
         <span class="c1"># Transform</span>
         <span class="n">lift</span> <span class="o">=</span> <span class="n">LiftOverSpark</span><span class="p">(</span>
             <span class="c1"># lift over variants to hg38</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">liftover_chain_file_path</span><span class="p">,</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">liftover_max_length_difference</span><span class="p">,</span>
+            <span class="n">liftover_chain_file_path</span><span class="p">,</span>
+            <span class="n">liftover_max_length_difference</span><span class="p">,</span>
         <span class="p">)</span>
         <span class="n">gene_index_filtered</span> <span class="o">=</span> <span class="n">gene_index</span><span class="o">.</span><span class="n">filter_by_biotypes</span><span class="p">(</span>
             <span class="c1"># Filter gene index by approved biotypes to define V2G gene universe</span>
-            <span class="nb">list</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">approved_biotypes</span><span class="p">)</span>
+            <span class="nb">list</span><span class="p">(</span><span class="n">approved_biotypes</span><span class="p">)</span>
         <span class="p">)</span>
         <span class="n">va_slimmed</span> <span class="o">=</span> <span class="n">va</span><span class="o">.</span><span class="n">filter_by_variant_df</span><span class="p">(</span>
             <span class="c1"># Variant annotation reduced to the variant index to define V2G variant universe</span>
@@ -2802,15 +3007,15 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
                 <span class="c1"># create interval instances by parsing each source</span>
                 <span class="p">[</span>
                     <span class="n">Intervals</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
-                        <span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">source_name</span><span class="p">,</span> <span class="n">source_path</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">,</span> <span class="n">lift</span>
+                        <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">source_name</span><span class="p">,</span> <span class="n">source_path</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">,</span> <span class="n">lift</span>
                     <span class="p">)</span><span class="o">.</span><span class="n">df</span>
-                    <span class="k">for</span> <span class="n">source_name</span><span class="p">,</span> <span class="n">source_path</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">intervals</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+                    <span class="k">for</span> <span class="n">source_name</span><span class="p">,</span> <span class="n">source_path</span> <span class="ow">in</span> <span class="n">interval_sources</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
                 <span class="p">],</span>
             <span class="p">),</span>
             <span class="n">_schema</span><span class="o">=</span><span class="n">Intervals</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
         <span class="p">)</span>
         <span class="n">v2g_datasets</span> <span class="o">=</span> <span class="p">[</span>
-            <span class="n">va_slimmed</span><span class="o">.</span><span class="n">get_distance_to_tss</span><span class="p">(</span><span class="n">gene_index_filtered</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_distance</span><span class="p">),</span>
+            <span class="n">va_slimmed</span><span class="o">.</span><span class="n">get_distance_to_tss</span><span class="p">(</span><span class="n">gene_index_filtered</span><span class="p">,</span> <span class="n">max_distance</span><span class="p">),</span>
             <span class="n">va_slimmed</span><span class="o">.</span><span class="n">get_most_severe_vep_v2g</span><span class="p">(</span><span class="n">vep_consequences</span><span class="p">,</span> <span class="n">gene_index_filtered</span><span class="p">),</span>
             <span class="n">va_slimmed</span><span class="o">.</span><span class="n">get_plof_v2g</span><span class="p">(</span><span class="n">gene_index_filtered</span><span class="p">),</span>
             <span class="n">intervals</span><span class="o">.</span><span class="n">v2g</span><span class="p">(</span><span class="n">vi</span><span class="p">),</span>
@@ -2826,8 +3031,8 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
         <span class="c1"># Load</span>
         <span class="p">(</span>
             <span class="n">v2g</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
-            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">v2g_path</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">v2g_path</span><span class="p">)</span>
         <span class="p">)</span>
 </code></pre></div></td></tr></table></div>
             </details>
@@ -2845,11 +3050,384 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
 
 
 
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.v2g.V2GStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">vep_consequences_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">liftover_chain_file_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">approved_biotypes</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span> <span class="n">interval_sources</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">],</span> <span class="n">v2g_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">max_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">500000</span><span class="p">,</span> <span class="n">liftover_max_length_difference</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">100</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.v2g.V2GStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run Variant-to-gene (V2G) step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>variant_index_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input variant index path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>variant_annotation_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input variant annotation path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>gene_index_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input gene index path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>vep_consequences_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Input VEP consequences path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>liftover_chain_file_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to GRCh37 to GRCh38 chain file.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>approved_biotypes</code></td>
+          <td>
+                <code>list[str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>List of approved biotypes.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>interval_sources</code></td>
+          <td>
+                <code>dict[str, str]</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Dictionary of interval sources.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>v2g_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Output V2G path.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>max_distance</code></td>
+          <td>
+                <code>int</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Maximum distance to consider.</p>
+            </div>
+          </td>
+          <td>
+                <code>500000</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>liftover_max_length_difference</code></td>
+          <td>
+                <code>int</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Maximum length difference for liftover.</p>
+            </div>
+          </td>
+          <td>
+                <code>100</code>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/v2g.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 40</span>
+<span class="normal"> 41</span>
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+<span class="normal">129</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">variant_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">variant_annotation_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">gene_index_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">vep_consequences_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">liftover_chain_file_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">approved_biotypes</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">],</span>
+    <span class="n">interval_sources</span><span class="p">:</span> <span class="nb">dict</span><span class="p">[</span><span class="nb">str</span><span class="p">,</span> <span class="nb">str</span><span class="p">],</span>
+    <span class="n">v2g_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">max_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">500_000</span><span class="p">,</span>
+    <span class="n">liftover_max_length_difference</span><span class="p">:</span> <span class="nb">int</span> <span class="o">=</span> <span class="mi">100</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run Variant-to-gene (V2G) step.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        session (Session): Session object.</span>
+<span class="sd">        variant_index_path (str): Input variant index path.</span>
+<span class="sd">        variant_annotation_path (str): Input variant annotation path.</span>
+<span class="sd">        gene_index_path (str): Input gene index path.</span>
+<span class="sd">        vep_consequences_path (str): Input VEP consequences path.</span>
+<span class="sd">        liftover_chain_file_path (str): Path to GRCh37 to GRCh38 chain file.</span>
+<span class="sd">        approved_biotypes (list[str]): List of approved biotypes.</span>
+<span class="sd">        interval_sources (dict[str, str]): Dictionary of interval sources.</span>
+<span class="sd">        v2g_path (str): Output V2G path.</span>
+<span class="sd">        max_distance (int): Maximum distance to consider.</span>
+<span class="sd">        liftover_max_length_difference (int): Maximum length difference for liftover.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># Read</span>
+    <span class="n">gene_index</span> <span class="o">=</span> <span class="n">GeneIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">gene_index_path</span><span class="p">)</span>
+    <span class="n">vi</span> <span class="o">=</span> <span class="n">VariantIndex</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_index_path</span><span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+    <span class="n">va</span> <span class="o">=</span> <span class="n">VariantAnnotation</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span><span class="n">session</span><span class="p">,</span> <span class="n">variant_annotation_path</span><span class="p">)</span>
+    <span class="n">vep_consequences</span> <span class="o">=</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">csv</span><span class="p">(</span>
+        <span class="n">vep_consequences_path</span><span class="p">,</span> <span class="n">sep</span><span class="o">=</span><span class="s2">&quot;</span><span class="se">\t</span><span class="s2">&quot;</span><span class="p">,</span> <span class="n">header</span><span class="o">=</span><span class="kc">True</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">element_at</span><span class="p">(</span><span class="n">f</span><span class="o">.</span><span class="n">split</span><span class="p">(</span><span class="s2">&quot;Accession&quot;</span><span class="p">,</span> <span class="sa">r</span><span class="s2">&quot;/&quot;</span><span class="p">),</span> <span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span>
+            <span class="s2">&quot;variantFunctionalConsequenceId&quot;</span>
+        <span class="p">),</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;Term&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;label&quot;</span><span class="p">),</span>
+        <span class="n">f</span><span class="o">.</span><span class="n">col</span><span class="p">(</span><span class="s2">&quot;v2g_score&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">cast</span><span class="p">(</span><span class="s2">&quot;double&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">alias</span><span class="p">(</span><span class="s2">&quot;score&quot;</span><span class="p">),</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Transform</span>
+    <span class="n">lift</span> <span class="o">=</span> <span class="n">LiftOverSpark</span><span class="p">(</span>
+        <span class="c1"># lift over variants to hg38</span>
+        <span class="n">liftover_chain_file_path</span><span class="p">,</span>
+        <span class="n">liftover_max_length_difference</span><span class="p">,</span>
+    <span class="p">)</span>
+    <span class="n">gene_index_filtered</span> <span class="o">=</span> <span class="n">gene_index</span><span class="o">.</span><span class="n">filter_by_biotypes</span><span class="p">(</span>
+        <span class="c1"># Filter gene index by approved biotypes to define V2G gene universe</span>
+        <span class="nb">list</span><span class="p">(</span><span class="n">approved_biotypes</span><span class="p">)</span>
+    <span class="p">)</span>
+    <span class="n">va_slimmed</span> <span class="o">=</span> <span class="n">va</span><span class="o">.</span><span class="n">filter_by_variant_df</span><span class="p">(</span>
+        <span class="c1"># Variant annotation reduced to the variant index to define V2G variant universe</span>
+        <span class="n">vi</span><span class="o">.</span><span class="n">df</span>
+    <span class="p">)</span><span class="o">.</span><span class="n">persist</span><span class="p">()</span>
+    <span class="n">intervals</span> <span class="o">=</span> <span class="n">Intervals</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="n">reduce</span><span class="p">(</span>
+            <span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">allowMissingColumns</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+            <span class="c1"># create interval instances by parsing each source</span>
+            <span class="p">[</span>
+                <span class="n">Intervals</span><span class="o">.</span><span class="n">from_source</span><span class="p">(</span>
+                    <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="p">,</span> <span class="n">source_name</span><span class="p">,</span> <span class="n">source_path</span><span class="p">,</span> <span class="n">gene_index</span><span class="p">,</span> <span class="n">lift</span>
+                <span class="p">)</span><span class="o">.</span><span class="n">df</span>
+                <span class="k">for</span> <span class="n">source_name</span><span class="p">,</span> <span class="n">source_path</span> <span class="ow">in</span> <span class="n">interval_sources</span><span class="o">.</span><span class="n">items</span><span class="p">()</span>
+            <span class="p">],</span>
+        <span class="p">),</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="n">Intervals</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+    <span class="p">)</span>
+    <span class="n">v2g_datasets</span> <span class="o">=</span> <span class="p">[</span>
+        <span class="n">va_slimmed</span><span class="o">.</span><span class="n">get_distance_to_tss</span><span class="p">(</span><span class="n">gene_index_filtered</span><span class="p">,</span> <span class="n">max_distance</span><span class="p">),</span>
+        <span class="n">va_slimmed</span><span class="o">.</span><span class="n">get_most_severe_vep_v2g</span><span class="p">(</span><span class="n">vep_consequences</span><span class="p">,</span> <span class="n">gene_index_filtered</span><span class="p">),</span>
+        <span class="n">va_slimmed</span><span class="o">.</span><span class="n">get_plof_v2g</span><span class="p">(</span><span class="n">gene_index_filtered</span><span class="p">),</span>
+        <span class="n">intervals</span><span class="o">.</span><span class="n">v2g</span><span class="p">(</span><span class="n">vi</span><span class="p">),</span>
+    <span class="p">]</span>
+    <span class="n">v2g</span> <span class="o">=</span> <span class="n">V2G</span><span class="p">(</span>
+        <span class="n">_df</span><span class="o">=</span><span class="n">reduce</span><span class="p">(</span>
+            <span class="k">lambda</span> <span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">:</span> <span class="n">x</span><span class="o">.</span><span class="n">unionByName</span><span class="p">(</span><span class="n">y</span><span class="p">,</span> <span class="n">allowMissingColumns</span><span class="o">=</span><span class="kc">True</span><span class="p">),</span>
+            <span class="p">[</span><span class="n">dataset</span><span class="o">.</span><span class="n">df</span> <span class="k">for</span> <span class="n">dataset</span> <span class="ow">in</span> <span class="n">v2g_datasets</span><span class="p">],</span>
+        <span class="p">)</span><span class="o">.</span><span class="n">repartition</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">),</span>
+        <span class="n">_schema</span><span class="o">=</span><span class="n">V2G</span><span class="o">.</span><span class="n">get_schema</span><span class="p">(),</span>
+    <span class="p">)</span>
+
+    <span class="c1"># Load</span>
+    <span class="p">(</span>
+        <span class="n">v2g</span><span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">partitionBy</span><span class="p">(</span><span class="s2">&quot;chromosome&quot;</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">v2g_path</span><span class="p">)</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
 
   </div>
 
   </div>
 
+
 </div>
 <hr />
 <div class="md-source-file">
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@@ -2932,7 +3510,7 @@ <h2 id="otg.v2g.V2GStep" class="doc doc-heading">
       
       
     
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diff --git a/python_api/steps/window_based_clumping/index.html b/python_api/steps/window_based_clumping/index.html
new file mode 100644
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+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/_datasources/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Datasources
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
+            <span class="md-nav__icon md-icon"></span>
+            Datasources
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Eqtl catalogue
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
+            <span class="md-nav__icon md-icon"></span>
+            Eqtl catalogue
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary Stats
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/finngen/_finngen/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Finngen
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
+            <span class="md-nav__icon md-icon"></span>
+            Finngen
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/finngen/summary_stats/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gnomad/_gnomad/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gnomad
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
+            <span class="md-nav__icon md-icon"></span>
+            Gnomad
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_ld/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LD Matrix
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gnomad/gnomad_variants/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Variants
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Gwas catalog
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
+            <span class="md-nav__icon md-icon"></span>
+            Gwas catalog
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/associations/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Associations
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/study_splitter/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Splitter
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Summary statistics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/intervals/_intervals/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Intervals
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
+            <span class="md-nav__icon md-icon"></span>
+            Intervals
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/andersson/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Andersson et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/javierre/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Javierre et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/jung/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Jung et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/intervals/thurman/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Thurman et al.
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../datasources/open_targets/_open_targets/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Open targets
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
+            <span class="md-nav__icon md-icon"></span>
+            Open targets
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Gold Standard
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../datasources/open_targets/target/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Target
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/_methods/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Methods
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
+            <span class="md-nav__icon md-icon"></span>
+            Methods
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/carma/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    CARMA
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/coloc/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Coloc
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ecaviar/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eCAVIAR
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/ld_annotator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    LDAnnotator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    PICS
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../../methods/l2g/_l2g/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    L2g
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
+            <span class="md-nav__icon md-icon"></span>
+            L2g
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/evaluator/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    W&B evaluator
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/feature_factory/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Feature Factory
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/model/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Model
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../../methods/l2g/trainer/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    L2G Trainer
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    
+    
+    
+    
+    
+    <li class="md-nav__item md-nav__item--active md-nav__item--nested">
+      
+        
+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" checked>
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../_steps/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Steps
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
+          </div>
+        
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="true">
+          <label class="md-nav__title" for="__nav_6_4">
+            <span class="md-nav__icon md-icon"></span>
+            Steps
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../colocalisation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    colocalisation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../eqtl_catalogue/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    eqtl_catalogue
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_studies/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_studies
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../finngen_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    finngen_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gene_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gene_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_curation/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_curation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_inclusion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_study_inclusion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_ingestion/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_ingestion
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    gwas_catalog_sumstat_preprocess
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../l2g/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    locus_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_clump/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_based_clumping
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../ld_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    ld_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../pics/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    pics
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_annotation_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+      
+        <label class="md-nav__link md-nav__link--active" for="__toc">
+          
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+          <span class="md-nav__icon md-icon"></span>
+        </label>
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
+  </span>
+  
+
+      </a>
+      
+        
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.window_based_clumping.WindowBasedClumpingStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      WindowBasedClumpingStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="WindowBasedClumpingStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.window_based_clumping.WindowBasedClumpingStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+  </ul>
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+            
+              
+              <div class="md-sidebar md-sidebar--secondary" data-md-component="sidebar" data-md-type="toc" >
+                <div class="md-sidebar__scrollwrap">
+                  <div class="md-sidebar__inner">
+                    
+
+<nav class="md-nav md-nav--secondary" aria-label="Table of contents">
+  
+  
+  
+  
+    <label class="md-nav__title" for="__toc">
+      <span class="md-nav__icon md-icon"></span>
+      Table of contents
+    </label>
+    <ul class="md-nav__list" data-md-component="toc" data-md-scrollfix>
+      
+        <li class="md-nav__item">
+  <a href="#gentropy.window_based_clumping.WindowBasedClumpingStep" class="md-nav__link">
+    <span class="md-ellipsis">
+      WindowBasedClumpingStep
+    </span>
+  </a>
+  
+    <nav class="md-nav" aria-label="WindowBasedClumpingStep">
+      <ul class="md-nav__list">
+        
+          <li class="md-nav__item">
+  <a href="#gentropy.window_based_clumping.WindowBasedClumpingStep.__init__" class="md-nav__link">
+    <span class="md-ellipsis">
+      __init__
+    </span>
+  </a>
+  
+</li>
+        
+      </ul>
+    </nav>
+  
+</li>
+      
+    </ul>
+  
+</nav>
+                  </div>
+                </div>
+              </div>
+            
+          
+          
+            <div class="md-content" data-md-component="content">
+              <article class="md-content__inner md-typeset">
+                
+                  
+
+  
+  
+
+
+  <h1>window_based_clumping</h1>
+
+<div class="doc doc-object doc-class">
+
+
+
+<h2 id="gentropy.window_based_clumping.WindowBasedClumpingStep" class="doc doc-heading">
+          <code>gentropy.window_based_clumping.WindowBasedClumpingStep</code>
+
+
+<a href="#gentropy.window_based_clumping.WindowBasedClumpingStep" class="headerlink" title="Permanent link">&para;</a></h2>
+
+
+  <div class="doc doc-contents first">
+
+  
+      <p>Apply window based clumping on summary statistics datasets.</p>
+
+            <details class="quote">
+              <summary>Source code in <code>src/gentropy/window_based_clumping.py</code></summary>
+              <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal"> 8</span>
+<span class="normal"> 9</span>
+<span class="normal">10</span>
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+<span class="normal">42</span>
+<span class="normal">43</span>
+<span class="normal">44</span>
+<span class="normal">45</span>
+<span class="normal">46</span>
+<span class="normal">47</span>
+<span class="normal">48</span>
+<span class="normal">49</span>
+<span class="normal">50</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">class</span> <span class="nc">WindowBasedClumpingStep</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Apply window based clumping on summary statistics datasets.&quot;&quot;&quot;</span>
+
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+        <span class="bp">self</span><span class="p">,</span>
+        <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+        <span class="n">summary_statistics_input_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">study_locus_output_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+        <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+        <span class="n">locus_collect_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;Run window-based clumping step.</span>
+
+<span class="sd">        Args:</span>
+<span class="sd">            session (Session): Session object.</span>
+<span class="sd">            summary_statistics_input_path (str): Path to the harmonized summary statistics dataset.</span>
+<span class="sd">            study_locus_output_path (str): Output path for the resulting study locus dataset.</span>
+<span class="sd">            inclusion_list_path (str | None): Path to the inclusion list (list of white-listed study identifier). Optional.</span>
+<span class="sd">            locus_collect_distance (int | None): Distance, within which tagging variants are collected around the semi-index. Optional.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="c1"># If inclusion list path is provided, only these studies will be read:</span>
+        <span class="k">if</span> <span class="n">inclusion_list_path</span><span class="p">:</span>
+            <span class="n">study_ids_to_ingest</span> <span class="o">=</span> <span class="p">[</span>
+                <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">summary_statistics_input_path</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">row</span><span class="p">[</span><span class="s2">&quot;studyId&quot;</span><span class="p">]</span><span class="si">}</span><span class="s1">.parquet&#39;</span>
+                <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">inclusion_list_path</span><span class="p">)</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span>
+            <span class="p">]</span>
+        <span class="k">else</span><span class="p">:</span>
+            <span class="c1"># If no inclusion list is provided, read all summary stats in folder:</span>
+            <span class="n">study_ids_to_ingest</span> <span class="o">=</span> <span class="p">[</span><span class="n">summary_statistics_input_path</span><span class="p">]</span>
+
+        <span class="p">(</span>
+            <span class="n">SummaryStatistics</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+                <span class="n">session</span><span class="p">,</span>
+                <span class="n">study_ids_to_ingest</span><span class="p">,</span>
+                <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+            <span class="p">)</span>
+            <span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="mi">4000</span><span class="p">)</span>
+            <span class="c1"># Applying window based clumping:</span>
+            <span class="o">.</span><span class="n">window_based_clumping</span><span class="p">(</span><span class="n">locus_collect_distance</span><span class="o">=</span><span class="n">locus_collect_distance</span><span class="p">)</span>
+            <span class="c1"># Save resulting study locus dataset:</span>
+            <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+            <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">study_locus_output_path</span><span class="p">)</span>
+        <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+            </details>
+
+  
+
+  <div class="doc doc-children">
+
+
+
+
+
+
+
+
+
+
+<div class="doc doc-object doc-function">
+
+
+
+<h3 id="gentropy.window_based_clumping.WindowBasedClumpingStep.__init__" class="doc doc-heading">
+          <code class="highlight language-python"><span class="fm">__init__</span><span class="p">(</span><span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span> <span class="n">summary_statistics_input_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">study_locus_output_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span> <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">locus_collect_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span></code>
+
+<a href="#gentropy.window_based_clumping.WindowBasedClumpingStep.__init__" class="headerlink" title="Permanent link">&para;</a></h3>
+
+
+  <div class="doc doc-contents ">
+  
+      <p>Run window-based clumping step.</p>
+
+
+
+  <p><strong>Parameters:</strong></p>
+  <table>
+    <thead>
+      <tr>
+        <th>Name</th>
+        <th>Type</th>
+        <th>Description</th>
+        <th>Default</th>
+      </tr>
+    </thead>
+    <tbody>
+        <tr>
+          <td><code>session</code></td>
+          <td>
+                <code><span title="gentropy.common.session.Session">Session</span></code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Session object.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>summary_statistics_input_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to the harmonized summary statistics dataset.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>study_locus_output_path</code></td>
+          <td>
+                <code>str</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Output path for the resulting study locus dataset.</p>
+            </div>
+          </td>
+          <td>
+              <em>required</em>
+          </td>
+        </tr>
+        <tr>
+          <td><code>inclusion_list_path</code></td>
+          <td>
+                <code>str | None</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Path to the inclusion list (list of white-listed study identifier). Optional.</p>
+            </div>
+          </td>
+          <td>
+                <code>None</code>
+          </td>
+        </tr>
+        <tr>
+          <td><code>locus_collect_distance</code></td>
+          <td>
+                <code>int | None</code>
+          </td>
+          <td>
+            <div class="doc-md-description">
+              <p>Distance, within which tagging variants are collected around the semi-index. Optional.</p>
+            </div>
+          </td>
+          <td>
+                <code>None</code>
+          </td>
+        </tr>
+    </tbody>
+  </table>
+
+          <details class="quote">
+            <summary>Source code in <code>src/gentropy/window_based_clumping.py</code></summary>
+            <div class="highlight"><table class="highlighttable"><tr><td class="linenos"><div class="linenodiv"><pre><span></span><span class="normal">11</span>
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+<span class="normal">47</span>
+<span class="normal">48</span>
+<span class="normal">49</span>
+<span class="normal">50</span></pre></div></td><td class="code"><div><pre><span></span><code><span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span>
+    <span class="bp">self</span><span class="p">,</span>
+    <span class="n">session</span><span class="p">:</span> <span class="n">Session</span><span class="p">,</span>
+    <span class="n">summary_statistics_input_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">study_locus_output_path</span><span class="p">:</span> <span class="nb">str</span><span class="p">,</span>
+    <span class="n">inclusion_list_path</span><span class="p">:</span> <span class="nb">str</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+    <span class="n">locus_collect_distance</span><span class="p">:</span> <span class="nb">int</span> <span class="o">|</span> <span class="kc">None</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span>
+<span class="p">)</span> <span class="o">-&gt;</span> <span class="kc">None</span><span class="p">:</span>
+<span class="w">    </span><span class="sd">&quot;&quot;&quot;Run window-based clumping step.</span>
+
+<span class="sd">    Args:</span>
+<span class="sd">        session (Session): Session object.</span>
+<span class="sd">        summary_statistics_input_path (str): Path to the harmonized summary statistics dataset.</span>
+<span class="sd">        study_locus_output_path (str): Output path for the resulting study locus dataset.</span>
+<span class="sd">        inclusion_list_path (str | None): Path to the inclusion list (list of white-listed study identifier). Optional.</span>
+<span class="sd">        locus_collect_distance (int | None): Distance, within which tagging variants are collected around the semi-index. Optional.</span>
+<span class="sd">    &quot;&quot;&quot;</span>
+    <span class="c1"># If inclusion list path is provided, only these studies will be read:</span>
+    <span class="k">if</span> <span class="n">inclusion_list_path</span><span class="p">:</span>
+        <span class="n">study_ids_to_ingest</span> <span class="o">=</span> <span class="p">[</span>
+            <span class="sa">f</span><span class="s1">&#39;</span><span class="si">{</span><span class="n">summary_statistics_input_path</span><span class="si">}</span><span class="s1">/</span><span class="si">{</span><span class="n">row</span><span class="p">[</span><span class="s2">&quot;studyId&quot;</span><span class="p">]</span><span class="si">}</span><span class="s1">.parquet&#39;</span>
+            <span class="k">for</span> <span class="n">row</span> <span class="ow">in</span> <span class="n">session</span><span class="o">.</span><span class="n">spark</span><span class="o">.</span><span class="n">read</span><span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">inclusion_list_path</span><span class="p">)</span><span class="o">.</span><span class="n">collect</span><span class="p">()</span>
+        <span class="p">]</span>
+    <span class="k">else</span><span class="p">:</span>
+        <span class="c1"># If no inclusion list is provided, read all summary stats in folder:</span>
+        <span class="n">study_ids_to_ingest</span> <span class="o">=</span> <span class="p">[</span><span class="n">summary_statistics_input_path</span><span class="p">]</span>
+
+    <span class="p">(</span>
+        <span class="n">SummaryStatistics</span><span class="o">.</span><span class="n">from_parquet</span><span class="p">(</span>
+            <span class="n">session</span><span class="p">,</span>
+            <span class="n">study_ids_to_ingest</span><span class="p">,</span>
+            <span class="n">recursiveFileLookup</span><span class="o">=</span><span class="kc">True</span><span class="p">,</span>
+        <span class="p">)</span>
+        <span class="o">.</span><span class="n">coalesce</span><span class="p">(</span><span class="mi">4000</span><span class="p">)</span>
+        <span class="c1"># Applying window based clumping:</span>
+        <span class="o">.</span><span class="n">window_based_clumping</span><span class="p">(</span><span class="n">locus_collect_distance</span><span class="o">=</span><span class="n">locus_collect_distance</span><span class="p">)</span>
+        <span class="c1"># Save resulting study locus dataset:</span>
+        <span class="o">.</span><span class="n">df</span><span class="o">.</span><span class="n">write</span><span class="o">.</span><span class="n">mode</span><span class="p">(</span><span class="n">session</span><span class="o">.</span><span class="n">write_mode</span><span class="p">)</span>
+        <span class="o">.</span><span class="n">parquet</span><span class="p">(</span><span class="n">study_locus_output_path</span><span class="p">)</span>
+    <span class="p">)</span>
+</code></pre></div></td></tr></table></div>
+          </details>
+  </div>
+
+</div>
+
+
+
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+
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+        </span>
+        <span class="label"> Contributors </span>
+      </li>
+      <li class="contributors-holder">
+        <ul class="contributors" data-bi-name="contributors"></ul>
+      </li>
+    </ul>
+  </small>
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+          
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\ No newline at end of file
diff --git a/roadmap/index.html b/roadmap/index.html
index 0fcfc8fb2..c7beb1d2a 100644
--- a/roadmap/index.html
+++ b/roadmap/index.html
@@ -9,18 +9,18 @@
       
       
       
-        <link rel="prev" href="../installation/">
+        <link rel="prev" href="../howto/run_step_using_config/">
       
       
-        <link rel="next" href="../usage/">
+        <link rel="next" href="../development/_development/">
       
       
       <link rel="icon" href="../assets/imgs/favicon.png">
-      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.2">
+      <meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.3">
     
     
       
-        <title>Roadmap - Open Targets Genetics</title>
+        <title>Roadmap - Open Targets Gentropy</title>
       
     
     
@@ -94,7 +94,7 @@
 
 <header class="md-header md-header--shadow md-header--lifted" data-md-component="header">
   <nav class="md-header__inner md-grid" aria-label="Header">
-    <a href=".." title="Open Targets Genetics" class="md-header__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href=".." title="Open Targets Gentropy" class="md-header__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../assets/imgs/otlogo.png" alt="logo">
 
@@ -107,7 +107,7 @@
       <div class="md-header__ellipsis">
         <div class="md-header__topic">
           <span class="md-ellipsis">
-            Open Targets Genetics
+            Open Targets Gentropy
           </span>
         </div>
         <div class="md-header__topic" data-md-component="header-topic">
@@ -192,13 +192,13 @@
     
     
       <div class="md-header__source">
-        <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+        <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
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   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
       </div>
@@ -215,6 +215,23 @@
   
   
   
+    <li class="md-tabs__item">
+      <a href=".." class="md-tabs__link">
+        
+  
+    
+  
+  Home
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
+  
     <li class="md-tabs__item">
       <a href="../installation/" class="md-tabs__link">
         
@@ -233,7 +250,7 @@
   
   
     <li class="md-tabs__item">
-      <a href="../usage/" class="md-tabs__link">
+      <a href="../howto/_howto/" class="md-tabs__link">
         
   
     
@@ -248,6 +265,25 @@
         
   
   
+    
+  
+  
+    <li class="md-tabs__item md-tabs__item--active">
+      <a href="./" class="md-tabs__link">
+        
+  
+    
+  
+  Roadmap
+
+      </a>
+    </li>
+  
+
+      
+        
+  
+  
   
     <li class="md-tabs__item">
       <a href="../development/_development/" class="md-tabs__link">
@@ -309,22 +345,22 @@
 
 <nav class="md-nav md-nav--primary md-nav--lifted" aria-label="Navigation" data-md-level="0">
   <label class="md-nav__title" for="__drawer">
-    <a href=".." title="Open Targets Genetics" class="md-nav__button md-logo" aria-label="Open Targets Genetics" data-md-component="logo">
+    <a href=".." title="Open Targets Gentropy" class="md-nav__button md-logo" aria-label="Open Targets Gentropy" data-md-component="logo">
       
   <img src="../assets/imgs/otlogo.png" alt="logo">
 
     </a>
-    Open Targets Genetics
+    Open Targets Gentropy
   </label>
   
     <div class="md-nav__source">
-      <a href="https://github.com/opentargets/genetics_etl_python" title="Go to repository" class="md-source" data-md-component="source">
+      <a href="https://github.com/opentargets/gentropy" title="Go to repository" class="md-source" data-md-component="source">
   <div class="md-source__icon md-icon">
     
     <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512"><!--! Font Awesome Free 6.5.1 by @fontawesome - https://fontawesome.com License - https://fontawesome.com/license/free (Icons: CC BY 4.0, Fonts: SIL OFL 1.1, Code: MIT License) Copyright 2023 Fonticons, Inc.--><path d="M439.55 236.05 244 40.45a28.87 28.87 0 0 0-40.81 0l-40.66 40.63 51.52 51.52c27.06-9.14 52.68 16.77 43.39 43.68l49.66 49.66c34.23-11.8 61.18 31 35.47 56.69-26.49 26.49-70.21-2.87-56-37.34L240.22 199v121.85c25.3 12.54 22.26 41.85 9.08 55a34.34 34.34 0 0 1-48.55 0c-17.57-17.6-11.07-46.91 11.25-56v-123c-20.8-8.51-24.6-30.74-18.64-45L142.57 101 8.45 235.14a28.86 28.86 0 0 0 0 40.81l195.61 195.6a28.86 28.86 0 0 0 40.8 0l194.69-194.69a28.86 28.86 0 0 0 0-40.81z"/></svg>
   </div>
   <div class="md-source__repository">
-    opentargets/genetics_etl_python
+    opentargets/gentropy
   </div>
 </a>
     </div>
@@ -338,11 +374,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../installation/" class="md-nav__link">
+      <a href=".." class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Installation
+    Home
   </span>
   
 
@@ -358,11 +394,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../usage/" class="md-nav__link">
+      <a href="../installation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    How-to
+    Installation
   </span>
   
 
@@ -395,11 +431,11 @@
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../development/_development/" class="md-nav__link ">
+            <a href="../howto/_howto/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Development
+    How-to
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@@ -414,6 +450,133 @@
         
         <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_3_label" aria-expanded="false">
           <label class="md-nav__title" for="__nav_3">
+            <span class="md-nav__icon md-icon"></span>
+            How-to
+          </label>
+          <ul class="md-nav__list" data-md-scrollfix>
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../howto/run_step_in_cli/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step in CLI
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../howto/run_step_using_config/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Run step using YAML config
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+          </ul>
+        </nav>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+    
+  
+  
+  
+    <li class="md-nav__item md-nav__item--active">
+      
+      <input class="md-nav__toggle md-toggle" type="checkbox" id="__toc">
+      
+      
+        
+      
+      
+      <a href="./" class="md-nav__link md-nav__link--active">
+        
+  
+  <span class="md-ellipsis">
+    Roadmap
+  </span>
+  
+
+      </a>
+      
+    </li>
+  
+
+    
+      
+      
+  
+  
+  
+  
+    
+    
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+    
+    
+      
+      
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+    <li class="md-nav__item md-nav__item--section md-nav__item--nested">
+      
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+        
+        
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_5" >
+        
+          
+          
+          <div class="md-nav__link md-nav__container">
+            <a href="../development/_development/" class="md-nav__link ">
+              
+  
+  <span class="md-ellipsis">
+    Development
+  </span>
+  
+
+            </a>
+            
+              
+              <label class="md-nav__link " for="__nav_5" id="__nav_5_label" tabindex="">
+                <span class="md-nav__icon md-icon"></span>
+              </label>
+            
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+        
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_5">
             <span class="md-nav__icon md-icon"></span>
             Development
           </label>
@@ -529,7 +692,7 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6" >
         
           
           
@@ -545,14 +708,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4" id="__nav_4_label" tabindex="">
+              <label class="md-nav__link " for="__nav_6" id="__nav_6_label" tabindex="">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4">
+        <nav class="md-nav" data-md-level="1" aria-labelledby="__nav_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6">
             <span class="md-nav__icon md-icon"></span>
             Python API
           </label>
@@ -574,32 +737,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/dataset/_dataset/" class="md-nav__link ">
+            <a href="../python_api/datasets/_datasets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Dataset
+    Datasets
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_1" id="__nav_4_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_1" id="__nav_6_1_label" tabindex="0">
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-          <label class="md-nav__title" for="__nav_4_1">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_1">
             <span class="md-nav__icon md-icon"></span>
-            Dataset
+            Datasets
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -610,7 +773,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/colocalisation/" class="md-nav__link">
+      <a href="../python_api/datasets/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -631,7 +794,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/gene_index/" class="md-nav__link">
+      <a href="../python_api/datasets/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -652,7 +815,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/intervals/" class="md-nav__link">
+      <a href="../python_api/datasets/intervals/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -673,7 +836,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_feature/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_feature/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -694,7 +857,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_feature_matrix/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_feature_matrix/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -715,7 +878,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_gold_standard/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -736,7 +899,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/l2g_prediction/" class="md-nav__link">
+      <a href="../python_api/datasets/l2g_prediction/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -757,7 +920,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/ld_index/" class="md-nav__link">
+      <a href="../python_api/datasets/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -778,7 +941,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/study_index/" class="md-nav__link">
+      <a href="../python_api/datasets/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -799,7 +962,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/study_locus/" class="md-nav__link">
+      <a href="../python_api/datasets/study_locus/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -820,7 +983,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/study_locus_overlap/" class="md-nav__link">
+      <a href="../python_api/datasets/study_locus_overlap/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -841,7 +1004,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/summary_statistics/" class="md-nav__link">
+      <a href="../python_api/datasets/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -862,7 +1025,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/variant_annotation/" class="md-nav__link">
+      <a href="../python_api/datasets/variant_annotation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -883,7 +1046,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/variant_index/" class="md-nav__link">
+      <a href="../python_api/datasets/variant_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -904,7 +1067,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/dataset/variant_to_gene/" class="md-nav__link">
+      <a href="../python_api/datasets/variant_to_gene/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -942,32 +1105,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/_datasource/" class="md-nav__link ">
+            <a href="../python_api/datasources/_datasources/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Datasource
+    Datasources
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2" id="__nav_4_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2" id="__nav_6_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
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           </div>
         
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-          <label class="md-nav__title" for="__nav_4_2">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2">
             <span class="md-nav__icon md-icon"></span>
-            Datasource
+            Datasources
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -987,12 +1150,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_1" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_1" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/eqtl_catalogue/study_index/" class="md-nav__link ">
+            <a href="../python_api/datasources/eqtl_catalogue/_eqtl_catalogue/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1003,14 +1166,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_1" id="__nav_4_2_1_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_1" id="__nav_6_2_1_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_1_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_1">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_1_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_1">
             <span class="md-nav__icon md-icon"></span>
             Eqtl catalogue
           </label>
@@ -1023,7 +1186,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/eqtl_catalogue/summary_stats/" class="md-nav__link">
+      <a href="../python_api/datasources/eqtl_catalogue/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/datasources/eqtl_catalogue/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1061,12 +1245,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_2" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_2" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/finngen/_finngen/" class="md-nav__link ">
+            <a href="../python_api/datasources/finngen/_finngen/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1077,14 +1261,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_2" id="__nav_4_2_2_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_2" id="__nav_6_2_2_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_2_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_2">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_2_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_2">
             <span class="md-nav__icon md-icon"></span>
             Finngen
           </label>
@@ -1097,7 +1281,28 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/finngen/study_index/" class="md-nav__link">
+      <a href="../python_api/datasources/finngen/study_index/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    Study Index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/datasources/finngen/summary_stats/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1135,12 +1340,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/gnomad/_gnomad/" class="md-nav__link ">
+            <a href="../python_api/datasources/gnomad/_gnomad/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1151,14 +1356,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_3" id="__nav_4_2_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_3" id="__nav_6_2_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-          <label class="md-nav__title" for="__nav_4_2_3">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_3">
             <span class="md-nav__icon md-icon"></span>
             Gnomad
           </label>
@@ -1171,7 +1376,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gnomad/gnomad_ld/" class="md-nav__link">
+      <a href="../python_api/datasources/gnomad/gnomad_ld/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1192,7 +1397,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gnomad/gnomad_variants/" class="md-nav__link">
+      <a href="../python_api/datasources/gnomad/gnomad_variants/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1230,12 +1435,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
+            <a href="../python_api/datasources/gwas_catalog/_gwas_catalog/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1246,14 +1451,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_4" id="__nav_4_2_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_4" id="__nav_6_2_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_4">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_4">
             <span class="md-nav__icon md-icon"></span>
             Gwas catalog
           </label>
@@ -1266,7 +1471,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/associations/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/associations/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1287,7 +1492,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/study_index/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/study_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1308,7 +1513,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/study_splitter/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/study_splitter/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1329,7 +1534,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/gwas_catalog/summary_statistics/" class="md-nav__link">
+      <a href="../python_api/datasources/gwas_catalog/summary_statistics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1367,12 +1572,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_5" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_5" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/intervals/_intervals/" class="md-nav__link ">
+            <a href="../python_api/datasources/intervals/_intervals/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1383,14 +1588,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_5" id="__nav_4_2_5_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_5" id="__nav_6_2_5_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_5_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_5">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_5_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_5">
             <span class="md-nav__icon md-icon"></span>
             Intervals
           </label>
@@ -1403,7 +1608,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/andersson/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/andersson/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1424,7 +1629,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/javierre/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/javierre/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1445,7 +1650,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/jung/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/jung/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1466,7 +1671,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/intervals/thurman/" class="md-nav__link">
+      <a href="../python_api/datasources/intervals/thurman/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1504,12 +1709,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_2_6" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_2_6" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/open_targets/_open_targets/" class="md-nav__link ">
+            <a href="../python_api/datasources/open_targets/_open_targets/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1520,14 +1725,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_2_6" id="__nav_4_2_6_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_2_6" id="__nav_6_2_6_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
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-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_6_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_6">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_2_6_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_2_6">
             <span class="md-nav__icon md-icon"></span>
             Open targets
           </label>
@@ -1540,7 +1745,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/open_targets/l2g_gold_standard/" class="md-nav__link">
+      <a href="../python_api/datasources/open_targets/l2g_gold_standard/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1561,7 +1766,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/datasource/open_targets/target/" class="md-nav__link">
+      <a href="../python_api/datasources/open_targets/target/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1583,80 +1788,6 @@
 
               
             
-              
-                
-  
-  
-  
-  
-    
-    
-    
-    
-    
-    <li class="md-nav__item md-nav__item--nested">
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-          
-          <div class="md-nav__link md-nav__container">
-            <a href="../python_api/datasource/ukbiobank/_ukbiobank/" class="md-nav__link ">
-              
-  
-  <span class="md-ellipsis">
-    Ukbiobank
-  </span>
-  
-
-            </a>
-            
-              
-              <label class="md-nav__link " for="__nav_4_2_7" id="__nav_4_2_7_label" tabindex="0">
-                <span class="md-nav__icon md-icon"></span>
-              </label>
-            
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-        
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_2_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_2_7">
-            <span class="md-nav__icon md-icon"></span>
-            Ukbiobank
-          </label>
-          <ul class="md-nav__list" data-md-scrollfix>
-            
-              
-                
-  
-  
-  
-  
-    <li class="md-nav__item">
-      <a href="../python_api/datasource/ukbiobank/study_index/" class="md-nav__link">
-        
-  
-  <span class="md-ellipsis">
-    Study Index
-  </span>
-  
-
-      </a>
-    </li>
-  
-
-              
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-          </ul>
-        </nav>
-      
-    </li>
-  
-
-              
-            
           </ul>
         </nav>
       
@@ -1681,32 +1812,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/method/_method/" class="md-nav__link ">
+            <a href="../python_api/methods/_methods/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Method
+    Methods
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3" id="__nav_4_3_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3" id="__nav_6_3_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_3_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_3_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3">
             <span class="md-nav__icon md-icon"></span>
-            Method
+            Methods
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -1717,11 +1848,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/clumping/" class="md-nav__link">
+      <a href="../python_api/methods/carma/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clumping
+    CARMA
   </span>
   
 
@@ -1738,11 +1869,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/coloc/" class="md-nav__link">
+      <a href="../python_api/methods/clumping/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Coloc
+    Clumping
   </span>
   
 
@@ -1759,11 +1890,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/ecaviar/" class="md-nav__link">
+      <a href="../python_api/methods/coloc/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eCAVIAR
+    Coloc
   </span>
   
 
@@ -1780,11 +1911,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/ld_annotator/" class="md-nav__link">
+      <a href="../python_api/methods/ecaviar/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LDAnnotator
+    eCAVIAR
   </span>
   
 
@@ -1801,11 +1932,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/pics/" class="md-nav__link">
+      <a href="../python_api/methods/ld_annotator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    LDAnnotator
   </span>
   
 
@@ -1822,11 +1953,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/window_based_clumping/" class="md-nav__link">
+      <a href="../python_api/methods/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Window-based clumping
+    PICS
   </span>
   
 
@@ -1852,12 +1983,12 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_3_7" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_3_7" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/method/l2g/_l2g/" class="md-nav__link ">
+            <a href="../python_api/methods/l2g/_l2g/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
@@ -1868,14 +1999,14 @@
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_3_7" id="__nav_4_3_7_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_3_7" id="__nav_6_3_7_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_4_3_7_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_3_7">
+        <nav class="md-nav" data-md-level="3" aria-labelledby="__nav_6_3_7_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_3_7">
             <span class="md-nav__icon md-icon"></span>
             L2g
           </label>
@@ -1888,7 +2019,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/evaluator/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/evaluator/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1909,7 +2040,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/feature_factory/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/feature_factory/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1930,7 +2061,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/model/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/model/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1951,7 +2082,7 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/method/l2g/trainer/" class="md-nav__link">
+      <a href="../python_api/methods/l2g/trainer/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
@@ -1997,32 +2128,32 @@
         
         
         
-        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_4_4" >
+        <input class="md-nav__toggle md-toggle " type="checkbox" id="__nav_6_4" >
         
           
           
           <div class="md-nav__link md-nav__container">
-            <a href="../python_api/step/_step/" class="md-nav__link ">
+            <a href="../python_api/steps/_steps/" class="md-nav__link ">
               
   
   <span class="md-ellipsis">
-    Step
+    Steps
   </span>
   
 
             </a>
             
               
-              <label class="md-nav__link " for="__nav_4_4" id="__nav_4_4_label" tabindex="0">
+              <label class="md-nav__link " for="__nav_6_4" id="__nav_6_4_label" tabindex="0">
                 <span class="md-nav__icon md-icon"></span>
               </label>
             
           </div>
         
-        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_4_4_label" aria-expanded="false">
-          <label class="md-nav__title" for="__nav_4_4">
+        <nav class="md-nav" data-md-level="2" aria-labelledby="__nav_6_4_label" aria-expanded="false">
+          <label class="md-nav__title" for="__nav_6_4">
             <span class="md-nav__icon md-icon"></span>
-            Step
+            Steps
           </label>
           <ul class="md-nav__list" data-md-scrollfix>
             
@@ -2033,11 +2164,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/clump/" class="md-nav__link">
+      <a href="../python_api/steps/colocalisation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Clump
+    colocalisation
   </span>
   
 
@@ -2054,11 +2185,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/colocalisation/" class="md-nav__link">
+      <a href="../python_api/steps/eqtl_catalogue/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Colocalisation
+    eqtl_catalogue
   </span>
   
 
@@ -2075,11 +2206,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/eqtl_catalogue/" class="md-nav__link">
+      <a href="../python_api/steps/finngen_studies/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    eQTL Catalogue
+    finngen_studies
   </span>
   
 
@@ -2096,11 +2227,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/finngen/" class="md-nav__link">
+      <a href="../python_api/steps/finngen_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    FinnGen
+    finngen_sumstat_preprocess
   </span>
   
 
@@ -2117,11 +2248,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/gene_index/" class="md-nav__link">
+      <a href="../python_api/steps/gene_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Gene Index
+    gene_index
   </span>
   
 
@@ -2138,11 +2269,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/gwas_catalog_ingestion/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_curation/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog
+    gwas_catalog_study_curation
   </span>
   
 
@@ -2159,11 +2290,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_inclusion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    GWAS Catalog sumstat preprocess
+    gwas_catalog_study_inclusion
   </span>
   
 
@@ -2180,11 +2311,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/l2g/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_ingestion/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Locus-to-gene (L2G)
+    gwas_catalog_ingestion
   </span>
   
 
@@ -2201,11 +2332,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/ld_index/" class="md-nav__link">
+      <a href="../python_api/steps/gwas_catalog_sumstat_preprocess/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    LD Index
+    gwas_catalog_sumstat_preprocess
   </span>
   
 
@@ -2222,11 +2353,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/pics/" class="md-nav__link">
+      <a href="../python_api/steps/l2g/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    PICS
+    locus_to_gene
   </span>
   
 
@@ -2243,11 +2374,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/ukbiobank/" class="md-nav__link">
+      <a href="../python_api/steps/ld_clump/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    UK Biobank
+    ld_based_clumping
   </span>
   
 
@@ -2264,11 +2395,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/variant_annotation_step/" class="md-nav__link">
+      <a href="../python_api/steps/ld_index/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Annotation
+    ld_index
   </span>
   
 
@@ -2285,11 +2416,11 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/variant_index_step/" class="md-nav__link">
+      <a href="../python_api/steps/pics/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant Index
+    pics
   </span>
   
 
@@ -2306,11 +2437,74 @@
   
   
     <li class="md-nav__item">
-      <a href="../python_api/step/variant_to_gene_step/" class="md-nav__link">
+      <a href="../python_api/steps/variant_annotation_step/" class="md-nav__link">
         
   
   <span class="md-ellipsis">
-    Variant-to-gene
+    variant_annotation
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/steps/variant_index_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_index
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/steps/variant_to_gene_step/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    variant_to_gene
+  </span>
+  
+
+      </a>
+    </li>
+  
+
+              
+            
+              
+                
+  
+  
+  
+  
+    <li class="md-nav__item">
+      <a href="../python_api/steps/window_based_clumping/" class="md-nav__link">
+        
+  
+  <span class="md-ellipsis">
+    window_based_clumping
   </span>
   
 
@@ -2483,7 +2677,7 @@ <h1 id="roadmap">Roadmap<a class="headerlink" href="#roadmap" title="Permanent l
       
       
     
-    <a href="https://github.com/genetics_etl_python" target="_blank" rel="noopener" title="github.com" class="md-social__link">
+    <a href="https://github.com/gentropy" target="_blank" rel="noopener" title="github.com" class="md-social__link">
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diff --git a/search/search_index.json b/search/search_index.json
index 33e0696d8..de70aa960 100644
--- a/search/search_index.json
+++ b/search/search_index.json
@@ -1 +1 @@
-{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Open Targets Genetics","text":"<p>Ingestion and analysis of genetic and functional genomic data for the identification and prioritisation of drug targets.</p> <p>This project is still in experimental phase. Please refer to the roadmap section for more information.</p> <p>For all development information, including running the code, troubleshooting, or contributing, see the development section.</p>"},{"location":"installation/","title":"Installation","text":"<p>TBC</p>"},{"location":"roadmap/","title":"Roadmap","text":"<p>The Open Targets core team is working on refactoring Open Targets Genetics, aiming to:</p> <ul> <li>Re-focus the product around Target ID</li> <li>Create a gold standard toolkit for post-GWAS analysis</li> <li>Faster/robust addition of new datasets and datatypes</li> <li>Reduce computational and financial cost</li> </ul> <p>See here for a list of open issues for this project.</p> <p>Schematic diagram representing the drafted process:</p> <p></p>"},{"location":"usage/","title":"How-to","text":"<p>TBC</p>"},{"location":"development/_development/","title":"Development","text":"<p>This section contains various technical information on how to develop and run the code.</p>"},{"location":"development/airflow/","title":"Airflow configuration","text":"<p>This section describes how to set up a local Airflow server which will orchestrate running workflows in Google Cloud Platform. This is useful for testing and debugging, but for production use, it is recommended to run Airflow on a dedicated server.</p>"},{"location":"development/airflow/#install-pre-requisites","title":"Install pre-requisites","text":"<ul> <li>Docker</li> <li>Google Cloud SDK</li> </ul> <p>Warning</p> <p>On macOS, the default amount of memory available for Docker might not be enough to get Airflow up and running. Allocate at least 4GB of memory for the Docker Engine (ideally 8GB). More info</p>"},{"location":"development/airflow/#configure-airflow-access-to-google-cloud-platform","title":"Configure Airflow access to Google Cloud Platform","text":"<p>Warning</p> <p>Run the next two command with the appropriate Google Cloud project ID and service account name to ensure the correct Google default application credentials are set up.</p> <p>Authenticate to Google Cloud:</p> <pre><code>gcloud auth application-default login --project=&lt;PROJECT&gt;\n</code></pre> <p>Create the service account key file that will be used by Airflow to access Google Cloud Platform resources:</p> <pre><code>gcloud iam service-accounts keys create ~/.config/gcloud/service_account_credentials.json --iam-account=&lt;PROJECT&gt;@appspot.gserviceaccount.com\n</code></pre>"},{"location":"development/airflow/#set-up-airflow","title":"Set up Airflow","text":"<p>Change the working directory so that all subsequent commands will work:</p> <pre><code>cd src/airflow\n</code></pre>"},{"location":"development/airflow/#build-docker-image","title":"Build Docker image","text":"<p>Note</p> <p>The custom Dockerfile built by the command below extends the official Airflow Docker Compose YAML. We add support for Google Cloud SDK, Google Dataproc operators, and access to GCP credentials.</p> <pre><code>docker build . --tag extending_airflow:latest\n</code></pre>"},{"location":"development/airflow/#set-airflow-user-id","title":"Set Airflow user ID","text":"<p>Note</p> <p>These commands allow Airflow running inside Docker to access the credentials file which was generated earlier.</p> <pre><code># If any user ID is already specified in .env, remove it.\ngrep -v \"AIRFLOW_UID\" .env &gt; .env.tmp\n# Add the correct user ID.\necho \"AIRFLOW_UID=$(id -u)\" &gt;&gt; .env.tmp\n# Move the file.\nmv .env.tmp .env\n</code></pre>"},{"location":"development/airflow/#initialise","title":"Initialise","text":"<p>Before starting Airflow, initialise the database:</p> <pre><code>docker compose up airflow-init\n</code></pre> <p>Now start all services:</p> <pre><code>docker compose up -d\n</code></pre> <p>Airflow UI will now be available at <code>http://localhost:8080/</code>. Default username and password are both <code>airflow</code>.</p> <p>For additional information on how to use Airflow visit the official documentation.</p>"},{"location":"development/airflow/#cleaning-up","title":"Cleaning up","text":"<p>At any time, you can check the status of your containers with:</p> <pre><code>docker ps\n</code></pre> <p>To stop Airflow, run:</p> <pre><code>docker compose down\n</code></pre> <p>To cleanup the Airflow database, run:</p> <pre><code>docker compose down --volumes --remove-orphans\n</code></pre>"},{"location":"development/airflow/#advanced-configuration","title":"Advanced configuration","text":"<p>More information on running Airflow with Docker Compose can be found in the official docs.</p> <ol> <li>Increase Airflow concurrency. Modify the <code>docker-compose.yaml</code> and add the following to the x-airflow-common \u2192 environment section:</li> </ol> <pre><code>AIRFLOW__CORE__PARALLELISM: 32\nAIRFLOW__CORE__MAX_ACTIVE_TASKS_PER_DAG: 32\nAIRFLOW__SCHEDULER__MAX_TIS_PER_QUERY: 16\nAIRFLOW__CORE__MAX_ACTIVE_RUNS_PER_DAG: 1\n# Also add the following line if you are using CeleryExecutor (by default, LocalExecutor is used).\nAIRFLOW__CELERY__WORKER_CONCURRENCY: 32\n</code></pre> <ol> <li>Additional pip packages. They can be added to the <code>requirements.txt</code> file.</li> </ol>"},{"location":"development/airflow/#troubleshooting","title":"Troubleshooting","text":"<p>Note that when you a a new workflow under <code>dags/</code>, Airflow will not pick that up immediately. By default the filesystem is only scanned for new DAGs every 300s. However, once the DAG is added, updates are applied nearly instantaneously.</p> <p>Also, if you edit the DAG while an instance of it is running, it might cause problems with the run, as Airflow will try to update the tasks and their properties in DAG according to the file changes.</p>"},{"location":"development/contributing/","title":"Contributing guidelines","text":""},{"location":"development/contributing/#one-time-configuration","title":"One-time configuration","text":"<p>The steps in this section only ever need to be done once on any particular system.</p> <p>Google Cloud configuration:</p> <ol> <li> <p>Install Google Cloud SDK: https://cloud.google.com/sdk/docs/install.</p> </li> <li> <p>Log in to your work Google Account: run <code>gcloud auth login</code> and follow instructions.</p> </li> <li> <p>Obtain Google application credentials: run <code>gcloud auth application-default login</code> and follow instructions.</p> </li> </ol> <p>Check that you have the <code>make</code> utility installed, and if not (which is unlikely), install it using your system package manager.</p> <p>Check that you have <code>java</code> installed.</p>"},{"location":"development/contributing/#environment-configuration","title":"Environment configuration","text":"<p>Run <code>make setup-dev</code> to install/update the necessary packages and activate the development environment. You need to do this every time you open a new shell.</p> <p>It is recommended to use VS Code as an IDE for development.</p>"},{"location":"development/contributing/#how-to-run-the-code","title":"How to run the code","text":"<p>All pipelines in this repository are intended to be run in Google Dataproc. Running them locally is not currently supported.</p> <p>In order to run the code:</p> <ol> <li> <p>Manually edit your local <code>src/airflow/dags/*</code> file and comment out the steps you do not want to run.</p> </li> <li> <p>Manually edit your local <code>pyproject.toml</code> file and modify the version of the code.</p> </li> <li> <p>This must be different from the version used by any other people working on the repository to avoid any deployment conflicts, so it's a good idea to use your name, for example: <code>1.2.3+jdoe</code>.</p> </li> <li>You can also add a brief branch description, for example: <code>1.2.3+jdoe.myfeature</code>.</li> <li>Note that the version must comply with PEP440 conventions, otherwise Poetry will not allow it to be deployed.</li> <li> <p>Do not use underscores or hyphens in your version name. When building the WHL file, they will be automatically converted to dots, which means the file name will no longer match the version and the build will fail. Use dots instead.</p> </li> <li> <p>Manually edit your local <code>src/airflow/dags/common_airflow.py</code> and set <code>OTG_VERSION</code> to the same version as you did in the previous step.</p> </li> <li> <p>Run <code>make build</code>.</p> </li> <li> <p>This will create a bundle containing the neccessary code, configuration and dependencies to run the ETL pipeline, and then upload this bundle to Google Cloud.</p> </li> <li>A version specific subpath is used, so uploading the code will not affect any branches but your own.</li> <li> <p>If there was already a code bundle uploaded with the same version number, it will be replaced.</p> </li> <li> <p>Open Airflow UI and run the DAG.</p> </li> </ol>"},{"location":"development/contributing/#contributing-checklist","title":"Contributing checklist","text":"<p>When making changes, and especially when implementing a new module or feature, it's essential to ensure that all relevant sections of the code base are modified.</p> <ul> <li>[ ] Run <code>make check</code>. This will run the linter and formatter to ensure that the code is compliant with the project conventions.</li> <li>[ ] Develop unit tests for your code and run <code>make test</code>. This will run all unit tests in the repository, including the examples appended in the docstrings of some methods.</li> <li>[ ] Update the configuration if necessary.</li> <li>[ ] Update the documentation and check it with <code>make build-documentation</code>. This will start a local server to browse it (URL will be printed, usually <code>http://127.0.0.1:8000/</code>)</li> </ul> <p>For more details on each of these steps, see the sections below.</p>"},{"location":"development/contributing/#documentation","title":"Documentation","text":"<ul> <li>If during development you had a question which wasn't covered in the documentation, and someone explained it to you, add it to the documentation. The same applies if you encountered any instructions in the documentation which were obsolete or incorrect.</li> <li>Documentation autogeneration expressions start with <code>:::</code>. They will automatically generate sections of the documentation based on class and method docstrings. Be sure to update them for:</li> <li>Dataset definitions in <code>docs/python_api/datasource/STEP</code> (example: <code>docs/python_api/datasource/finngen/study_index.md</code>)</li> <li>Step definition in <code>docs/python_api/step/STEP.md</code> (example: <code>docs/python_api/step/finngen.md</code>)</li> </ul>"},{"location":"development/contributing/#configuration","title":"Configuration","text":"<ul> <li>Input and output paths in <code>config/datasets/gcp.yaml</code></li> <li>Step configuration in <code>config/step/STEP.yaml</code> (example: <code>config/step/finngen.yaml</code>)</li> </ul>"},{"location":"development/contributing/#classes","title":"Classes","text":"<ul> <li>Dataset class in <code>src/otg/datasource/STEP</code> (example: <code>src/otg/datasource/finngen/study_index.py</code> \u2192 <code>FinnGenStudyIndex</code>)</li> <li>Step main running class in <code>src/otg/STEP.py</code> (example: <code>src/otg/finngen.py</code>)</li> </ul>"},{"location":"development/contributing/#tests","title":"Tests","text":"<ul> <li>Test study fixture in <code>tests/conftest.py</code> (example: <code>mock_study_index_finngen</code> in that module)</li> <li>Test sample data in <code>tests/data_samples</code> (example: <code>tests/data_samples/finngen_studies_sample.json</code>)</li> <li>Test definition in <code>tests/</code> (example: <code>tests/dataset/test_study_index.py</code> \u2192 <code>test_study_index_finngen_creation</code>)</li> </ul>"},{"location":"development/troubleshooting/","title":"Troubleshooting","text":""},{"location":"development/troubleshooting/#blaslapack","title":"BLAS/LAPACK","text":"<p>If you see errors related to BLAS/LAPACK libraries, see this StackOverflow post for guidance.</p>"},{"location":"development/troubleshooting/#pyenv-and-poetry","title":"Pyenv and Poetry","text":"<p>If you see various errors thrown by Pyenv or Poetry, they can be hard to specifically diagnose and resolve. In this case, it often helps to remove those tools from the system completely. Follow these steps:</p> <ol> <li>Close your currently activated environment, if any: <code>exit</code></li> <li>Uninstall Poetry: <code>curl -sSL https://install.python-poetry.org | python3 - --uninstall</code></li> <li>Clear Poetry cache: <code>rm -rf ~/.cache/pypoetry</code></li> <li>Clear pre-commit cache: <code>rm -rf ~/.cache/pre-commit</code></li> <li>Switch to system Python shell: <code>pyenv shell system</code></li> <li>Edit <code>~/.bashrc</code> to remove the lines related to Pyenv configuration</li> <li>Remove Pyenv configuration and cache: <code>rm -rf ~/.pyenv</code></li> </ol> <p>After that, open a fresh shell session and run <code>make setup-dev</code> again.</p>"},{"location":"development/troubleshooting/#java","title":"Java","text":"<p>Officially, PySpark requires Java version 8 (a.k.a. 1.8) or above to work. However, if you have a very recent version of Java, you may experience issues, as it may introduce breaking changes that PySpark hasn't had time to integrate. For example, as of May 2023, PySpark did not work with Java 20.</p> <p>If you are encountering problems with initialising a Spark session, try using Java 11.</p>"},{"location":"development/troubleshooting/#pre-commit","title":"Pre-commit","text":"<p>If you see an error message thrown by pre-commit, which looks like this (<code>SyntaxError: Unexpected token '?'</code>), followed by a JavaScript traceback, the issue is likely with your system NodeJS version.</p> <p>One solution which can help in this case is to upgrade your system NodeJS version. However, this may not always be possible. For example, Ubuntu repository is several major versions behind the latest version as of July 2023.</p> <p>Another solution which helps is to remove Node, NodeJS, and npm from your system entirely. In this case, pre-commit will not try to rely on a system version of NodeJS and will install its own, suitable one.</p> <p>On Ubuntu, this can be done using <code>sudo apt remove node nodejs npm</code>, followed by <code>sudo apt autoremove</code>. But in some cases, depending on your existing installation, you may need to also manually remove some files. See this StackOverflow answer for guidance.</p> <p>After running these commands, you are advised to open a fresh shell, and then also reinstall Pyenv and Poetry to make sure they pick up the changes (see relevant section above).</p>"},{"location":"development/workflows/","title":"Pipeline workflows","text":"<p>This page describes the high level components of the pipeline, which are organised as Airflow DAGs (directed acyclic graphs).</p>"},{"location":"development/workflows/#note-on-dags-and-dataproc-clusters","title":"Note on DAGs and Dataproc clusters","text":"<p>Each DAG consists of the following general stages:</p> <ol> <li> <p>Create cluster (if it already exists, this step is skipped)</p> </li> <li> <p>Install dependencies on the cluster</p> </li> <li> <p>Run data processing steps for this DAG</p> </li> <li> <p>Delete the cluster</p> </li> </ol> <p>Within a DAG, all data processing steps run on the same Dataproc cluster as separate jobs.</p> <p>There is no need to configure DAGs or steps depending on the size of the input data. Clusters have autoscaling enabled, which means they will increase or decrease the number of worker VMs to accommodate the load.</p>"},{"location":"development/workflows/#dag-1-preprocess","title":"DAG 1: Preprocess","text":"<p>This DAG contains steps which are only supposed to be run once, or very rarely. They ingest external data and apply bespoke transformations specific for each particular data source. The output is normalised according to the data schemas used by the pipeline.</p>"},{"location":"development/workflows/#dag-2-etl","title":"DAG 2: ETL","text":"<p>The ETL DAG takes the inputs of the previous step and performs the main algorithmic processing. This processing is supposed to be data source agnostic.</p>"},{"location":"python_api/dataset/_dataset/","title":"Dataset","text":""},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset","title":"<code>otg.dataset.dataset.Dataset</code>  <code>dataclass</code>","text":"<p>             Bases: <code>ABC</code></p> <p>Open Targets Genetics Dataset.</p> <p><code>Dataset</code> is a wrapper around a Spark DataFrame with a predefined schema. Schemas for each child dataset are described in the <code>schemas</code> module.</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>@dataclass\nclass Dataset(ABC):\n    \"\"\"Open Targets Genetics Dataset.\n\n    `Dataset` is a wrapper around a Spark DataFrame with a predefined schema. Schemas for each child dataset are described in the `schemas` module.\n    \"\"\"\n\n    _df: DataFrame\n    _schema: StructType\n\n    def __post_init__(self: Dataset) -&gt; None:\n        \"\"\"Post init.\"\"\"\n        self.validate_schema()\n\n    @property\n    def df(self: Dataset) -&gt; DataFrame:\n        \"\"\"Dataframe included in the Dataset.\n\n        Returns:\n            DataFrame: Dataframe included in the Dataset\n        \"\"\"\n        return self._df\n\n    @df.setter\n    def df(self: Dataset, new_df: DataFrame) -&gt; None:  # noqa: CCE001\n        \"\"\"Dataframe setter.\n\n        Args:\n            new_df (DataFrame): New dataframe to be included in the Dataset\n        \"\"\"\n        self._df: DataFrame = new_df\n        self.validate_schema()\n\n    @property\n    def schema(self: Dataset) -&gt; StructType:\n        \"\"\"Dataframe expected schema.\n\n        Returns:\n            StructType: Dataframe expected schema\n        \"\"\"\n        return self._schema\n\n    @classmethod\n    @abstractmethod\n    def get_schema(cls: type[Self]) -&gt; StructType:\n        \"\"\"Abstract method to get the schema. Must be implemented by child classes.\n\n        Returns:\n            StructType: Schema for the Dataset\n        \"\"\"\n        pass\n\n    @classmethod\n    def from_parquet(\n        cls: type[Self],\n        session: Session,\n        path: str,\n        **kwargs: bool | float | int | str | None,\n    ) -&gt; Self:\n        \"\"\"Reads a parquet file into a Dataset with a given schema.\n\n        Args:\n            session (Session): Spark session\n            path (str): Path to the parquet file\n            **kwargs (bool | float | int | str | None): Additional arguments to pass to spark.read.parquet\n\n        Returns:\n            Self: Dataset with the parquet file contents\n\n        Raises:\n            ValueError: Parquet file is empty\n        \"\"\"\n        schema = cls.get_schema()\n        df = session.read_parquet(path=path, schema=schema, **kwargs)\n        if df.isEmpty():\n            raise ValueError(f\"Parquet file is empty: {path}\")\n        return cls(_df=df, _schema=schema)\n\n    def validate_schema(self: Dataset) -&gt; None:\n        \"\"\"Validate DataFrame schema against expected class schema.\n\n        Raises:\n            ValueError: DataFrame schema is not valid\n        \"\"\"\n        expected_schema = self._schema\n        expected_fields = flatten_schema(expected_schema)\n        observed_schema = self._df.schema\n        observed_fields = flatten_schema(observed_schema)\n\n        # Unexpected fields in dataset\n        if unexpected_field_names := [\n            x.name\n            for x in observed_fields\n            if x.name not in [y.name for y in expected_fields]\n        ]:\n            raise ValueError(\n                f\"The {unexpected_field_names} fields are not included in DataFrame schema: {expected_fields}\"\n            )\n\n        # Required fields not in dataset\n        required_fields = [x.name for x in expected_schema if not x.nullable]\n        if missing_required_fields := [\n            req\n            for req in required_fields\n            if not any(field.name == req for field in observed_fields)\n        ]:\n            raise ValueError(\n                f\"The {missing_required_fields} fields are required but missing: {required_fields}\"\n            )\n\n        # Fields with duplicated names\n        if duplicated_fields := [\n            x for x in set(observed_fields) if observed_fields.count(x) &gt; 1\n        ]:\n            raise ValueError(\n                f\"The following fields are duplicated in DataFrame schema: {duplicated_fields}\"\n            )\n\n        # Fields with different datatype\n        observed_field_types = {\n            field.name: type(field.dataType) for field in observed_fields\n        }\n        expected_field_types = {\n            field.name: type(field.dataType) for field in expected_fields\n        }\n        if fields_with_different_observed_datatype := [\n            name\n            for name, observed_type in observed_field_types.items()\n            if name in expected_field_types\n            and observed_type != expected_field_types[name]\n        ]:\n            raise ValueError(\n                f\"The following fields present differences in their datatypes: {fields_with_different_observed_datatype}.\"\n            )\n\n    def persist(self: Self) -&gt; Self:\n        \"\"\"Persist in memory the DataFrame included in the Dataset.\n\n        Returns:\n            Self: Persisted Dataset\n        \"\"\"\n        self.df = self._df.persist()\n        return self\n\n    def unpersist(self: Self) -&gt; Self:\n        \"\"\"Remove the persisted DataFrame from memory.\n\n        Returns:\n            Self: Unpersisted Dataset\n        \"\"\"\n        self.df = self._df.unpersist()\n        return self\n\n    def coalesce(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n        \"\"\"Coalesce the DataFrame included in the Dataset.\n\n        Coalescing is efficient for decreasing the number of partitions because it avoids a full shuffle of the data.\n\n        Args:\n            num_partitions (int): Number of partitions to coalesce to\n            **kwargs (Any): Arguments to pass to the coalesce method\n\n        Returns:\n            Self: Coalesced Dataset\n        \"\"\"\n        self.df = self._df.coalesce(num_partitions, **kwargs)\n        return self\n\n    def repartition(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n        \"\"\"Repartition the DataFrame included in the Dataset.\n\n        Repartitioning creates new partitions with data that is distributed evenly.\n\n        Args:\n            num_partitions (int): Number of partitions to repartition to\n            **kwargs (Any): Arguments to pass to the repartition method\n\n        Returns:\n            Self: Repartitioned Dataset\n        \"\"\"\n        self.df = self._df.repartition(num_partitions, **kwargs)\n        return self\n</code></pre>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.df","title":"<code>df: DataFrame</code>  <code>property</code> <code>writable</code>","text":"<p>Dataframe included in the Dataset.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Dataframe included in the Dataset</p>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.schema","title":"<code>schema: StructType</code>  <code>property</code>","text":"<p>Dataframe expected schema.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Dataframe expected schema</p>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.coalesce","title":"<code>coalesce(num_partitions: int, **kwargs: Any) -&gt; Self</code>","text":"<p>Coalesce the DataFrame included in the Dataset.</p> <p>Coalescing is efficient for decreasing the number of partitions because it avoids a full shuffle of the data.</p> <p>Parameters:</p> Name Type Description Default <code>num_partitions</code> <code>int</code> <p>Number of partitions to coalesce to</p> required <code>**kwargs</code> <code>Any</code> <p>Arguments to pass to the coalesce method</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Coalesced Dataset</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>def coalesce(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n    \"\"\"Coalesce the DataFrame included in the Dataset.\n\n    Coalescing is efficient for decreasing the number of partitions because it avoids a full shuffle of the data.\n\n    Args:\n        num_partitions (int): Number of partitions to coalesce to\n        **kwargs (Any): Arguments to pass to the coalesce method\n\n    Returns:\n        Self: Coalesced Dataset\n    \"\"\"\n    self.df = self._df.coalesce(num_partitions, **kwargs)\n    return self\n</code></pre>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.from_parquet","title":"<code>from_parquet(session: Session, path: str, **kwargs: bool | float | int | str | None) -&gt; Self</code>  <code>classmethod</code>","text":"<p>Reads a parquet file into a Dataset with a given schema.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to the parquet file</p> required <code>**kwargs</code> <code>bool | float | int | str | None</code> <p>Additional arguments to pass to spark.read.parquet</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Dataset with the parquet file contents</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>Parquet file is empty</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>@classmethod\ndef from_parquet(\n    cls: type[Self],\n    session: Session,\n    path: str,\n    **kwargs: bool | float | int | str | None,\n) -&gt; Self:\n    \"\"\"Reads a parquet file into a Dataset with a given schema.\n\n    Args:\n        session (Session): Spark session\n        path (str): Path to the parquet file\n        **kwargs (bool | float | int | str | None): Additional arguments to pass to spark.read.parquet\n\n    Returns:\n        Self: Dataset with the parquet file contents\n\n    Raises:\n        ValueError: Parquet file is empty\n    \"\"\"\n    schema = cls.get_schema()\n    df = session.read_parquet(path=path, schema=schema, **kwargs)\n    if df.isEmpty():\n        raise ValueError(f\"Parquet file is empty: {path}\")\n    return cls(_df=df, _schema=schema)\n</code></pre>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>abstractmethod</code> <code>classmethod</code>","text":"<p>Abstract method to get the schema. Must be implemented by child classes.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the Dataset</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>@classmethod\n@abstractmethod\ndef get_schema(cls: type[Self]) -&gt; StructType:\n    \"\"\"Abstract method to get the schema. Must be implemented by child classes.\n\n    Returns:\n        StructType: Schema for the Dataset\n    \"\"\"\n    pass\n</code></pre>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.persist","title":"<code>persist() -&gt; Self</code>","text":"<p>Persist in memory the DataFrame included in the Dataset.</p> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Persisted Dataset</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>def persist(self: Self) -&gt; Self:\n    \"\"\"Persist in memory the DataFrame included in the Dataset.\n\n    Returns:\n        Self: Persisted Dataset\n    \"\"\"\n    self.df = self._df.persist()\n    return self\n</code></pre>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.repartition","title":"<code>repartition(num_partitions: int, **kwargs: Any) -&gt; Self</code>","text":"<p>Repartition the DataFrame included in the Dataset.</p> <p>Repartitioning creates new partitions with data that is distributed evenly.</p> <p>Parameters:</p> Name Type Description Default <code>num_partitions</code> <code>int</code> <p>Number of partitions to repartition to</p> required <code>**kwargs</code> <code>Any</code> <p>Arguments to pass to the repartition method</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Repartitioned Dataset</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>def repartition(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n    \"\"\"Repartition the DataFrame included in the Dataset.\n\n    Repartitioning creates new partitions with data that is distributed evenly.\n\n    Args:\n        num_partitions (int): Number of partitions to repartition to\n        **kwargs (Any): Arguments to pass to the repartition method\n\n    Returns:\n        Self: Repartitioned Dataset\n    \"\"\"\n    self.df = self._df.repartition(num_partitions, **kwargs)\n    return self\n</code></pre>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.unpersist","title":"<code>unpersist() -&gt; Self</code>","text":"<p>Remove the persisted DataFrame from memory.</p> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Unpersisted Dataset</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>def unpersist(self: Self) -&gt; Self:\n    \"\"\"Remove the persisted DataFrame from memory.\n\n    Returns:\n        Self: Unpersisted Dataset\n    \"\"\"\n    self.df = self._df.unpersist()\n    return self\n</code></pre>"},{"location":"python_api/dataset/_dataset/#otg.dataset.dataset.Dataset.validate_schema","title":"<code>validate_schema() -&gt; None</code>","text":"<p>Validate DataFrame schema against expected class schema.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>DataFrame schema is not valid</p> Source code in <code>src/otg/dataset/dataset.py</code> <pre><code>def validate_schema(self: Dataset) -&gt; None:\n    \"\"\"Validate DataFrame schema against expected class schema.\n\n    Raises:\n        ValueError: DataFrame schema is not valid\n    \"\"\"\n    expected_schema = self._schema\n    expected_fields = flatten_schema(expected_schema)\n    observed_schema = self._df.schema\n    observed_fields = flatten_schema(observed_schema)\n\n    # Unexpected fields in dataset\n    if unexpected_field_names := [\n        x.name\n        for x in observed_fields\n        if x.name not in [y.name for y in expected_fields]\n    ]:\n        raise ValueError(\n            f\"The {unexpected_field_names} fields are not included in DataFrame schema: {expected_fields}\"\n        )\n\n    # Required fields not in dataset\n    required_fields = [x.name for x in expected_schema if not x.nullable]\n    if missing_required_fields := [\n        req\n        for req in required_fields\n        if not any(field.name == req for field in observed_fields)\n    ]:\n        raise ValueError(\n            f\"The {missing_required_fields} fields are required but missing: {required_fields}\"\n        )\n\n    # Fields with duplicated names\n    if duplicated_fields := [\n        x for x in set(observed_fields) if observed_fields.count(x) &gt; 1\n    ]:\n        raise ValueError(\n            f\"The following fields are duplicated in DataFrame schema: {duplicated_fields}\"\n        )\n\n    # Fields with different datatype\n    observed_field_types = {\n        field.name: type(field.dataType) for field in observed_fields\n    }\n    expected_field_types = {\n        field.name: type(field.dataType) for field in expected_fields\n    }\n    if fields_with_different_observed_datatype := [\n        name\n        for name, observed_type in observed_field_types.items()\n        if name in expected_field_types\n        and observed_type != expected_field_types[name]\n    ]:\n        raise ValueError(\n            f\"The following fields present differences in their datatypes: {fields_with_different_observed_datatype}.\"\n        )\n</code></pre>"},{"location":"python_api/dataset/colocalisation/","title":"Colocalisation","text":""},{"location":"python_api/dataset/colocalisation/#otg.dataset.colocalisation.Colocalisation","title":"<code>otg.dataset.colocalisation.Colocalisation</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Colocalisation results for pairs of overlapping study-locus.</p> Source code in <code>src/otg/dataset/colocalisation.py</code> <pre><code>@dataclass\nclass Colocalisation(Dataset):\n    \"\"\"Colocalisation results for pairs of overlapping study-locus.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[Colocalisation]) -&gt; StructType:\n        \"\"\"Provides the schema for the Colocalisation dataset.\n\n        Returns:\n            StructType: Schema for the Colocalisation dataset\n        \"\"\"\n        return parse_spark_schema(\"colocalisation.json\")\n</code></pre>"},{"location":"python_api/dataset/colocalisation/#otg.dataset.colocalisation.Colocalisation.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the Colocalisation dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the Colocalisation dataset</p> Source code in <code>src/otg/dataset/colocalisation.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[Colocalisation]) -&gt; StructType:\n    \"\"\"Provides the schema for the Colocalisation dataset.\n\n    Returns:\n        StructType: Schema for the Colocalisation dataset\n    \"\"\"\n    return parse_spark_schema(\"colocalisation.json\")\n</code></pre>"},{"location":"python_api/dataset/colocalisation/#schema","title":"Schema","text":"<pre><code>root\n |-- leftStudyLocusId: long (nullable = false)\n |-- rightStudyLocusId: long (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- colocalisationMethod: string (nullable = false)\n |-- numberColocalisingVariants: long (nullable = false)\n |-- h0: double (nullable = true)\n |-- h1: double (nullable = true)\n |-- h2: double (nullable = true)\n |-- h3: double (nullable = true)\n |-- h4: double (nullable = true)\n |-- log2h4h3: double (nullable = true)\n |-- clpp: double (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/gene_index/","title":"Gene Index","text":""},{"location":"python_api/dataset/gene_index/#otg.dataset.gene_index.GeneIndex","title":"<code>otg.dataset.gene_index.GeneIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Gene index dataset.</p> <p>Gene-based annotation.</p> Source code in <code>src/otg/dataset/gene_index.py</code> <pre><code>@dataclass\nclass GeneIndex(Dataset):\n    \"\"\"Gene index dataset.\n\n    Gene-based annotation.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[GeneIndex]) -&gt; StructType:\n        \"\"\"Provides the schema for the GeneIndex dataset.\n\n        Returns:\n            StructType: Schema for the GeneIndex dataset\n        \"\"\"\n        return parse_spark_schema(\"gene_index.json\")\n\n    def filter_by_biotypes(self: GeneIndex, biotypes: list[str]) -&gt; GeneIndex:\n        \"\"\"Filter by approved biotypes.\n\n        Args:\n            biotypes (list[str]): List of Ensembl biotypes to keep.\n\n        Returns:\n            GeneIndex: Gene index dataset filtered by biotypes.\n        \"\"\"\n        self.df = self._df.filter(f.col(\"biotype\").isin(biotypes))\n        return self\n\n    def locations_lut(self: GeneIndex) -&gt; DataFrame:\n        \"\"\"Gene location information.\n\n        Returns:\n            DataFrame: Gene LUT including genomic location information.\n        \"\"\"\n        return self.df.select(\n            \"geneId\",\n            \"chromosome\",\n            \"start\",\n            \"end\",\n            \"strand\",\n            \"tss\",\n        )\n\n    def symbols_lut(self: GeneIndex) -&gt; DataFrame:\n        \"\"\"Gene symbol lookup table.\n\n        Pre-processess gene/target dataset to create lookup table of gene symbols, including\n        obsoleted gene symbols.\n\n        Returns:\n            DataFrame: Gene LUT for symbol mapping containing `geneId` and `geneSymbol` columns.\n        \"\"\"\n        return self.df.select(\n            f.explode(\n                f.array_union(f.array(\"approvedSymbol\"), f.col(\"obsoleteSymbols\"))\n            ).alias(\"geneSymbol\"),\n            \"*\",\n        )\n</code></pre>"},{"location":"python_api/dataset/gene_index/#otg.dataset.gene_index.GeneIndex.filter_by_biotypes","title":"<code>filter_by_biotypes(biotypes: list[str]) -&gt; GeneIndex</code>","text":"<p>Filter by approved biotypes.</p> <p>Parameters:</p> Name Type Description Default <code>biotypes</code> <code>list[str]</code> <p>List of Ensembl biotypes to keep.</p> required <p>Returns:</p> Name Type Description <code>GeneIndex</code> <code>GeneIndex</code> <p>Gene index dataset filtered by biotypes.</p> Source code in <code>src/otg/dataset/gene_index.py</code> <pre><code>def filter_by_biotypes(self: GeneIndex, biotypes: list[str]) -&gt; GeneIndex:\n    \"\"\"Filter by approved biotypes.\n\n    Args:\n        biotypes (list[str]): List of Ensembl biotypes to keep.\n\n    Returns:\n        GeneIndex: Gene index dataset filtered by biotypes.\n    \"\"\"\n    self.df = self._df.filter(f.col(\"biotype\").isin(biotypes))\n    return self\n</code></pre>"},{"location":"python_api/dataset/gene_index/#otg.dataset.gene_index.GeneIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the GeneIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the GeneIndex dataset</p> Source code in <code>src/otg/dataset/gene_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[GeneIndex]) -&gt; StructType:\n    \"\"\"Provides the schema for the GeneIndex dataset.\n\n    Returns:\n        StructType: Schema for the GeneIndex dataset\n    \"\"\"\n    return parse_spark_schema(\"gene_index.json\")\n</code></pre>"},{"location":"python_api/dataset/gene_index/#otg.dataset.gene_index.GeneIndex.locations_lut","title":"<code>locations_lut() -&gt; DataFrame</code>","text":"<p>Gene location information.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Gene LUT including genomic location information.</p> Source code in <code>src/otg/dataset/gene_index.py</code> <pre><code>def locations_lut(self: GeneIndex) -&gt; DataFrame:\n    \"\"\"Gene location information.\n\n    Returns:\n        DataFrame: Gene LUT including genomic location information.\n    \"\"\"\n    return self.df.select(\n        \"geneId\",\n        \"chromosome\",\n        \"start\",\n        \"end\",\n        \"strand\",\n        \"tss\",\n    )\n</code></pre>"},{"location":"python_api/dataset/gene_index/#otg.dataset.gene_index.GeneIndex.symbols_lut","title":"<code>symbols_lut() -&gt; DataFrame</code>","text":"<p>Gene symbol lookup table.</p> <p>Pre-processess gene/target dataset to create lookup table of gene symbols, including obsoleted gene symbols.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Gene LUT for symbol mapping containing <code>geneId</code> and <code>geneSymbol</code> columns.</p> Source code in <code>src/otg/dataset/gene_index.py</code> <pre><code>def symbols_lut(self: GeneIndex) -&gt; DataFrame:\n    \"\"\"Gene symbol lookup table.\n\n    Pre-processess gene/target dataset to create lookup table of gene symbols, including\n    obsoleted gene symbols.\n\n    Returns:\n        DataFrame: Gene LUT for symbol mapping containing `geneId` and `geneSymbol` columns.\n    \"\"\"\n    return self.df.select(\n        f.explode(\n            f.array_union(f.array(\"approvedSymbol\"), f.col(\"obsoleteSymbols\"))\n        ).alias(\"geneSymbol\"),\n        \"*\",\n    )\n</code></pre>"},{"location":"python_api/dataset/gene_index/#schema","title":"Schema","text":"<pre><code>root\n |-- geneId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- approvedSymbol: string (nullable = true)\n |-- biotype: string (nullable = true)\n |-- approvedName: string (nullable = true)\n |-- obsoleteSymbols: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- tss: long (nullable = true)\n |-- start: long (nullable = true)\n |-- end: long (nullable = true)\n |-- strand: integer (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/intervals/","title":"Intervals","text":""},{"location":"python_api/dataset/intervals/#otg.dataset.intervals.Intervals","title":"<code>otg.dataset.intervals.Intervals</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Intervals dataset links genes to genomic regions based on genome interaction studies.</p> Source code in <code>src/otg/dataset/intervals.py</code> <pre><code>@dataclass\nclass Intervals(Dataset):\n    \"\"\"Intervals dataset links genes to genomic regions based on genome interaction studies.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[Intervals]) -&gt; StructType:\n        \"\"\"Provides the schema for the Intervals dataset.\n\n        Returns:\n            StructType: Schema for the Intervals dataset\n        \"\"\"\n        return parse_spark_schema(\"intervals.json\")\n\n    @classmethod\n    def from_source(\n        cls: type[Intervals],\n        spark: SparkSession,\n        source_name: str,\n        source_path: str,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Collect interval data for a particular source.\n\n        Args:\n            spark (SparkSession): Spark session\n            source_name (str): Name of the interval source\n            source_path (str): Path to the interval source file\n            gene_index (GeneIndex): Gene index\n            lift (LiftOverSpark): LiftOverSpark instance to convert coordinats from hg37 to hg38\n\n        Returns:\n            Intervals: Intervals dataset\n\n        Raises:\n            ValueError: If the source name is not recognised\n        \"\"\"\n        from otg.datasource.intervals.andersson import IntervalsAndersson\n        from otg.datasource.intervals.javierre import IntervalsJavierre\n        from otg.datasource.intervals.jung import IntervalsJung\n        from otg.datasource.intervals.thurman import IntervalsThurman\n\n        source_to_class = {\n            \"andersson\": IntervalsAndersson,\n            \"javierre\": IntervalsJavierre,\n            \"jung\": IntervalsJung,\n            \"thurman\": IntervalsThurman,\n        }\n\n        if source_name not in source_to_class:\n            raise ValueError(f\"Unknown interval source: {source_name}\")\n\n        source_class = source_to_class[source_name]\n        data = source_class.read(spark, source_path)  # type: ignore\n        return source_class.parse(data, gene_index, lift)  # type: ignore\n\n    def v2g(self: Intervals, variant_index: VariantIndex) -&gt; V2G:\n        \"\"\"Convert intervals into V2G by intersecting with a variant index.\n\n        Args:\n            variant_index (VariantIndex): Variant index dataset\n\n        Returns:\n            V2G: Variant-to-gene evidence dataset\n        \"\"\"\n        return V2G(\n            _df=(\n                self.df.alias(\"interval\")\n                .join(\n                    variant_index.df.selectExpr(\n                        \"chromosome as vi_chromosome\", \"variantId\", \"position\"\n                    ).alias(\"vi\"),\n                    on=[\n                        f.col(\"vi.vi_chromosome\") == f.col(\"interval.chromosome\"),\n                        f.col(\"vi.position\").between(\n                            f.col(\"interval.start\"), f.col(\"interval.end\")\n                        ),\n                    ],\n                    how=\"inner\",\n                )\n                .drop(\"start\", \"end\", \"vi_chromosome\", \"position\")\n            ),\n            _schema=V2G.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/dataset/intervals/#otg.dataset.intervals.Intervals.from_source","title":"<code>from_source(spark: SparkSession, source_name: str, source_path: str, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Collect interval data for a particular source.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>source_name</code> <code>str</code> <p>Name of the interval source</p> required <code>source_path</code> <code>str</code> <p>Path to the interval source file</p> required <code>gene_index</code> <code>GeneIndex</code> <p>Gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance to convert coordinats from hg37 to hg38</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Intervals dataset</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the source name is not recognised</p> Source code in <code>src/otg/dataset/intervals.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[Intervals],\n    spark: SparkSession,\n    source_name: str,\n    source_path: str,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Collect interval data for a particular source.\n\n    Args:\n        spark (SparkSession): Spark session\n        source_name (str): Name of the interval source\n        source_path (str): Path to the interval source file\n        gene_index (GeneIndex): Gene index\n        lift (LiftOverSpark): LiftOverSpark instance to convert coordinats from hg37 to hg38\n\n    Returns:\n        Intervals: Intervals dataset\n\n    Raises:\n        ValueError: If the source name is not recognised\n    \"\"\"\n    from otg.datasource.intervals.andersson import IntervalsAndersson\n    from otg.datasource.intervals.javierre import IntervalsJavierre\n    from otg.datasource.intervals.jung import IntervalsJung\n    from otg.datasource.intervals.thurman import IntervalsThurman\n\n    source_to_class = {\n        \"andersson\": IntervalsAndersson,\n        \"javierre\": IntervalsJavierre,\n        \"jung\": IntervalsJung,\n        \"thurman\": IntervalsThurman,\n    }\n\n    if source_name not in source_to_class:\n        raise ValueError(f\"Unknown interval source: {source_name}\")\n\n    source_class = source_to_class[source_name]\n    data = source_class.read(spark, source_path)  # type: ignore\n    return source_class.parse(data, gene_index, lift)  # type: ignore\n</code></pre>"},{"location":"python_api/dataset/intervals/#otg.dataset.intervals.Intervals.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the Intervals dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the Intervals dataset</p> Source code in <code>src/otg/dataset/intervals.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[Intervals]) -&gt; StructType:\n    \"\"\"Provides the schema for the Intervals dataset.\n\n    Returns:\n        StructType: Schema for the Intervals dataset\n    \"\"\"\n    return parse_spark_schema(\"intervals.json\")\n</code></pre>"},{"location":"python_api/dataset/intervals/#otg.dataset.intervals.Intervals.v2g","title":"<code>v2g(variant_index: VariantIndex) -&gt; V2G</code>","text":"<p>Convert intervals into V2G by intersecting with a variant index.</p> <p>Parameters:</p> Name Type Description Default <code>variant_index</code> <code>VariantIndex</code> <p>Variant index dataset</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>Variant-to-gene evidence dataset</p> Source code in <code>src/otg/dataset/intervals.py</code> <pre><code>def v2g(self: Intervals, variant_index: VariantIndex) -&gt; V2G:\n    \"\"\"Convert intervals into V2G by intersecting with a variant index.\n\n    Args:\n        variant_index (VariantIndex): Variant index dataset\n\n    Returns:\n        V2G: Variant-to-gene evidence dataset\n    \"\"\"\n    return V2G(\n        _df=(\n            self.df.alias(\"interval\")\n            .join(\n                variant_index.df.selectExpr(\n                    \"chromosome as vi_chromosome\", \"variantId\", \"position\"\n                ).alias(\"vi\"),\n                on=[\n                    f.col(\"vi.vi_chromosome\") == f.col(\"interval.chromosome\"),\n                    f.col(\"vi.position\").between(\n                        f.col(\"interval.start\"), f.col(\"interval.end\")\n                    ),\n                ],\n                how=\"inner\",\n            )\n            .drop(\"start\", \"end\", \"vi_chromosome\", \"position\")\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/dataset/intervals/#schema","title":"Schema","text":"<pre><code>root\n |-- chromosome: string (nullable = false)\n |-- start: string (nullable = false)\n |-- end: string (nullable = false)\n |-- geneId: string (nullable = false)\n |-- resourceScore: double (nullable = true)\n |-- score: double (nullable = true)\n |-- datasourceId: string (nullable = false)\n |-- datatypeId: string (nullable = false)\n |-- pmid: string (nullable = true)\n |-- biofeature: string (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/l2g_feature/","title":"L2G Feature","text":""},{"location":"python_api/dataset/l2g_feature/#otg.method.l2g.feature_factory.L2GFeature","title":"<code>otg.method.l2g.feature_factory.L2GFeature</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Locus-to-gene feature dataset.</p> Source code in <code>src/otg/dataset/l2g_feature.py</code> <pre><code>@dataclass\nclass L2GFeature(Dataset):\n    \"\"\"Locus-to-gene feature dataset.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[L2GFeature]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2GFeature dataset.\n\n        Returns:\n            StructType: Schema for the L2GFeature dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_feature.json\")\n</code></pre>"},{"location":"python_api/dataset/l2g_feature/#otg.method.l2g.feature_factory.L2GFeature.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2GFeature dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the L2GFeature dataset</p> Source code in <code>src/otg/dataset/l2g_feature.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GFeature]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2GFeature dataset.\n\n    Returns:\n        StructType: Schema for the L2GFeature dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_feature.json\")\n</code></pre>"},{"location":"python_api/dataset/l2g_feature/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- geneId: string (nullable = false)\n |-- featureName: string (nullable = false)\n |-- featureValue: float (nullable = false)\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/","title":"L2G Feature Matrix","text":""},{"location":"python_api/dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix","title":"<code>otg.dataset.l2g_feature_matrix.L2GFeatureMatrix</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset with features for Locus to Gene prediction.</p> <p>Attributes:</p> Name Type Description <code>features_list</code> <code>list[str] | None</code> <p>List of features to use. If None, all possible features are used.</p> Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code> <pre><code>@dataclass\nclass L2GFeatureMatrix(Dataset):\n    \"\"\"Dataset with features for Locus to Gene prediction.\n\n    Attributes:\n        features_list (list[str] | None): List of features to use. If None, all possible features are used.\n    \"\"\"\n\n    features_list: list[str] | None = None\n\n    def __post_init__(self: L2GFeatureMatrix) -&gt; None:\n        \"\"\"Post-initialisation to set the features list. If not provided, all columns except the fixed ones are used.\"\"\"\n        fixed_cols = [\"studyLocusId\", \"geneId\", \"goldStandardSet\"]\n        self.features_list = self.features_list or [\n            col for col in self._df.columns if col not in fixed_cols\n        ]\n\n    @classmethod\n    def generate_features(\n        cls: Type[L2GFeatureMatrix],\n        features_list: list[str],\n        study_locus: StudyLocus,\n        study_index: StudyIndex,\n        variant_gene: V2G,\n        # colocalisation: Colocalisation,\n    ) -&gt; L2GFeatureMatrix:\n        \"\"\"Generate features from the OTG datasets.\n\n        Args:\n            features_list (list[str]): List of features to generate\n            study_locus (StudyLocus): Study locus dataset\n            study_index (StudyIndex): Study index dataset\n            variant_gene (V2G): Variant to gene dataset\n\n        Returns:\n            L2GFeatureMatrix: L2G feature matrix dataset\n\n        Raises:\n            ValueError: If the feature matrix is empty\n        \"\"\"\n        if features_dfs := [\n            # Extract features\n            # ColocalisationFactory._get_coloc_features(\n            #     study_locus, study_index, colocalisation\n            # ).df,\n            StudyLocusFactory._get_tss_distance_features(study_locus, variant_gene).df,\n        ]:\n            fm = reduce(\n                lambda x, y: x.unionByName(y),\n                features_dfs,\n            )\n        else:\n            raise ValueError(\"No features found\")\n\n        # raise error if the feature matrix is empty\n        if fm.limit(1).count() != 0:\n            return cls(\n                _df=convert_from_long_to_wide(\n                    fm, [\"studyLocusId\", \"geneId\"], \"featureName\", \"featureValue\"\n                ),\n                _schema=cls.get_schema(),\n                features_list=features_list,\n            )\n        raise ValueError(\"L2G Feature matrix is empty\")\n\n    @classmethod\n    def get_schema(cls: type[L2GFeatureMatrix]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2gFeatureMatrix dataset.\n\n        Returns:\n            StructType: Schema for the L2gFeatureMatrix dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_feature_matrix.json\")\n\n    def calculate_feature_missingness_rate(\n        self: L2GFeatureMatrix,\n    ) -&gt; dict[str, float]:\n        \"\"\"Calculate the proportion of missing values in each feature.\n\n        Returns:\n            dict[str, float]: Dictionary of feature names and their missingness rate.\n\n        Raises:\n            ValueError: If no features are found.\n        \"\"\"\n        total_count = self._df.count()\n        if not self.features_list:\n            raise ValueError(\"No features found\")\n\n        return {\n            feature: (self._df.filter(self._df[feature].isNull()).count() / total_count)\n            for feature in self.features_list\n        }\n\n    def fill_na(\n        self: L2GFeatureMatrix, value: float = 0.0, subset: list[str] | None = None\n    ) -&gt; L2GFeatureMatrix:\n        \"\"\"Fill missing values in a column with a given value.\n\n        Args:\n            value (float): Value to replace missing values with. Defaults to 0.0.\n            subset (list[str] | None): Subset of columns to consider. Defaults to None.\n\n        Returns:\n            L2GFeatureMatrix: L2G feature matrix dataset\n        \"\"\"\n        self.df = self._df.fillna(value, subset=subset)\n        return self\n\n    def select_features(\n        self: L2GFeatureMatrix, features_list: list[str] | None\n    ) -&gt; L2GFeatureMatrix:\n        \"\"\"Select a subset of features from the feature matrix.\n\n        Args:\n            features_list (list[str] | None): List of features to select\n\n        Returns:\n            L2GFeatureMatrix: L2G feature matrix dataset\n        \"\"\"\n        features_list = features_list or self.features_list\n        fixed_cols = [\"studyLocusId\", \"geneId\", \"goldStandardSet\"]\n        self.df = self._df.select(fixed_cols + features_list)  # type: ignore\n        return self\n\n    def train_test_split(\n        self: L2GFeatureMatrix, fraction: float\n    ) -&gt; tuple[L2GFeatureMatrix, L2GFeatureMatrix]:\n        \"\"\"Split the dataset into training and test sets.\n\n        Args:\n            fraction (float): Fraction of the dataset to use for training\n\n        Returns:\n            tuple[L2GFeatureMatrix, L2GFeatureMatrix]: Training and test datasets\n        \"\"\"\n        train, test = self._df.randomSplit([fraction, 1 - fraction], seed=42)\n        return (\n            L2GFeatureMatrix(\n                _df=train, _schema=L2GFeatureMatrix.get_schema()\n            ).persist(),\n            L2GFeatureMatrix(_df=test, _schema=L2GFeatureMatrix.get_schema()).persist(),\n        )\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate","title":"<code>calculate_feature_missingness_rate() -&gt; dict[str, float]</code>","text":"<p>Calculate the proportion of missing values in each feature.</p> <p>Returns:</p> Type Description <code>dict[str, float]</code> <p>dict[str, float]: Dictionary of feature names and their missingness rate.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If no features are found.</p> Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code> <pre><code>def calculate_feature_missingness_rate(\n    self: L2GFeatureMatrix,\n) -&gt; dict[str, float]:\n    \"\"\"Calculate the proportion of missing values in each feature.\n\n    Returns:\n        dict[str, float]: Dictionary of feature names and their missingness rate.\n\n    Raises:\n        ValueError: If no features are found.\n    \"\"\"\n    total_count = self._df.count()\n    if not self.features_list:\n        raise ValueError(\"No features found\")\n\n    return {\n        feature: (self._df.filter(self._df[feature].isNull()).count() / total_count)\n        for feature in self.features_list\n    }\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na","title":"<code>fill_na(value: float = 0.0, subset: list[str] | None = None) -&gt; L2GFeatureMatrix</code>","text":"<p>Fill missing values in a column with a given value.</p> <p>Parameters:</p> Name Type Description Default <code>value</code> <code>float</code> <p>Value to replace missing values with. Defaults to 0.0.</p> <code>0.0</code> <code>subset</code> <code>list[str] | None</code> <p>Subset of columns to consider. Defaults to None.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>L2GFeatureMatrix</code> <code>L2GFeatureMatrix</code> <p>L2G feature matrix dataset</p> Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code> <pre><code>def fill_na(\n    self: L2GFeatureMatrix, value: float = 0.0, subset: list[str] | None = None\n) -&gt; L2GFeatureMatrix:\n    \"\"\"Fill missing values in a column with a given value.\n\n    Args:\n        value (float): Value to replace missing values with. Defaults to 0.0.\n        subset (list[str] | None): Subset of columns to consider. Defaults to None.\n\n    Returns:\n        L2GFeatureMatrix: L2G feature matrix dataset\n    \"\"\"\n    self.df = self._df.fillna(value, subset=subset)\n    return self\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features","title":"<code>generate_features(features_list: list[str], study_locus: StudyLocus, study_index: StudyIndex, variant_gene: V2G) -&gt; L2GFeatureMatrix</code>  <code>classmethod</code>","text":"<p>Generate features from the OTG datasets.</p> <p>Parameters:</p> Name Type Description Default <code>features_list</code> <code>list[str]</code> <p>List of features to generate</p> required <code>study_locus</code> <code>StudyLocus</code> <p>Study locus dataset</p> required <code>study_index</code> <code>StudyIndex</code> <p>Study index dataset</p> required <code>variant_gene</code> <code>V2G</code> <p>Variant to gene dataset</p> required <p>Returns:</p> Name Type Description <code>L2GFeatureMatrix</code> <code>L2GFeatureMatrix</code> <p>L2G feature matrix dataset</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the feature matrix is empty</p> Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code> <pre><code>@classmethod\ndef generate_features(\n    cls: Type[L2GFeatureMatrix],\n    features_list: list[str],\n    study_locus: StudyLocus,\n    study_index: StudyIndex,\n    variant_gene: V2G,\n    # colocalisation: Colocalisation,\n) -&gt; L2GFeatureMatrix:\n    \"\"\"Generate features from the OTG datasets.\n\n    Args:\n        features_list (list[str]): List of features to generate\n        study_locus (StudyLocus): Study locus dataset\n        study_index (StudyIndex): Study index dataset\n        variant_gene (V2G): Variant to gene dataset\n\n    Returns:\n        L2GFeatureMatrix: L2G feature matrix dataset\n\n    Raises:\n        ValueError: If the feature matrix is empty\n    \"\"\"\n    if features_dfs := [\n        # Extract features\n        # ColocalisationFactory._get_coloc_features(\n        #     study_locus, study_index, colocalisation\n        # ).df,\n        StudyLocusFactory._get_tss_distance_features(study_locus, variant_gene).df,\n    ]:\n        fm = reduce(\n            lambda x, y: x.unionByName(y),\n            features_dfs,\n        )\n    else:\n        raise ValueError(\"No features found\")\n\n    # raise error if the feature matrix is empty\n    if fm.limit(1).count() != 0:\n        return cls(\n            _df=convert_from_long_to_wide(\n                fm, [\"studyLocusId\", \"geneId\"], \"featureName\", \"featureValue\"\n            ),\n            _schema=cls.get_schema(),\n            features_list=features_list,\n        )\n    raise ValueError(\"L2G Feature matrix is empty\")\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2gFeatureMatrix dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the L2gFeatureMatrix dataset</p> Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GFeatureMatrix]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2gFeatureMatrix dataset.\n\n    Returns:\n        StructType: Schema for the L2gFeatureMatrix dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_feature_matrix.json\")\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features","title":"<code>select_features(features_list: list[str] | None) -&gt; L2GFeatureMatrix</code>","text":"<p>Select a subset of features from the feature matrix.</p> <p>Parameters:</p> Name Type Description Default <code>features_list</code> <code>list[str] | None</code> <p>List of features to select</p> required <p>Returns:</p> Name Type Description <code>L2GFeatureMatrix</code> <code>L2GFeatureMatrix</code> <p>L2G feature matrix dataset</p> Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code> <pre><code>def select_features(\n    self: L2GFeatureMatrix, features_list: list[str] | None\n) -&gt; L2GFeatureMatrix:\n    \"\"\"Select a subset of features from the feature matrix.\n\n    Args:\n        features_list (list[str] | None): List of features to select\n\n    Returns:\n        L2GFeatureMatrix: L2G feature matrix dataset\n    \"\"\"\n    features_list = features_list or self.features_list\n    fixed_cols = [\"studyLocusId\", \"geneId\", \"goldStandardSet\"]\n    self.df = self._df.select(fixed_cols + features_list)  # type: ignore\n    return self\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/#otg.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split","title":"<code>train_test_split(fraction: float) -&gt; tuple[L2GFeatureMatrix, L2GFeatureMatrix]</code>","text":"<p>Split the dataset into training and test sets.</p> <p>Parameters:</p> Name Type Description Default <code>fraction</code> <code>float</code> <p>Fraction of the dataset to use for training</p> required <p>Returns:</p> Type Description <code>tuple[L2GFeatureMatrix, L2GFeatureMatrix]</code> <p>tuple[L2GFeatureMatrix, L2GFeatureMatrix]: Training and test datasets</p> Source code in <code>src/otg/dataset/l2g_feature_matrix.py</code> <pre><code>def train_test_split(\n    self: L2GFeatureMatrix, fraction: float\n) -&gt; tuple[L2GFeatureMatrix, L2GFeatureMatrix]:\n    \"\"\"Split the dataset into training and test sets.\n\n    Args:\n        fraction (float): Fraction of the dataset to use for training\n\n    Returns:\n        tuple[L2GFeatureMatrix, L2GFeatureMatrix]: Training and test datasets\n    \"\"\"\n    train, test = self._df.randomSplit([fraction, 1 - fraction], seed=42)\n    return (\n        L2GFeatureMatrix(\n            _df=train, _schema=L2GFeatureMatrix.get_schema()\n        ).persist(),\n        L2GFeatureMatrix(_df=test, _schema=L2GFeatureMatrix.get_schema()).persist(),\n    )\n</code></pre>"},{"location":"python_api/dataset/l2g_feature_matrix/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- geneId: string (nullable = false)\n |-- goldStandardSet: string (nullable = true)\n |-- distanceTssMean: float (nullable = true)\n |-- distanceTssMinimum: float (nullable = true)\n |-- eqtlColocClppLocalMaximum: double (nullable = true)\n |-- eqtlColocClppNeighborhoodMaximum: double (nullable = true)\n |-- eqtlColocLlrLocalMaximum: double (nullable = true)\n |-- eqtlColocLlrNeighborhoodMaximum: double (nullable = true)\n |-- pqtlColocClppLocalMaximum: double (nullable = true)\n |-- pqtlColocClppNeighborhoodMaximum: double (nullable = true)\n |-- pqtlColocLlrLocalMaximum: double (nullable = true)\n |-- pqtlColocLlrNeighborhoodMaximum: double (nullable = true)\n |-- sqtlColocClppLocalMaximum: double (nullable = true)\n |-- sqtlColocClppNeighborhoodMaximum: double (nullable = true)\n |-- sqtlColocLlrLocalMaximum: double (nullable = true)\n |-- sqtlColocLlrNeighborhoodMaximum: double (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/l2g_gold_standard/","title":"L2G Gold Standard","text":""},{"location":"python_api/dataset/l2g_gold_standard/#otg.dataset.l2g_gold_standard.L2GGoldStandard","title":"<code>otg.dataset.l2g_gold_standard.L2GGoldStandard</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>L2G gold standard dataset.</p> Source code in <code>src/otg/dataset/l2g_gold_standard.py</code> <pre><code>@dataclass\nclass L2GGoldStandard(Dataset):\n    \"\"\"L2G gold standard dataset.\"\"\"\n\n    INTERACTION_THRESHOLD = 0.7\n    GS_POSITIVE_LABEL = \"positive\"\n    GS_NEGATIVE_LABEL = \"negative\"\n\n    @classmethod\n    def from_otg_curation(\n        cls: type[L2GGoldStandard],\n        gold_standard_curation: DataFrame,\n        v2g: V2G,\n        study_locus_overlap: StudyLocusOverlap,\n        interactions: DataFrame,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Initialise L2GGoldStandard from source dataset.\n\n        Args:\n            gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from\n            v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n            study_locus_overlap (StudyLocusOverlap): Study locus overlap dataset to remove duplicated loci\n            interactions (DataFrame): Gene-gene interactions dataset to remove negative cases where the gene interacts with a positive gene\n\n        Returns:\n            L2GGoldStandard: L2G Gold Standard dataset\n        \"\"\"\n        from otg.datasource.open_targets.l2g_gold_standard import (\n            OpenTargetsL2GGoldStandard,\n        )\n\n        interactions_df = cls.process_gene_interactions(interactions)\n\n        return (\n            OpenTargetsL2GGoldStandard.as_l2g_gold_standard(gold_standard_curation, v2g)\n            # .filter_unique_associations(study_locus_overlap)\n            .remove_false_negatives(interactions_df)\n        )\n\n    @classmethod\n    def get_schema(cls: type[L2GGoldStandard]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2GGoldStandard dataset.\n\n        Returns:\n            StructType: Spark schema for the L2GGoldStandard dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_gold_standard.json\")\n\n    @classmethod\n    def process_gene_interactions(\n        cls: Type[L2GGoldStandard], interactions: DataFrame\n    ) -&gt; DataFrame:\n        \"\"\"Extract top scoring gene-gene interaction from the interactions dataset of the Platform.\n\n        Args:\n            interactions (DataFrame): Gene-gene interactions dataset from the Open Targets Platform\n\n        Returns:\n            DataFrame: Top scoring gene-gene interaction per pair of genes\n\n        Examples:\n            &gt;&gt;&gt; interactions = spark.createDataFrame([(\"gene1\", \"gene2\", 0.8), (\"gene1\", \"gene2\", 0.5), (\"gene2\", \"gene3\", 0.7)], [\"targetA\", \"targetB\", \"scoring\"])\n            &gt;&gt;&gt; L2GGoldStandard.process_gene_interactions(interactions).show()\n            +-------+-------+-----+\n            |geneIdA|geneIdB|score|\n            +-------+-------+-----+\n            |  gene1|  gene2|  0.8|\n            |  gene2|  gene3|  0.7|\n            +-------+-------+-----+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        return get_record_with_maximum_value(\n            interactions,\n            [\"targetA\", \"targetB\"],\n            \"scoring\",\n        ).selectExpr(\n            \"targetA as geneIdA\",\n            \"targetB as geneIdB\",\n            \"scoring as score\",\n        )\n\n    def filter_unique_associations(\n        self: L2GGoldStandard,\n        study_locus_overlap: StudyLocusOverlap,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Refines the gold standard to filter out loci that are not independent.\n\n        Rules:\n        - If two loci point to the same gene, one positive and one negative, and have overlapping variants, we keep the positive one.\n        - If two loci point to the same gene, both positive or negative, and have overlapping variants, we drop one.\n        - If two loci point to different genes, and have overlapping variants, we keep both.\n\n        Args:\n            study_locus_overlap (StudyLocusOverlap): A dataset detailing variants that overlap between StudyLocus.\n\n        Returns:\n            L2GGoldStandard: L2GGoldStandard updated to exclude false negatives and redundant positives.\n        \"\"\"\n        squared_overlaps = study_locus_overlap._convert_to_square_matrix()\n        unique_associations = (\n            self.df.alias(\"left\")\n            # identify all the study loci that point to the same gene\n            .withColumn(\n                \"sl_same_gene\",\n                f.collect_set(\"studyLocusId\").over(Window.partitionBy(\"geneId\")),\n            )\n            # identify all the study loci that have an overlapping variant\n            .join(\n                squared_overlaps.df.alias(\"right\"),\n                (f.col(\"left.studyLocusId\") == f.col(\"right.leftStudyLocusId\"))\n                &amp; (f.col(\"left.variantId\") == f.col(\"right.tagVariantId\")),\n                \"left\",\n            )\n            .withColumn(\n                \"overlaps\",\n                f.when(f.col(\"right.tagVariantId\").isNotNull(), f.lit(True)).otherwise(\n                    f.lit(False)\n                ),\n            )\n            # drop redundant rows: where the variantid overlaps and the gene is \"explained\" by more than one study locus\n            .filter(~((f.size(\"sl_same_gene\") &gt; 1) &amp; (f.col(\"overlaps\") == 1)))\n            .select(*self.df.columns)\n        )\n        return L2GGoldStandard(_df=unique_associations, _schema=self.get_schema())\n\n    def remove_false_negatives(\n        self: L2GGoldStandard,\n        interactions_df: DataFrame,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Refines the gold standard to remove negative gold standard instances where the gene interacts with a positive gene.\n\n        Args:\n            interactions_df (DataFrame): Top scoring gene-gene interaction per pair of genes\n\n        Returns:\n            L2GGoldStandard: A refined set of locus-to-gene associations with increased reliability, having excluded loci that were likely false negatives due to gene-gene interaction confounding.\n        \"\"\"\n        squared_interactions = interactions_df.unionByName(\n            interactions_df.selectExpr(\n                \"geneIdB as geneIdA\", \"geneIdA as geneIdB\", \"score\"\n            )\n        ).filter(f.col(\"score\") &gt; self.INTERACTION_THRESHOLD)\n        df = (\n            self.df.alias(\"left\")\n            .join(\n                # bring gene partners\n                squared_interactions.alias(\"right\"),\n                f.col(\"left.geneId\") == f.col(\"right.geneIdA\"),\n                \"left\",\n            )\n            .withColumnRenamed(\"geneIdB\", \"interactorGeneId\")\n            .join(\n                # bring gold standard status for gene partners\n                self.df.selectExpr(\n                    \"geneId as interactorGeneId\",\n                    \"goldStandardSet as interactorGeneIdGoldStandardSet\",\n                ),\n                \"interactorGeneId\",\n                \"left\",\n            )\n            # remove self-interactions\n            .filter(\n                (f.col(\"geneId\") != f.col(\"interactorGeneId\"))\n                | (f.col(\"interactorGeneId\").isNull())\n            )\n            # remove false negatives\n            .filter(\n                # drop rows where the GS gene is negative but the interactor is a GS positive\n                ~(f.col(\"goldStandardSet\") == \"negative\")\n                &amp; (f.col(\"interactorGeneIdGoldStandardSet\") == \"positive\")\n                |\n                # keep rows where the gene does not interact\n                (f.col(\"interactorGeneId\").isNull())\n            )\n            .select(*self.df.columns)\n            .distinct()\n        )\n        return L2GGoldStandard(_df=df, _schema=self.get_schema())\n</code></pre>"},{"location":"python_api/dataset/l2g_gold_standard/#otg.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations","title":"<code>filter_unique_associations(study_locus_overlap: StudyLocusOverlap) -&gt; L2GGoldStandard</code>","text":"<p>Refines the gold standard to filter out loci that are not independent.</p> <p>Rules: - If two loci point to the same gene, one positive and one negative, and have overlapping variants, we keep the positive one. - If two loci point to the same gene, both positive or negative, and have overlapping variants, we drop one. - If two loci point to different genes, and have overlapping variants, we keep both.</p> <p>Parameters:</p> Name Type Description Default <code>study_locus_overlap</code> <code>StudyLocusOverlap</code> <p>A dataset detailing variants that overlap between StudyLocus.</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>L2GGoldStandard updated to exclude false negatives and redundant positives.</p> Source code in <code>src/otg/dataset/l2g_gold_standard.py</code> <pre><code>def filter_unique_associations(\n    self: L2GGoldStandard,\n    study_locus_overlap: StudyLocusOverlap,\n) -&gt; L2GGoldStandard:\n    \"\"\"Refines the gold standard to filter out loci that are not independent.\n\n    Rules:\n    - If two loci point to the same gene, one positive and one negative, and have overlapping variants, we keep the positive one.\n    - If two loci point to the same gene, both positive or negative, and have overlapping variants, we drop one.\n    - If two loci point to different genes, and have overlapping variants, we keep both.\n\n    Args:\n        study_locus_overlap (StudyLocusOverlap): A dataset detailing variants that overlap between StudyLocus.\n\n    Returns:\n        L2GGoldStandard: L2GGoldStandard updated to exclude false negatives and redundant positives.\n    \"\"\"\n    squared_overlaps = study_locus_overlap._convert_to_square_matrix()\n    unique_associations = (\n        self.df.alias(\"left\")\n        # identify all the study loci that point to the same gene\n        .withColumn(\n            \"sl_same_gene\",\n            f.collect_set(\"studyLocusId\").over(Window.partitionBy(\"geneId\")),\n        )\n        # identify all the study loci that have an overlapping variant\n        .join(\n            squared_overlaps.df.alias(\"right\"),\n            (f.col(\"left.studyLocusId\") == f.col(\"right.leftStudyLocusId\"))\n            &amp; (f.col(\"left.variantId\") == f.col(\"right.tagVariantId\")),\n            \"left\",\n        )\n        .withColumn(\n            \"overlaps\",\n            f.when(f.col(\"right.tagVariantId\").isNotNull(), f.lit(True)).otherwise(\n                f.lit(False)\n            ),\n        )\n        # drop redundant rows: where the variantid overlaps and the gene is \"explained\" by more than one study locus\n        .filter(~((f.size(\"sl_same_gene\") &gt; 1) &amp; (f.col(\"overlaps\") == 1)))\n        .select(*self.df.columns)\n    )\n    return L2GGoldStandard(_df=unique_associations, _schema=self.get_schema())\n</code></pre>"},{"location":"python_api/dataset/l2g_gold_standard/#otg.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation","title":"<code>from_otg_curation(gold_standard_curation: DataFrame, v2g: V2G, study_locus_overlap: StudyLocusOverlap, interactions: DataFrame) -&gt; L2GGoldStandard</code>  <code>classmethod</code>","text":"<p>Initialise L2GGoldStandard from source dataset.</p> <p>Parameters:</p> Name Type Description Default <code>gold_standard_curation</code> <code>DataFrame</code> <p>Gold standard curation dataframe, extracted from</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset to bring distance between a variant and a gene's TSS</p> required <code>study_locus_overlap</code> <code>StudyLocusOverlap</code> <p>Study locus overlap dataset to remove duplicated loci</p> required <code>interactions</code> <code>DataFrame</code> <p>Gene-gene interactions dataset to remove negative cases where the gene interacts with a positive gene</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>L2G Gold Standard dataset</p> Source code in <code>src/otg/dataset/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef from_otg_curation(\n    cls: type[L2GGoldStandard],\n    gold_standard_curation: DataFrame,\n    v2g: V2G,\n    study_locus_overlap: StudyLocusOverlap,\n    interactions: DataFrame,\n) -&gt; L2GGoldStandard:\n    \"\"\"Initialise L2GGoldStandard from source dataset.\n\n    Args:\n        gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from\n        v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n        study_locus_overlap (StudyLocusOverlap): Study locus overlap dataset to remove duplicated loci\n        interactions (DataFrame): Gene-gene interactions dataset to remove negative cases where the gene interacts with a positive gene\n\n    Returns:\n        L2GGoldStandard: L2G Gold Standard dataset\n    \"\"\"\n    from otg.datasource.open_targets.l2g_gold_standard import (\n        OpenTargetsL2GGoldStandard,\n    )\n\n    interactions_df = cls.process_gene_interactions(interactions)\n\n    return (\n        OpenTargetsL2GGoldStandard.as_l2g_gold_standard(gold_standard_curation, v2g)\n        # .filter_unique_associations(study_locus_overlap)\n        .remove_false_negatives(interactions_df)\n    )\n</code></pre>"},{"location":"python_api/dataset/l2g_gold_standard/#otg.dataset.l2g_gold_standard.L2GGoldStandard.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2GGoldStandard dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Spark schema for the L2GGoldStandard dataset</p> Source code in <code>src/otg/dataset/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GGoldStandard]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2GGoldStandard dataset.\n\n    Returns:\n        StructType: Spark schema for the L2GGoldStandard dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_gold_standard.json\")\n</code></pre>"},{"location":"python_api/dataset/l2g_gold_standard/#otg.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions","title":"<code>process_gene_interactions(interactions: DataFrame) -&gt; DataFrame</code>  <code>classmethod</code>","text":"<p>Extract top scoring gene-gene interaction from the interactions dataset of the Platform.</p> <p>Parameters:</p> Name Type Description Default <code>interactions</code> <code>DataFrame</code> <p>Gene-gene interactions dataset from the Open Targets Platform</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Top scoring gene-gene interaction per pair of genes</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; interactions = spark.createDataFrame([(\"gene1\", \"gene2\", 0.8), (\"gene1\", \"gene2\", 0.5), (\"gene2\", \"gene3\", 0.7)], [\"targetA\", \"targetB\", \"scoring\"])\n&gt;&gt;&gt; L2GGoldStandard.process_gene_interactions(interactions).show()\n+-------+-------+-----+\n|geneIdA|geneIdB|score|\n+-------+-------+-----+\n|  gene1|  gene2|  0.8|\n|  gene2|  gene3|  0.7|\n+-------+-------+-----+\n</code></pre> Source code in <code>src/otg/dataset/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef process_gene_interactions(\n    cls: Type[L2GGoldStandard], interactions: DataFrame\n) -&gt; DataFrame:\n    \"\"\"Extract top scoring gene-gene interaction from the interactions dataset of the Platform.\n\n    Args:\n        interactions (DataFrame): Gene-gene interactions dataset from the Open Targets Platform\n\n    Returns:\n        DataFrame: Top scoring gene-gene interaction per pair of genes\n\n    Examples:\n        &gt;&gt;&gt; interactions = spark.createDataFrame([(\"gene1\", \"gene2\", 0.8), (\"gene1\", \"gene2\", 0.5), (\"gene2\", \"gene3\", 0.7)], [\"targetA\", \"targetB\", \"scoring\"])\n        &gt;&gt;&gt; L2GGoldStandard.process_gene_interactions(interactions).show()\n        +-------+-------+-----+\n        |geneIdA|geneIdB|score|\n        +-------+-------+-----+\n        |  gene1|  gene2|  0.8|\n        |  gene2|  gene3|  0.7|\n        +-------+-------+-----+\n        &lt;BLANKLINE&gt;\n    \"\"\"\n    return get_record_with_maximum_value(\n        interactions,\n        [\"targetA\", \"targetB\"],\n        \"scoring\",\n    ).selectExpr(\n        \"targetA as geneIdA\",\n        \"targetB as geneIdB\",\n        \"scoring as score\",\n    )\n</code></pre>"},{"location":"python_api/dataset/l2g_gold_standard/#otg.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives","title":"<code>remove_false_negatives(interactions_df: DataFrame) -&gt; L2GGoldStandard</code>","text":"<p>Refines the gold standard to remove negative gold standard instances where the gene interacts with a positive gene.</p> <p>Parameters:</p> Name Type Description Default <code>interactions_df</code> <code>DataFrame</code> <p>Top scoring gene-gene interaction per pair of genes</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>A refined set of locus-to-gene associations with increased reliability, having excluded loci that were likely false negatives due to gene-gene interaction confounding.</p> Source code in <code>src/otg/dataset/l2g_gold_standard.py</code> <pre><code>def remove_false_negatives(\n    self: L2GGoldStandard,\n    interactions_df: DataFrame,\n) -&gt; L2GGoldStandard:\n    \"\"\"Refines the gold standard to remove negative gold standard instances where the gene interacts with a positive gene.\n\n    Args:\n        interactions_df (DataFrame): Top scoring gene-gene interaction per pair of genes\n\n    Returns:\n        L2GGoldStandard: A refined set of locus-to-gene associations with increased reliability, having excluded loci that were likely false negatives due to gene-gene interaction confounding.\n    \"\"\"\n    squared_interactions = interactions_df.unionByName(\n        interactions_df.selectExpr(\n            \"geneIdB as geneIdA\", \"geneIdA as geneIdB\", \"score\"\n        )\n    ).filter(f.col(\"score\") &gt; self.INTERACTION_THRESHOLD)\n    df = (\n        self.df.alias(\"left\")\n        .join(\n            # bring gene partners\n            squared_interactions.alias(\"right\"),\n            f.col(\"left.geneId\") == f.col(\"right.geneIdA\"),\n            \"left\",\n        )\n        .withColumnRenamed(\"geneIdB\", \"interactorGeneId\")\n        .join(\n            # bring gold standard status for gene partners\n            self.df.selectExpr(\n                \"geneId as interactorGeneId\",\n                \"goldStandardSet as interactorGeneIdGoldStandardSet\",\n            ),\n            \"interactorGeneId\",\n            \"left\",\n        )\n        # remove self-interactions\n        .filter(\n            (f.col(\"geneId\") != f.col(\"interactorGeneId\"))\n            | (f.col(\"interactorGeneId\").isNull())\n        )\n        # remove false negatives\n        .filter(\n            # drop rows where the GS gene is negative but the interactor is a GS positive\n            ~(f.col(\"goldStandardSet\") == \"negative\")\n            &amp; (f.col(\"interactorGeneIdGoldStandardSet\") == \"positive\")\n            |\n            # keep rows where the gene does not interact\n            (f.col(\"interactorGeneId\").isNull())\n        )\n        .select(*self.df.columns)\n        .distinct()\n    )\n    return L2GGoldStandard(_df=df, _schema=self.get_schema())\n</code></pre>"},{"location":"python_api/dataset/l2g_gold_standard/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- variantId: string (nullable = false)\n |-- studyId: string (nullable = false)\n |-- geneId: string (nullable = false)\n |-- goldStandardSet: string (nullable = false)\n |-- sources: array (nullable = true)\n |    |-- element: string (containsNull = true)\n</code></pre>"},{"location":"python_api/dataset/l2g_prediction/","title":"L2G Prediction","text":""},{"location":"python_api/dataset/l2g_prediction/#otg.dataset.l2g_prediction.L2GPrediction","title":"<code>otg.dataset.l2g_prediction.L2GPrediction</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset that contains the Locus to Gene predictions.</p> <p>It is the result of applying the L2G model on a feature matrix, which contains all the study/locus pairs and their functional annotations. The score column informs the confidence of the prediction that a gene is causal to an association.</p> Source code in <code>src/otg/dataset/l2g_prediction.py</code> <pre><code>@dataclass\nclass L2GPrediction(Dataset):\n    \"\"\"Dataset that contains the Locus to Gene predictions.\n\n    It is the result of applying the L2G model on a feature matrix, which contains all\n    the study/locus pairs and their functional annotations. The score column informs the\n    confidence of the prediction that a gene is causal to an association.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[L2GPrediction]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2GPrediction dataset.\n\n        Returns:\n            StructType: Schema for the L2GPrediction dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_predictions.json\")\n\n    @classmethod\n    def from_credible_set(\n        cls: Type[L2GPrediction],\n        model_path: str,\n        features_list: list[str],\n        study_locus: StudyLocus,\n        study_index: StudyIndex,\n        v2g: V2G,\n        # coloc: Colocalisation,\n    ) -&gt; L2GPrediction:\n        \"\"\"Initialise L2G from feature matrix.\n\n        Args:\n            model_path (str): Path to the fitted model\n            features_list (list[str]): List of features to use for the model\n            study_locus (StudyLocus): Study locus dataset\n            study_index (StudyIndex): Study index dataset\n            v2g (V2G): Variant to gene dataset\n\n        Returns:\n            L2GPrediction: L2G dataset\n        \"\"\"\n        fm = L2GFeatureMatrix.generate_features(\n            features_list=features_list,\n            study_locus=study_locus,\n            study_index=study_index,\n            variant_gene=v2g,\n            # colocalisation=coloc,\n        ).fill_na()\n        return L2GPrediction(\n            # Load and apply fitted model\n            _df=(\n                LocusToGeneModel.load_from_disk(\n                    model_path,\n                    features_list=features_list,\n                )\n                .predict(fm)\n                # the probability of the positive class is the second element inside the probability array\n                # - this is selected as the L2G probability\n                .select(\n                    \"studyLocusId\",\n                    \"geneId\",\n                    vector_to_array(f.col(\"probability\"))[1].alias(\"score\"),\n                )\n            ),\n            _schema=cls.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/dataset/l2g_prediction/#otg.dataset.l2g_prediction.L2GPrediction.from_credible_set","title":"<code>from_credible_set(model_path: str, features_list: list[str], study_locus: StudyLocus, study_index: StudyIndex, v2g: V2G) -&gt; L2GPrediction</code>  <code>classmethod</code>","text":"<p>Initialise L2G from feature matrix.</p> <p>Parameters:</p> Name Type Description Default <code>model_path</code> <code>str</code> <p>Path to the fitted model</p> required <code>features_list</code> <code>list[str]</code> <p>List of features to use for the model</p> required <code>study_locus</code> <code>StudyLocus</code> <p>Study locus dataset</p> required <code>study_index</code> <code>StudyIndex</code> <p>Study index dataset</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset</p> required <p>Returns:</p> Name Type Description <code>L2GPrediction</code> <code>L2GPrediction</code> <p>L2G dataset</p> Source code in <code>src/otg/dataset/l2g_prediction.py</code> <pre><code>@classmethod\ndef from_credible_set(\n    cls: Type[L2GPrediction],\n    model_path: str,\n    features_list: list[str],\n    study_locus: StudyLocus,\n    study_index: StudyIndex,\n    v2g: V2G,\n    # coloc: Colocalisation,\n) -&gt; L2GPrediction:\n    \"\"\"Initialise L2G from feature matrix.\n\n    Args:\n        model_path (str): Path to the fitted model\n        features_list (list[str]): List of features to use for the model\n        study_locus (StudyLocus): Study locus dataset\n        study_index (StudyIndex): Study index dataset\n        v2g (V2G): Variant to gene dataset\n\n    Returns:\n        L2GPrediction: L2G dataset\n    \"\"\"\n    fm = L2GFeatureMatrix.generate_features(\n        features_list=features_list,\n        study_locus=study_locus,\n        study_index=study_index,\n        variant_gene=v2g,\n        # colocalisation=coloc,\n    ).fill_na()\n    return L2GPrediction(\n        # Load and apply fitted model\n        _df=(\n            LocusToGeneModel.load_from_disk(\n                model_path,\n                features_list=features_list,\n            )\n            .predict(fm)\n            # the probability of the positive class is the second element inside the probability array\n            # - this is selected as the L2G probability\n            .select(\n                \"studyLocusId\",\n                \"geneId\",\n                vector_to_array(f.col(\"probability\"))[1].alias(\"score\"),\n            )\n        ),\n        _schema=cls.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/dataset/l2g_prediction/#otg.dataset.l2g_prediction.L2GPrediction.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2GPrediction dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the L2GPrediction dataset</p> Source code in <code>src/otg/dataset/l2g_prediction.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GPrediction]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2GPrediction dataset.\n\n    Returns:\n        StructType: Schema for the L2GPrediction dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_predictions.json\")\n</code></pre>"},{"location":"python_api/dataset/l2g_prediction/#schema","title":"Schema","text":""},{"location":"python_api/dataset/ld_index/","title":"LD Index","text":""},{"location":"python_api/dataset/ld_index/#otg.dataset.ld_index.LDIndex","title":"<code>otg.dataset.ld_index.LDIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset containing linkage desequilibrium information between variants.</p> Source code in <code>src/otg/dataset/ld_index.py</code> <pre><code>@dataclass\nclass LDIndex(Dataset):\n    \"\"\"Dataset containing linkage desequilibrium information between variants.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[LDIndex]) -&gt; StructType:\n        \"\"\"Provides the schema for the LDIndex dataset.\n\n        Returns:\n            StructType: Schema for the LDIndex dataset\n        \"\"\"\n        return parse_spark_schema(\"ld_index.json\")\n</code></pre>"},{"location":"python_api/dataset/ld_index/#otg.dataset.ld_index.LDIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the LDIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the LDIndex dataset</p> Source code in <code>src/otg/dataset/ld_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[LDIndex]) -&gt; StructType:\n    \"\"\"Provides the schema for the LDIndex dataset.\n\n    Returns:\n        StructType: Schema for the LDIndex dataset\n    \"\"\"\n    return parse_spark_schema(\"ld_index.json\")\n</code></pre>"},{"location":"python_api/dataset/ld_index/#schema","title":"Schema","text":"<pre><code>root\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- ldSet: array (nullable = false)\n |    |-- element: struct (containsNull = false)\n |    |    |-- tagVariantId: string (nullable = false)\n |    |    |-- rValues: array (nullable = false)\n |    |    |    |-- element: struct (containsNull = false)\n |    |    |    |    |-- population: string (nullable = false)\n |    |    |    |    |-- r: double (nullable = false)\n</code></pre>"},{"location":"python_api/dataset/study_index/","title":"Study Index","text":""},{"location":"python_api/dataset/study_index/#otg.dataset.study_index.StudyIndex","title":"<code>otg.dataset.study_index.StudyIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Study index dataset.</p> <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p> Source code in <code>src/otg/dataset/study_index.py</code> <pre><code>@dataclass\nclass StudyIndex(Dataset):\n    \"\"\"Study index dataset.\n\n    A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.\n    \"\"\"\n\n    @staticmethod\n    def _aggregate_samples_by_ancestry(merged: Column, ancestry: Column) -&gt; Column:\n        \"\"\"Aggregate sample counts by ancestry in a list of struct colmns.\n\n        Args:\n            merged (Column): A column representing merged data (list of structs).\n            ancestry (Column): The `ancestry` parameter is a column that represents the ancestry of each\n                sample. (a struct)\n\n        Returns:\n            Column: the modified \"merged\" column after aggregating the samples by ancestry.\n        \"\"\"\n        # Iterating over the list of ancestries and adding the sample size if label matches:\n        return f.transform(\n            merged,\n            lambda a: f.when(\n                a.ancestry == ancestry.ancestry,\n                f.struct(\n                    a.ancestry.alias(\"ancestry\"),\n                    (a.sampleSize + ancestry.sampleSize).alias(\"sampleSize\"),\n                ),\n            ).otherwise(a),\n        )\n\n    @staticmethod\n    def _map_ancestries_to_ld_population(gwas_ancestry_label: Column) -&gt; Column:\n        \"\"\"Normalise ancestry column from GWAS studies into reference LD panel based on a pre-defined map.\n\n        This function assumes all possible ancestry categories have a corresponding\n        LD panel in the LD index. It is very important to have the ancestry labels\n        moved to the LD panel map.\n\n        Args:\n            gwas_ancestry_label (Column): A struct column with ancestry label like Finnish,\n                European, African etc. and the corresponding sample size.\n\n        Returns:\n            Column: Struct column with the mapped LD population label and the sample size.\n        \"\"\"\n        # Loading ancestry label to LD population label:\n        json_dict = json.loads(\n            pkg_resources.read_text(\n                data, \"gwas_population_2_LD_panel_map.json\", encoding=\"utf-8\"\n            )\n        )\n        map_expr = f.create_map(*[f.lit(x) for x in chain(*json_dict.items())])\n\n        return f.struct(\n            map_expr[gwas_ancestry_label.ancestry].alias(\"ancestry\"),\n            gwas_ancestry_label.sampleSize.alias(\"sampleSize\"),\n        )\n\n    @classmethod\n    def get_schema(cls: type[StudyIndex]) -&gt; StructType:\n        \"\"\"Provide the schema for the StudyIndex dataset.\n\n        Returns:\n            StructType: The schema of the StudyIndex dataset.\n        \"\"\"\n        return parse_spark_schema(\"study_index.json\")\n\n    @classmethod\n    def aggregate_and_map_ancestries(\n        cls: type[StudyIndex], discovery_samples: Column\n    ) -&gt; Column:\n        \"\"\"Map ancestries to populations in the LD reference and calculate relative sample size.\n\n        Args:\n            discovery_samples (Column): A list of struct column. Has an `ancestry` column and a `sampleSize` columns\n\n        Returns:\n            Column: A list of struct with mapped LD population and their relative sample size.\n        \"\"\"\n        # Map ancestry categories to population labels of the LD index:\n        mapped_ancestries = f.transform(\n            discovery_samples, cls._map_ancestries_to_ld_population\n        )\n\n        # Aggregate sample sizes belonging to the same LD population:\n        aggregated_counts = f.aggregate(\n            mapped_ancestries,\n            f.array_distinct(\n                f.transform(\n                    mapped_ancestries,\n                    lambda x: f.struct(\n                        x.ancestry.alias(\"ancestry\"), f.lit(0.0).alias(\"sampleSize\")\n                    ),\n                )\n            ),\n            cls._aggregate_samples_by_ancestry,\n        )\n        # Getting total sample count:\n        total_sample_count = f.aggregate(\n            aggregated_counts, f.lit(0.0), lambda total, pop: total + pop.sampleSize\n        ).alias(\"sampleSize\")\n\n        # Calculating relative sample size for each LD population:\n        return f.transform(\n            aggregated_counts,\n            lambda ld_population: f.struct(\n                ld_population.ancestry.alias(\"ldPopulation\"),\n                (ld_population.sampleSize / total_sample_count).alias(\n                    \"relativeSampleSize\"\n                ),\n            ),\n        )\n\n    def study_type_lut(self: StudyIndex) -&gt; DataFrame:\n        \"\"\"Return a lookup table of study type.\n\n        Returns:\n            DataFrame: A dataframe containing `studyId` and `studyType` columns.\n        \"\"\"\n        return self.df.select(\"studyId\", \"studyType\")\n</code></pre>"},{"location":"python_api/dataset/study_index/#otg.dataset.study_index.StudyIndex.aggregate_and_map_ancestries","title":"<code>aggregate_and_map_ancestries(discovery_samples: Column) -&gt; Column</code>  <code>classmethod</code>","text":"<p>Map ancestries to populations in the LD reference and calculate relative sample size.</p> <p>Parameters:</p> Name Type Description Default <code>discovery_samples</code> <code>Column</code> <p>A list of struct column. Has an <code>ancestry</code> column and a <code>sampleSize</code> columns</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>A list of struct with mapped LD population and their relative sample size.</p> Source code in <code>src/otg/dataset/study_index.py</code> <pre><code>@classmethod\ndef aggregate_and_map_ancestries(\n    cls: type[StudyIndex], discovery_samples: Column\n) -&gt; Column:\n    \"\"\"Map ancestries to populations in the LD reference and calculate relative sample size.\n\n    Args:\n        discovery_samples (Column): A list of struct column. Has an `ancestry` column and a `sampleSize` columns\n\n    Returns:\n        Column: A list of struct with mapped LD population and their relative sample size.\n    \"\"\"\n    # Map ancestry categories to population labels of the LD index:\n    mapped_ancestries = f.transform(\n        discovery_samples, cls._map_ancestries_to_ld_population\n    )\n\n    # Aggregate sample sizes belonging to the same LD population:\n    aggregated_counts = f.aggregate(\n        mapped_ancestries,\n        f.array_distinct(\n            f.transform(\n                mapped_ancestries,\n                lambda x: f.struct(\n                    x.ancestry.alias(\"ancestry\"), f.lit(0.0).alias(\"sampleSize\")\n                ),\n            )\n        ),\n        cls._aggregate_samples_by_ancestry,\n    )\n    # Getting total sample count:\n    total_sample_count = f.aggregate(\n        aggregated_counts, f.lit(0.0), lambda total, pop: total + pop.sampleSize\n    ).alias(\"sampleSize\")\n\n    # Calculating relative sample size for each LD population:\n    return f.transform(\n        aggregated_counts,\n        lambda ld_population: f.struct(\n            ld_population.ancestry.alias(\"ldPopulation\"),\n            (ld_population.sampleSize / total_sample_count).alias(\n                \"relativeSampleSize\"\n            ),\n        ),\n    )\n</code></pre>"},{"location":"python_api/dataset/study_index/#otg.dataset.study_index.StudyIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provide the schema for the StudyIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>The schema of the StudyIndex dataset.</p> Source code in <code>src/otg/dataset/study_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[StudyIndex]) -&gt; StructType:\n    \"\"\"Provide the schema for the StudyIndex dataset.\n\n    Returns:\n        StructType: The schema of the StudyIndex dataset.\n    \"\"\"\n    return parse_spark_schema(\"study_index.json\")\n</code></pre>"},{"location":"python_api/dataset/study_index/#otg.dataset.study_index.StudyIndex.study_type_lut","title":"<code>study_type_lut() -&gt; DataFrame</code>","text":"<p>Return a lookup table of study type.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>A dataframe containing <code>studyId</code> and <code>studyType</code> columns.</p> Source code in <code>src/otg/dataset/study_index.py</code> <pre><code>def study_type_lut(self: StudyIndex) -&gt; DataFrame:\n    \"\"\"Return a lookup table of study type.\n\n    Returns:\n        DataFrame: A dataframe containing `studyId` and `studyType` columns.\n    \"\"\"\n    return self.df.select(\"studyId\", \"studyType\")\n</code></pre>"},{"location":"python_api/dataset/study_index/#schema","title":"Schema","text":"<pre><code>root\n |-- studyId: string (nullable = false)\n |-- projectId: string (nullable = false)\n |-- studyType: string (nullable = false)\n |-- traitFromSource: string (nullable = false)\n |-- traitFromSourceMappedIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- geneId: string (nullable = true)\n |-- pubmedId: string (nullable = true)\n |-- publicationTitle: string (nullable = true)\n |-- publicationFirstAuthor: string (nullable = true)\n |-- publicationDate: string (nullable = true)\n |-- publicationJournal: string (nullable = true)\n |-- backgroundTraitFromSourceMappedIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- initialSampleSize: string (nullable = true)\n |-- nCases: long (nullable = true)\n |-- nControls: long (nullable = true)\n |-- nSamples: long (nullable = true)\n |-- cohorts: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- ldPopulationStructure: array (nullable = true)\n |    |-- element: struct (containsNull = false)\n |    |    |-- ldPopulation: string (nullable = true)\n |    |    |-- relativeSampleSize: double (nullable = true)\n |-- discoverySamples: array (nullable = true)\n |    |-- element: struct (containsNull = false)\n |    |    |-- sampleSize: long (nullable = true)\n |    |    |-- ancestry: string (nullable = true)\n |-- replicationSamples: array (nullable = true)\n |    |-- element: struct (containsNull = false)\n |    |    |-- sampleSize: long (nullable = true)\n |    |    |-- ancestry: string (nullable = true)\n |-- summarystatsLocation: string (nullable = true)\n |-- hasSumstats: boolean (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/study_locus/","title":"Study Locus","text":""},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus","title":"<code>otg.dataset.study_locus.StudyLocus</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Study-Locus dataset.</p> <p>This dataset captures associations between study/traits and a genetic loci as provided by finemapping methods.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>@dataclass\nclass StudyLocus(Dataset):\n    \"\"\"Study-Locus dataset.\n\n    This dataset captures associations between study/traits and a genetic loci as provided by finemapping methods.\n    \"\"\"\n\n    @staticmethod\n    def _overlapping_peaks(credset_to_overlap: DataFrame) -&gt; DataFrame:\n        \"\"\"Calculate overlapping signals (study-locus) between GWAS-GWAS and GWAS-Molecular trait.\n\n        Args:\n            credset_to_overlap (DataFrame): DataFrame containing at least `studyLocusId`, `studyType`, `chromosome` and `tagVariantId` columns.\n\n        Returns:\n            DataFrame: containing `leftStudyLocusId`, `rightStudyLocusId` and `chromosome` columns.\n        \"\"\"\n        # Reduce columns to the minimum to reduce the size of the dataframe\n        credset_to_overlap = credset_to_overlap.select(\n            \"studyLocusId\", \"studyType\", \"chromosome\", \"tagVariantId\"\n        )\n        return (\n            credset_to_overlap.alias(\"left\")\n            .filter(f.col(\"studyType\") == \"gwas\")\n            # Self join with complex condition. Left it's all gwas and right can be gwas or molecular trait\n            .join(\n                credset_to_overlap.alias(\"right\"),\n                on=[\n                    f.col(\"left.chromosome\") == f.col(\"right.chromosome\"),\n                    f.col(\"left.tagVariantId\") == f.col(\"right.tagVariantId\"),\n                    (f.col(\"right.studyType\") != \"gwas\")\n                    | (f.col(\"left.studyLocusId\") &gt; f.col(\"right.studyLocusId\")),\n                ],\n                how=\"inner\",\n            )\n            .select(\n                f.col(\"left.studyLocusId\").alias(\"leftStudyLocusId\"),\n                f.col(\"right.studyLocusId\").alias(\"rightStudyLocusId\"),\n                f.col(\"left.chromosome\").alias(\"chromosome\"),\n            )\n            .distinct()\n            .repartition(\"chromosome\")\n            .persist()\n        )\n\n    @staticmethod\n    def _align_overlapping_tags(\n        loci_to_overlap: DataFrame, peak_overlaps: DataFrame\n    ) -&gt; StudyLocusOverlap:\n        \"\"\"Align overlapping tags in pairs of overlapping study-locus, keeping all tags in both loci.\n\n        Args:\n            loci_to_overlap (DataFrame): containing `studyLocusId`, `studyType`, `chromosome`, `tagVariantId`, `logABF` and `posteriorProbability` columns.\n            peak_overlaps (DataFrame): containing `leftStudyLocusId`, `rightStudyLocusId` and `chromosome` columns.\n\n        Returns:\n            StudyLocusOverlap: Pairs of overlapping study-locus with aligned tags.\n        \"\"\"\n        # Complete information about all tags in the left study-locus of the overlap\n        stats_cols = [\n            \"logABF\",\n            \"posteriorProbability\",\n            \"beta\",\n            \"pValueMantissa\",\n            \"pValueExponent\",\n        ]\n        overlapping_left = loci_to_overlap.select(\n            f.col(\"chromosome\"),\n            f.col(\"tagVariantId\"),\n            f.col(\"studyLocusId\").alias(\"leftStudyLocusId\"),\n            *[f.col(col).alias(f\"left_{col}\") for col in stats_cols],\n        ).join(peak_overlaps, on=[\"chromosome\", \"leftStudyLocusId\"], how=\"inner\")\n\n        # Complete information about all tags in the right study-locus of the overlap\n        overlapping_right = loci_to_overlap.select(\n            f.col(\"chromosome\"),\n            f.col(\"tagVariantId\"),\n            f.col(\"studyLocusId\").alias(\"rightStudyLocusId\"),\n            *[f.col(col).alias(f\"right_{col}\") for col in stats_cols],\n        ).join(peak_overlaps, on=[\"chromosome\", \"rightStudyLocusId\"], how=\"inner\")\n\n        # Include information about all tag variants in both study-locus aligned by tag variant id\n        overlaps = overlapping_left.join(\n            overlapping_right,\n            on=[\n                \"chromosome\",\n                \"rightStudyLocusId\",\n                \"leftStudyLocusId\",\n                \"tagVariantId\",\n            ],\n            how=\"outer\",\n        ).select(\n            \"leftStudyLocusId\",\n            \"rightStudyLocusId\",\n            \"chromosome\",\n            \"tagVariantId\",\n            f.struct(\n                *[f\"left_{e}\" for e in stats_cols] + [f\"right_{e}\" for e in stats_cols]\n            ).alias(\"statistics\"),\n        )\n        return StudyLocusOverlap(\n            _df=overlaps,\n            _schema=StudyLocusOverlap.get_schema(),\n        )\n\n    @staticmethod\n    def update_quality_flag(\n        qc: Column, flag_condition: Column, flag_text: StudyLocusQualityCheck\n    ) -&gt; Column:\n        \"\"\"Update the provided quality control list with a new flag if condition is met.\n\n        Args:\n            qc (Column): Array column with the current list of qc flags.\n            flag_condition (Column): This is a column of booleans, signing which row should be flagged\n            flag_text (StudyLocusQualityCheck): Text for the new quality control flag\n\n        Returns:\n            Column: Array column with the updated list of qc flags.\n        \"\"\"\n        qc = f.when(qc.isNull(), f.array()).otherwise(qc)\n        return f.when(\n            flag_condition,\n            f.array_union(qc, f.array(f.lit(flag_text.value))),\n        ).otherwise(qc)\n\n    @staticmethod\n    def assign_study_locus_id(study_id_col: Column, variant_id_col: Column) -&gt; Column:\n        \"\"\"Hashes a column with a variant ID and a study ID to extract a consistent studyLocusId.\n\n        Args:\n            study_id_col (Column): column name with a study ID\n            variant_id_col (Column): column name with a variant ID\n\n        Returns:\n            Column: column with a study locus ID\n\n        Examples:\n            &gt;&gt;&gt; df = spark.createDataFrame([(\"GCST000001\", \"1_1000_A_C\"), (\"GCST000002\", \"1_1000_A_C\")]).toDF(\"studyId\", \"variantId\")\n            &gt;&gt;&gt; df.withColumn(\"study_locus_id\", StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\"))).show()\n            +----------+----------+-------------------+\n            |   studyId| variantId|     study_locus_id|\n            +----------+----------+-------------------+\n            |GCST000001|1_1000_A_C|1553357789130151995|\n            |GCST000002|1_1000_A_C|-415050894682709184|\n            +----------+----------+-------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        variant_id_col = f.coalesce(variant_id_col, f.rand().cast(\"string\"))\n        return f.xxhash64(study_id_col, variant_id_col).alias(\"studyLocusId\")\n\n    @classmethod\n    def get_schema(cls: type[StudyLocus]) -&gt; StructType:\n        \"\"\"Provides the schema for the StudyLocus dataset.\n\n        Returns:\n            StructType: schema for the StudyLocus dataset.\n        \"\"\"\n        return parse_spark_schema(\"study_locus.json\")\n\n    def filter_credible_set(\n        self: StudyLocus,\n        credible_interval: CredibleInterval,\n    ) -&gt; StudyLocus:\n        \"\"\"Filter study-locus tag variants based on given credible interval.\n\n        Args:\n            credible_interval (CredibleInterval): Credible interval to filter for.\n\n        Returns:\n            StudyLocus: Filtered study-locus dataset.\n        \"\"\"\n        self.df = self._df.withColumn(\n            \"locus\",\n            f.filter(\n                f.col(\"locus\"),\n                lambda tag: (tag[credible_interval.value]),\n            ),\n        )\n        return self\n\n    def find_overlaps(self: StudyLocus, study_index: StudyIndex) -&gt; StudyLocusOverlap:\n        \"\"\"Calculate overlapping study-locus.\n\n        Find overlapping study-locus that share at least one tagging variant. All GWAS-GWAS and all GWAS-Molecular traits are computed with the Molecular traits always\n        appearing on the right side.\n\n        Args:\n            study_index (StudyIndex): Study index to resolve study types.\n\n        Returns:\n            StudyLocusOverlap: Pairs of overlapping study-locus with aligned tags.\n        \"\"\"\n        loci_to_overlap = (\n            self.df.join(study_index.study_type_lut(), on=\"studyId\", how=\"inner\")\n            .withColumn(\"locus\", f.explode(\"locus\"))\n            .select(\n                \"studyLocusId\",\n                \"studyType\",\n                \"chromosome\",\n                f.col(\"locus.variantId\").alias(\"tagVariantId\"),\n                f.col(\"locus.logABF\").alias(\"logABF\"),\n                f.col(\"locus.posteriorProbability\").alias(\"posteriorProbability\"),\n                f.col(\"locus.pValueMantissa\").alias(\"pValueMantissa\"),\n                f.col(\"locus.pValueExponent\").alias(\"pValueExponent\"),\n                f.col(\"locus.beta\").alias(\"beta\"),\n            )\n            .persist()\n        )\n\n        # overlapping study-locus\n        peak_overlaps = self._overlapping_peaks(loci_to_overlap)\n\n        # study-locus overlap by aligning overlapping variants\n        return self._align_overlapping_tags(loci_to_overlap, peak_overlaps)\n\n    def unique_variants_in_locus(self: StudyLocus) -&gt; DataFrame:\n        \"\"\"All unique variants collected in a `StudyLocus` dataframe.\n\n        Returns:\n            DataFrame: A dataframe containing `variantId` and `chromosome` columns.\n        \"\"\"\n        return (\n            self.df.withColumn(\n                \"variantId\",\n                # Joint array of variants in that studylocus. Locus can be null\n                f.explode(\n                    f.array_union(\n                        f.array(f.col(\"variantId\")),\n                        f.coalesce(f.col(\"locus.variantId\"), f.array()),\n                    )\n                ),\n            )\n            .select(\n                \"variantId\", f.split(f.col(\"variantId\"), \"_\")[0].alias(\"chromosome\")\n            )\n            .distinct()\n        )\n\n    def neglog_pvalue(self: StudyLocus) -&gt; Column:\n        \"\"\"Returns the negative log p-value.\n\n        Returns:\n            Column: Negative log p-value\n        \"\"\"\n        return calculate_neglog_pvalue(\n            self.df.pValueMantissa,\n            self.df.pValueExponent,\n        )\n\n    def annotate_credible_sets(self: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Annotate study-locus dataset with credible set flags.\n\n        Sorts the array in the `locus` column elements by their `posteriorProbability` values in descending order and adds\n        `is95CredibleSet` and `is99CredibleSet` fields to the elements, indicating which are the tagging variants whose cumulative sum\n        of their `posteriorProbability` values is below 0.95 and 0.99, respectively.\n\n        Returns:\n            StudyLocus: including annotation on `is95CredibleSet` and `is99CredibleSet`.\n\n        Raises:\n            ValueError: If `locus` column is not available.\n        \"\"\"\n        if \"locus\" not in self.df.columns:\n            raise ValueError(\"Locus column not available.\")\n\n        self.df = self.df.withColumn(\n            # Sort credible set by posterior probability in descending order\n            \"locus\",\n            f.when(\n                f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n                order_array_of_structs_by_field(\"locus\", \"posteriorProbability\"),\n            ),\n        ).withColumn(\n            # Calculate array of cumulative sums of posterior probabilities to determine which variants are in the 95% and 99% credible sets\n            # and zip the cumulative sums array with the credible set array to add the flags\n            \"locus\",\n            f.when(\n                f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n                f.zip_with(\n                    f.col(\"locus\"),\n                    f.transform(\n                        f.sequence(f.lit(1), f.size(f.col(\"locus\"))),\n                        lambda index: f.aggregate(\n                            f.slice(\n                                # By using `index - 1` we introduce a value of `0.0` in the cumulative sums array. to ensure that the last variant\n                                # that exceeds the 0.95 threshold is included in the cumulative sum, as its probability is necessary to satisfy the threshold.\n                                f.col(\"locus.posteriorProbability\"),\n                                1,\n                                index - 1,\n                            ),\n                            f.lit(0.0),\n                            lambda acc, el: acc + el,\n                        ),\n                    ),\n                    lambda struct_e, acc: struct_e.withField(\n                        CredibleInterval.IS95.value, (acc &lt; 0.95) &amp; acc.isNotNull()\n                    ).withField(\n                        CredibleInterval.IS99.value, (acc &lt; 0.99) &amp; acc.isNotNull()\n                    ),\n                ),\n            ),\n        )\n        return self\n\n    def annotate_ld(\n        self: StudyLocus, study_index: StudyIndex, ld_index: LDIndex\n    ) -&gt; StudyLocus:\n        \"\"\"Annotate LD information to study-locus.\n\n        Args:\n            study_index (StudyIndex): Study index to resolve ancestries.\n            ld_index (LDIndex): LD index to resolve LD information.\n\n        Returns:\n            StudyLocus: Study locus annotated with ld information from LD index.\n        \"\"\"\n        from otg.method.ld import LDAnnotator\n\n        return LDAnnotator.ld_annotate(self, study_index, ld_index)\n\n    def clump(self: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Perform LD clumping of the studyLocus.\n\n        Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.\n\n        Returns:\n            StudyLocus: with empty credible sets for linked variants and QC flag.\n        \"\"\"\n        self.df = (\n            self.df.withColumn(\n                \"is_lead_linked\",\n                LDclumping._is_lead_linked(\n                    self.df.studyId,\n                    self.df.variantId,\n                    self.df.pValueExponent,\n                    self.df.pValueMantissa,\n                    self.df.ldSet,\n                ),\n            )\n            .withColumn(\n                \"ldSet\",\n                f.when(f.col(\"is_lead_linked\"), f.array()).otherwise(f.col(\"ldSet\")),\n            )\n            .withColumn(\n                \"qualityControls\",\n                StudyLocus.update_quality_flag(\n                    f.col(\"qualityControls\"),\n                    f.col(\"is_lead_linked\"),\n                    StudyLocusQualityCheck.LD_CLUMPED,\n                ),\n            )\n            .drop(\"is_lead_linked\")\n        )\n        return self\n\n    def _qc_unresolved_ld(\n        self: StudyLocus,\n    ) -&gt; StudyLocus:\n        \"\"\"Flag associations with variants that are not found in the LD reference.\n\n        Returns:\n            StudyLocus: Updated study locus.\n        \"\"\"\n        self.df = self.df.withColumn(\n            \"qualityControls\",\n            self.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.col(\"ldSet\").isNull(),\n                StudyLocusQualityCheck.UNRESOLVED_LD,\n            ),\n        )\n        return self\n\n    def _qc_no_population(self: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Flag associations where the study doesn't have population information to resolve LD.\n\n        Returns:\n            StudyLocus: Updated study locus.\n        \"\"\"\n        # If the tested column is not present, return self unchanged:\n        if \"ldPopulationStructure\" not in self.df.columns:\n            return self\n\n        self.df = self.df.withColumn(\n            \"qualityControls\",\n            self.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.col(\"ldPopulationStructure\").isNull(),\n                StudyLocusQualityCheck.NO_POPULATION,\n            ),\n        )\n        return self\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.annotate_credible_sets","title":"<code>annotate_credible_sets() -&gt; StudyLocus</code>","text":"<p>Annotate study-locus dataset with credible set flags.</p> <p>Sorts the array in the <code>locus</code> column elements by their <code>posteriorProbability</code> values in descending order and adds <code>is95CredibleSet</code> and <code>is99CredibleSet</code> fields to the elements, indicating which are the tagging variants whose cumulative sum of their <code>posteriorProbability</code> values is below 0.95 and 0.99, respectively.</p> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>including annotation on <code>is95CredibleSet</code> and <code>is99CredibleSet</code>.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If <code>locus</code> column is not available.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>def annotate_credible_sets(self: StudyLocus) -&gt; StudyLocus:\n    \"\"\"Annotate study-locus dataset with credible set flags.\n\n    Sorts the array in the `locus` column elements by their `posteriorProbability` values in descending order and adds\n    `is95CredibleSet` and `is99CredibleSet` fields to the elements, indicating which are the tagging variants whose cumulative sum\n    of their `posteriorProbability` values is below 0.95 and 0.99, respectively.\n\n    Returns:\n        StudyLocus: including annotation on `is95CredibleSet` and `is99CredibleSet`.\n\n    Raises:\n        ValueError: If `locus` column is not available.\n    \"\"\"\n    if \"locus\" not in self.df.columns:\n        raise ValueError(\"Locus column not available.\")\n\n    self.df = self.df.withColumn(\n        # Sort credible set by posterior probability in descending order\n        \"locus\",\n        f.when(\n            f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n            order_array_of_structs_by_field(\"locus\", \"posteriorProbability\"),\n        ),\n    ).withColumn(\n        # Calculate array of cumulative sums of posterior probabilities to determine which variants are in the 95% and 99% credible sets\n        # and zip the cumulative sums array with the credible set array to add the flags\n        \"locus\",\n        f.when(\n            f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n            f.zip_with(\n                f.col(\"locus\"),\n                f.transform(\n                    f.sequence(f.lit(1), f.size(f.col(\"locus\"))),\n                    lambda index: f.aggregate(\n                        f.slice(\n                            # By using `index - 1` we introduce a value of `0.0` in the cumulative sums array. to ensure that the last variant\n                            # that exceeds the 0.95 threshold is included in the cumulative sum, as its probability is necessary to satisfy the threshold.\n                            f.col(\"locus.posteriorProbability\"),\n                            1,\n                            index - 1,\n                        ),\n                        f.lit(0.0),\n                        lambda acc, el: acc + el,\n                    ),\n                ),\n                lambda struct_e, acc: struct_e.withField(\n                    CredibleInterval.IS95.value, (acc &lt; 0.95) &amp; acc.isNotNull()\n                ).withField(\n                    CredibleInterval.IS99.value, (acc &lt; 0.99) &amp; acc.isNotNull()\n                ),\n            ),\n        ),\n    )\n    return self\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.annotate_ld","title":"<code>annotate_ld(study_index: StudyIndex, ld_index: LDIndex) -&gt; StudyLocus</code>","text":"<p>Annotate LD information to study-locus.</p> <p>Parameters:</p> Name Type Description Default <code>study_index</code> <code>StudyIndex</code> <p>Study index to resolve ancestries.</p> required <code>ld_index</code> <code>LDIndex</code> <p>LD index to resolve LD information.</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Study locus annotated with ld information from LD index.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>def annotate_ld(\n    self: StudyLocus, study_index: StudyIndex, ld_index: LDIndex\n) -&gt; StudyLocus:\n    \"\"\"Annotate LD information to study-locus.\n\n    Args:\n        study_index (StudyIndex): Study index to resolve ancestries.\n        ld_index (LDIndex): LD index to resolve LD information.\n\n    Returns:\n        StudyLocus: Study locus annotated with ld information from LD index.\n    \"\"\"\n    from otg.method.ld import LDAnnotator\n\n    return LDAnnotator.ld_annotate(self, study_index, ld_index)\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.assign_study_locus_id","title":"<code>assign_study_locus_id(study_id_col: Column, variant_id_col: Column) -&gt; Column</code>  <code>staticmethod</code>","text":"<p>Hashes a column with a variant ID and a study ID to extract a consistent studyLocusId.</p> <p>Parameters:</p> Name Type Description Default <code>study_id_col</code> <code>Column</code> <p>column name with a study ID</p> required <code>variant_id_col</code> <code>Column</code> <p>column name with a variant ID</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>column with a study locus ID</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; df = spark.createDataFrame([(\"GCST000001\", \"1_1000_A_C\"), (\"GCST000002\", \"1_1000_A_C\")]).toDF(\"studyId\", \"variantId\")\n&gt;&gt;&gt; df.withColumn(\"study_locus_id\", StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\"))).show()\n+----------+----------+-------------------+\n|   studyId| variantId|     study_locus_id|\n+----------+----------+-------------------+\n|GCST000001|1_1000_A_C|1553357789130151995|\n|GCST000002|1_1000_A_C|-415050894682709184|\n+----------+----------+-------------------+\n</code></pre> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>@staticmethod\ndef assign_study_locus_id(study_id_col: Column, variant_id_col: Column) -&gt; Column:\n    \"\"\"Hashes a column with a variant ID and a study ID to extract a consistent studyLocusId.\n\n    Args:\n        study_id_col (Column): column name with a study ID\n        variant_id_col (Column): column name with a variant ID\n\n    Returns:\n        Column: column with a study locus ID\n\n    Examples:\n        &gt;&gt;&gt; df = spark.createDataFrame([(\"GCST000001\", \"1_1000_A_C\"), (\"GCST000002\", \"1_1000_A_C\")]).toDF(\"studyId\", \"variantId\")\n        &gt;&gt;&gt; df.withColumn(\"study_locus_id\", StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\"))).show()\n        +----------+----------+-------------------+\n        |   studyId| variantId|     study_locus_id|\n        +----------+----------+-------------------+\n        |GCST000001|1_1000_A_C|1553357789130151995|\n        |GCST000002|1_1000_A_C|-415050894682709184|\n        +----------+----------+-------------------+\n        &lt;BLANKLINE&gt;\n    \"\"\"\n    variant_id_col = f.coalesce(variant_id_col, f.rand().cast(\"string\"))\n    return f.xxhash64(study_id_col, variant_id_col).alias(\"studyLocusId\")\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.clump","title":"<code>clump() -&gt; StudyLocus</code>","text":"<p>Perform LD clumping of the studyLocus.</p> <p>Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.</p> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>with empty credible sets for linked variants and QC flag.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>def clump(self: StudyLocus) -&gt; StudyLocus:\n    \"\"\"Perform LD clumping of the studyLocus.\n\n    Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.\n\n    Returns:\n        StudyLocus: with empty credible sets for linked variants and QC flag.\n    \"\"\"\n    self.df = (\n        self.df.withColumn(\n            \"is_lead_linked\",\n            LDclumping._is_lead_linked(\n                self.df.studyId,\n                self.df.variantId,\n                self.df.pValueExponent,\n                self.df.pValueMantissa,\n                self.df.ldSet,\n            ),\n        )\n        .withColumn(\n            \"ldSet\",\n            f.when(f.col(\"is_lead_linked\"), f.array()).otherwise(f.col(\"ldSet\")),\n        )\n        .withColumn(\n            \"qualityControls\",\n            StudyLocus.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.col(\"is_lead_linked\"),\n                StudyLocusQualityCheck.LD_CLUMPED,\n            ),\n        )\n        .drop(\"is_lead_linked\")\n    )\n    return self\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.filter_credible_set","title":"<code>filter_credible_set(credible_interval: CredibleInterval) -&gt; StudyLocus</code>","text":"<p>Filter study-locus tag variants based on given credible interval.</p> <p>Parameters:</p> Name Type Description Default <code>credible_interval</code> <code>CredibleInterval</code> <p>Credible interval to filter for.</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Filtered study-locus dataset.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>def filter_credible_set(\n    self: StudyLocus,\n    credible_interval: CredibleInterval,\n) -&gt; StudyLocus:\n    \"\"\"Filter study-locus tag variants based on given credible interval.\n\n    Args:\n        credible_interval (CredibleInterval): Credible interval to filter for.\n\n    Returns:\n        StudyLocus: Filtered study-locus dataset.\n    \"\"\"\n    self.df = self._df.withColumn(\n        \"locus\",\n        f.filter(\n            f.col(\"locus\"),\n            lambda tag: (tag[credible_interval.value]),\n        ),\n    )\n    return self\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.find_overlaps","title":"<code>find_overlaps(study_index: StudyIndex) -&gt; StudyLocusOverlap</code>","text":"<p>Calculate overlapping study-locus.</p> <p>Find overlapping study-locus that share at least one tagging variant. All GWAS-GWAS and all GWAS-Molecular traits are computed with the Molecular traits always appearing on the right side.</p> <p>Parameters:</p> Name Type Description Default <code>study_index</code> <code>StudyIndex</code> <p>Study index to resolve study types.</p> required <p>Returns:</p> Name Type Description <code>StudyLocusOverlap</code> <code>StudyLocusOverlap</code> <p>Pairs of overlapping study-locus with aligned tags.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>def find_overlaps(self: StudyLocus, study_index: StudyIndex) -&gt; StudyLocusOverlap:\n    \"\"\"Calculate overlapping study-locus.\n\n    Find overlapping study-locus that share at least one tagging variant. All GWAS-GWAS and all GWAS-Molecular traits are computed with the Molecular traits always\n    appearing on the right side.\n\n    Args:\n        study_index (StudyIndex): Study index to resolve study types.\n\n    Returns:\n        StudyLocusOverlap: Pairs of overlapping study-locus with aligned tags.\n    \"\"\"\n    loci_to_overlap = (\n        self.df.join(study_index.study_type_lut(), on=\"studyId\", how=\"inner\")\n        .withColumn(\"locus\", f.explode(\"locus\"))\n        .select(\n            \"studyLocusId\",\n            \"studyType\",\n            \"chromosome\",\n            f.col(\"locus.variantId\").alias(\"tagVariantId\"),\n            f.col(\"locus.logABF\").alias(\"logABF\"),\n            f.col(\"locus.posteriorProbability\").alias(\"posteriorProbability\"),\n            f.col(\"locus.pValueMantissa\").alias(\"pValueMantissa\"),\n            f.col(\"locus.pValueExponent\").alias(\"pValueExponent\"),\n            f.col(\"locus.beta\").alias(\"beta\"),\n        )\n        .persist()\n    )\n\n    # overlapping study-locus\n    peak_overlaps = self._overlapping_peaks(loci_to_overlap)\n\n    # study-locus overlap by aligning overlapping variants\n    return self._align_overlapping_tags(loci_to_overlap, peak_overlaps)\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the StudyLocus dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>schema for the StudyLocus dataset.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[StudyLocus]) -&gt; StructType:\n    \"\"\"Provides the schema for the StudyLocus dataset.\n\n    Returns:\n        StructType: schema for the StudyLocus dataset.\n    \"\"\"\n    return parse_spark_schema(\"study_locus.json\")\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.neglog_pvalue","title":"<code>neglog_pvalue() -&gt; Column</code>","text":"<p>Returns the negative log p-value.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>Negative log p-value</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>def neglog_pvalue(self: StudyLocus) -&gt; Column:\n    \"\"\"Returns the negative log p-value.\n\n    Returns:\n        Column: Negative log p-value\n    \"\"\"\n    return calculate_neglog_pvalue(\n        self.df.pValueMantissa,\n        self.df.pValueExponent,\n    )\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.unique_variants_in_locus","title":"<code>unique_variants_in_locus() -&gt; DataFrame</code>","text":"<p>All unique variants collected in a <code>StudyLocus</code> dataframe.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>A dataframe containing <code>variantId</code> and <code>chromosome</code> columns.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>def unique_variants_in_locus(self: StudyLocus) -&gt; DataFrame:\n    \"\"\"All unique variants collected in a `StudyLocus` dataframe.\n\n    Returns:\n        DataFrame: A dataframe containing `variantId` and `chromosome` columns.\n    \"\"\"\n    return (\n        self.df.withColumn(\n            \"variantId\",\n            # Joint array of variants in that studylocus. Locus can be null\n            f.explode(\n                f.array_union(\n                    f.array(f.col(\"variantId\")),\n                    f.coalesce(f.col(\"locus.variantId\"), f.array()),\n                )\n            ),\n        )\n        .select(\n            \"variantId\", f.split(f.col(\"variantId\"), \"_\")[0].alias(\"chromosome\")\n        )\n        .distinct()\n    )\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocus.update_quality_flag","title":"<code>update_quality_flag(qc: Column, flag_condition: Column, flag_text: StudyLocusQualityCheck) -&gt; Column</code>  <code>staticmethod</code>","text":"<p>Update the provided quality control list with a new flag if condition is met.</p> <p>Parameters:</p> Name Type Description Default <code>qc</code> <code>Column</code> <p>Array column with the current list of qc flags.</p> required <code>flag_condition</code> <code>Column</code> <p>This is a column of booleans, signing which row should be flagged</p> required <code>flag_text</code> <code>StudyLocusQualityCheck</code> <p>Text for the new quality control flag</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>Array column with the updated list of qc flags.</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>@staticmethod\ndef update_quality_flag(\n    qc: Column, flag_condition: Column, flag_text: StudyLocusQualityCheck\n) -&gt; Column:\n    \"\"\"Update the provided quality control list with a new flag if condition is met.\n\n    Args:\n        qc (Column): Array column with the current list of qc flags.\n        flag_condition (Column): This is a column of booleans, signing which row should be flagged\n        flag_text (StudyLocusQualityCheck): Text for the new quality control flag\n\n    Returns:\n        Column: Array column with the updated list of qc flags.\n    \"\"\"\n    qc = f.when(qc.isNull(), f.array()).otherwise(qc)\n    return f.when(\n        flag_condition,\n        f.array_union(qc, f.array(f.lit(flag_text.value))),\n    ).otherwise(qc)\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.StudyLocusQualityCheck","title":"<code>otg.dataset.study_locus.StudyLocusQualityCheck</code>","text":"<p>             Bases: <code>Enum</code></p> <p>Study-Locus quality control options listing concerns on the quality of the association.</p> <p>Attributes:</p> Name Type Description <code>SUBSIGNIFICANT_FLAG</code> <code>str</code> <p>p-value below significance threshold</p> <code>NO_GENOMIC_LOCATION_FLAG</code> <code>str</code> <p>Incomplete genomic mapping</p> <code>COMPOSITE_FLAG</code> <code>str</code> <p>Composite association due to variant x variant interactions</p> <code>VARIANT_INCONSISTENCY_FLAG</code> <code>str</code> <p>Inconsistencies in the reported variants</p> <code>NON_MAPPED_VARIANT_FLAG</code> <code>str</code> <p>Variant not mapped to GnomAd</p> <code>PALINDROMIC_ALLELE_FLAG</code> <code>str</code> <p>Alleles are palindromic - cannot harmonize</p> <code>AMBIGUOUS_STUDY</code> <code>str</code> <p>Association with ambiguous study</p> <code>UNRESOLVED_LD</code> <code>str</code> <p>Variant not found in LD reference</p> <code>LD_CLUMPED</code> <code>str</code> <p>Explained by a more significant variant in high LD (clumped)</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>class StudyLocusQualityCheck(Enum):\n    \"\"\"Study-Locus quality control options listing concerns on the quality of the association.\n\n    Attributes:\n        SUBSIGNIFICANT_FLAG (str): p-value below significance threshold\n        NO_GENOMIC_LOCATION_FLAG (str): Incomplete genomic mapping\n        COMPOSITE_FLAG (str): Composite association due to variant x variant interactions\n        VARIANT_INCONSISTENCY_FLAG (str): Inconsistencies in the reported variants\n        NON_MAPPED_VARIANT_FLAG (str): Variant not mapped to GnomAd\n        PALINDROMIC_ALLELE_FLAG (str): Alleles are palindromic - cannot harmonize\n        AMBIGUOUS_STUDY (str): Association with ambiguous study\n        UNRESOLVED_LD (str): Variant not found in LD reference\n        LD_CLUMPED (str): Explained by a more significant variant in high LD (clumped)\n    \"\"\"\n\n    SUBSIGNIFICANT_FLAG = \"Subsignificant p-value\"\n    NO_GENOMIC_LOCATION_FLAG = \"Incomplete genomic mapping\"\n    COMPOSITE_FLAG = \"Composite association\"\n    INCONSISTENCY_FLAG = \"Variant inconsistency\"\n    NON_MAPPED_VARIANT_FLAG = \"No mapping in GnomAd\"\n    PALINDROMIC_ALLELE_FLAG = \"Palindrome alleles - cannot harmonize\"\n    AMBIGUOUS_STUDY = \"Association with ambiguous study\"\n    UNRESOLVED_LD = \"Variant not found in LD reference\"\n    LD_CLUMPED = \"Explained by a more significant variant in high LD (clumped)\"\n    NO_POPULATION = \"Study does not have population annotation to resolve LD\"\n</code></pre>"},{"location":"python_api/dataset/study_locus/#otg.dataset.study_locus.CredibleInterval","title":"<code>otg.dataset.study_locus.CredibleInterval</code>","text":"<p>             Bases: <code>Enum</code></p> <p>Credible interval enum.</p> <p>Interval within which an unobserved parameter value falls with a particular probability.</p> <p>Attributes:</p> Name Type Description <code>IS95</code> <code>str</code> <p>95% credible interval</p> <code>IS99</code> <code>str</code> <p>99% credible interval</p> Source code in <code>src/otg/dataset/study_locus.py</code> <pre><code>class CredibleInterval(Enum):\n    \"\"\"Credible interval enum.\n\n    Interval within which an unobserved parameter value falls with a particular probability.\n\n    Attributes:\n        IS95 (str): 95% credible interval\n        IS99 (str): 99% credible interval\n    \"\"\"\n\n    IS95 = \"is95CredibleSet\"\n    IS99 = \"is99CredibleSet\"\n</code></pre>"},{"location":"python_api/dataset/study_locus/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = true)\n |-- position: integer (nullable = true)\n |-- studyId: string (nullable = false)\n |-- beta: double (nullable = true)\n |-- pValueMantissa: float (nullable = true)\n |-- pValueExponent: integer (nullable = true)\n |-- effectAlleleFrequencyFromSource: float (nullable = true)\n |-- standardError: double (nullable = true)\n |-- subStudyDescription: string (nullable = true)\n |-- qualityControls: array (nullable = true)\n |    |-- element: string (containsNull = false)\n |-- finemappingMethod: string (nullable = true)\n |-- sampleSize: integer (nullable = true)\n |-- ldSet: array (nullable = true)\n |    |-- element: struct (containsNull = true)\n |    |    |-- tagVariantId: string (nullable = true)\n |    |    |-- r2Overall: double (nullable = true)\n |-- locus: array (nullable = true)\n |    |-- element: struct (containsNull = true)\n |    |    |-- is95CredibleSet: boolean (nullable = true)\n |    |    |-- is99CredibleSet: boolean (nullable = true)\n |    |    |-- logABF: double (nullable = true)\n |    |    |-- posteriorProbability: double (nullable = true)\n |    |    |-- variantId: string (nullable = true)\n |    |    |-- pValueMantissa: float (nullable = true)\n |    |    |-- pValueExponent: integer (nullable = true)\n |    |    |-- pValueMantissaConditioned: float (nullable = true)\n |    |    |-- pValueExponentConditioned: integer (nullable = true)\n |    |    |-- beta: double (nullable = true)\n |    |    |-- standardError: double (nullable = true)\n |    |    |-- betaConditioned: double (nullable = true)\n |    |    |-- standardErrorConditioned: double (nullable = true)\n |    |    |-- r2Overall: double (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/study_locus_overlap/","title":"Study Locus Overlap","text":""},{"location":"python_api/dataset/study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap","title":"<code>otg.dataset.study_locus_overlap.StudyLocusOverlap</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Study-Locus overlap.</p> <p>This dataset captures pairs of overlapping <code>StudyLocus</code>: that is associations whose credible sets share at least one tagging variant.</p> <p>Note</p> <p>This is a helpful dataset for other downstream analyses, such as colocalisation. This dataset will contain the overlapping signals between studyLocus associations once they have been clumped and fine-mapped.</p> Source code in <code>src/otg/dataset/study_locus_overlap.py</code> <pre><code>@dataclass\nclass StudyLocusOverlap(Dataset):\n    \"\"\"Study-Locus overlap.\n\n    This dataset captures pairs of overlapping `StudyLocus`: that is associations whose credible sets share at least one tagging variant.\n\n    !!! note\n        This is a helpful dataset for other downstream analyses, such as colocalisation. This dataset will contain the overlapping signals between studyLocus associations once they have been clumped and fine-mapped.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[StudyLocusOverlap]) -&gt; StructType:\n        \"\"\"Provides the schema for the StudyLocusOverlap dataset.\n\n        Returns:\n            StructType: Schema for the StudyLocusOverlap dataset\n        \"\"\"\n        return parse_spark_schema(\"study_locus_overlap.json\")\n\n    @classmethod\n    def from_associations(\n        cls: type[StudyLocusOverlap], study_locus: StudyLocus, study_index: StudyIndex\n    ) -&gt; StudyLocusOverlap:\n        \"\"\"Find the overlapping signals in a particular set of associations (StudyLocus dataset).\n\n        Args:\n            study_locus (StudyLocus): Study-locus associations to find the overlapping signals\n            study_index (StudyIndex): Study index to find the overlapping signals\n\n        Returns:\n            StudyLocusOverlap: Study-locus overlap dataset\n        \"\"\"\n        return study_locus.find_overlaps(study_index)\n\n    def _convert_to_square_matrix(self: StudyLocusOverlap) -&gt; StudyLocusOverlap:\n        \"\"\"Convert the dataset to a square matrix.\n\n        Returns:\n            StudyLocusOverlap: Square matrix of the dataset\n        \"\"\"\n        return StudyLocusOverlap(\n            _df=self.df.unionByName(\n                self.df.selectExpr(\n                    \"leftStudyLocusId as rightStudyLocusId\",\n                    \"rightStudyLocusId as leftStudyLocusId\",\n                    \"tagVariantId\",\n                )\n            ).distinct(),\n            _schema=self.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/dataset/study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap.from_associations","title":"<code>from_associations(study_locus: StudyLocus, study_index: StudyIndex) -&gt; StudyLocusOverlap</code>  <code>classmethod</code>","text":"<p>Find the overlapping signals in a particular set of associations (StudyLocus dataset).</p> <p>Parameters:</p> Name Type Description Default <code>study_locus</code> <code>StudyLocus</code> <p>Study-locus associations to find the overlapping signals</p> required <code>study_index</code> <code>StudyIndex</code> <p>Study index to find the overlapping signals</p> required <p>Returns:</p> Name Type Description <code>StudyLocusOverlap</code> <code>StudyLocusOverlap</code> <p>Study-locus overlap dataset</p> Source code in <code>src/otg/dataset/study_locus_overlap.py</code> <pre><code>@classmethod\ndef from_associations(\n    cls: type[StudyLocusOverlap], study_locus: StudyLocus, study_index: StudyIndex\n) -&gt; StudyLocusOverlap:\n    \"\"\"Find the overlapping signals in a particular set of associations (StudyLocus dataset).\n\n    Args:\n        study_locus (StudyLocus): Study-locus associations to find the overlapping signals\n        study_index (StudyIndex): Study index to find the overlapping signals\n\n    Returns:\n        StudyLocusOverlap: Study-locus overlap dataset\n    \"\"\"\n    return study_locus.find_overlaps(study_index)\n</code></pre>"},{"location":"python_api/dataset/study_locus_overlap/#otg.dataset.study_locus_overlap.StudyLocusOverlap.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the StudyLocusOverlap dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the StudyLocusOverlap dataset</p> Source code in <code>src/otg/dataset/study_locus_overlap.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[StudyLocusOverlap]) -&gt; StructType:\n    \"\"\"Provides the schema for the StudyLocusOverlap dataset.\n\n    Returns:\n        StructType: Schema for the StudyLocusOverlap dataset\n    \"\"\"\n    return parse_spark_schema(\"study_locus_overlap.json\")\n</code></pre>"},{"location":"python_api/dataset/study_locus_overlap/#schema","title":"Schema","text":"<pre><code>root\n |-- leftStudyLocusId: long (nullable = false)\n |-- rightStudyLocusId: long (nullable = false)\n |-- chromosome: string (nullable = true)\n |-- tagVariantId: string (nullable = false)\n |-- statistics: struct (nullable = true)\n |    |-- left_pValueMantissa: float (nullable = true)\n |    |-- left_pValueExponent: integer (nullable = true)\n |    |-- right_pValueMantissa: float (nullable = true)\n |    |-- right_pValueExponent: integer (nullable = true)\n |    |-- left_beta: double (nullable = true)\n |    |-- right_beta: double (nullable = true)\n |    |-- left_logABF: double (nullable = true)\n |    |-- right_logABF: double (nullable = true)\n |    |-- left_posteriorProbability: double (nullable = true)\n |    |-- right_posteriorProbability: double (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/summary_statistics/","title":"Summary Statistics","text":""},{"location":"python_api/dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics","title":"<code>otg.dataset.summary_statistics.SummaryStatistics</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Summary Statistics dataset.</p> <p>A summary statistics dataset contains all single point statistics resulting from a GWAS.</p> Source code in <code>src/otg/dataset/summary_statistics.py</code> <pre><code>@dataclass\nclass SummaryStatistics(Dataset):\n    \"\"\"Summary Statistics dataset.\n\n    A summary statistics dataset contains all single point statistics resulting from a GWAS.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[SummaryStatistics]) -&gt; StructType:\n        \"\"\"Provides the schema for the SummaryStatistics dataset.\n\n        Returns:\n            StructType: Schema for the SummaryStatistics dataset\n        \"\"\"\n        return parse_spark_schema(\"summary_statistics.json\")\n\n    def pvalue_filter(self: SummaryStatistics, pvalue: float) -&gt; SummaryStatistics:\n        \"\"\"Filter summary statistics based on the provided p-value threshold.\n\n        Args:\n            pvalue (float): upper limit of the p-value to be filtered upon.\n\n        Returns:\n            SummaryStatistics: summary statistics object containing single point associations with p-values at least as significant as the provided threshold.\n        \"\"\"\n        # Converting p-value to mantissa and exponent:\n        (mantissa, exponent) = split_pvalue(pvalue)\n\n        # Applying filter:\n        df = self._df.filter(\n            (f.col(\"pValueExponent\") &lt; exponent)\n            | (\n                (f.col(\"pValueExponent\") == exponent)\n                &amp; (f.col(\"pValueMantissa\") &lt;= mantissa)\n            )\n        )\n        return SummaryStatistics(_df=df, _schema=self._schema)\n\n    def window_based_clumping(\n        self: SummaryStatistics,\n        distance: int = 500_000,\n        gwas_significance: float = 5e-8,\n        baseline_significance: float = 0.05,\n        locus_collect_distance: int | None = None,\n    ) -&gt; StudyLocus:\n        \"\"\"Generate study-locus from summary statistics by distance based clumping + collect locus.\n\n        Args:\n            distance (int): Distance in base pairs to be used for clumping. Defaults to 500_000.\n            gwas_significance (float, optional): GWAS significance threshold. Defaults to 5e-8.\n            baseline_significance (float, optional): Baseline significance threshold for inclusion in the locus. Defaults to 0.05.\n            locus_collect_distance (int | None): The distance to collect locus around semi-indices. If not provided, locus is not collected.\n\n        Returns:\n            StudyLocus: Clumped study-locus containing variants based on window.\n        \"\"\"\n        return (\n            WindowBasedClumping.clump_with_locus(\n                self,\n                window_length=distance,\n                p_value_significance=gwas_significance,\n                p_value_baseline=baseline_significance,\n                locus_window_length=locus_collect_distance,\n            )\n            if locus_collect_distance\n            else WindowBasedClumping.clump(\n                self,\n                window_length=distance,\n                p_value_significance=gwas_significance,\n            )\n        )\n\n    def exclude_region(self: SummaryStatistics, region: str) -&gt; SummaryStatistics:\n        \"\"\"Exclude a region from the summary stats dataset.\n\n        Args:\n            region (str): region given in \"chr##:#####-####\" format\n\n        Returns:\n            SummaryStatistics: filtered summary statistics.\n        \"\"\"\n        (chromosome, start_position, end_position) = parse_region(region)\n\n        return SummaryStatistics(\n            _df=(\n                self.df.filter(\n                    ~(\n                        (f.col(\"chromosome\") == chromosome)\n                        &amp; (\n                            (f.col(\"position\") &gt;= start_position)\n                            &amp; (f.col(\"position\") &lt;= end_position)\n                        )\n                    )\n                )\n            ),\n            _schema=SummaryStatistics.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics.exclude_region","title":"<code>exclude_region(region: str) -&gt; SummaryStatistics</code>","text":"<p>Exclude a region from the summary stats dataset.</p> <p>Parameters:</p> Name Type Description Default <code>region</code> <code>str</code> <p>region given in \"chr##:#####-####\" format</p> required <p>Returns:</p> Name Type Description <code>SummaryStatistics</code> <code>SummaryStatistics</code> <p>filtered summary statistics.</p> Source code in <code>src/otg/dataset/summary_statistics.py</code> <pre><code>def exclude_region(self: SummaryStatistics, region: str) -&gt; SummaryStatistics:\n    \"\"\"Exclude a region from the summary stats dataset.\n\n    Args:\n        region (str): region given in \"chr##:#####-####\" format\n\n    Returns:\n        SummaryStatistics: filtered summary statistics.\n    \"\"\"\n    (chromosome, start_position, end_position) = parse_region(region)\n\n    return SummaryStatistics(\n        _df=(\n            self.df.filter(\n                ~(\n                    (f.col(\"chromosome\") == chromosome)\n                    &amp; (\n                        (f.col(\"position\") &gt;= start_position)\n                        &amp; (f.col(\"position\") &lt;= end_position)\n                    )\n                )\n            )\n        ),\n        _schema=SummaryStatistics.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the SummaryStatistics dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the SummaryStatistics dataset</p> Source code in <code>src/otg/dataset/summary_statistics.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[SummaryStatistics]) -&gt; StructType:\n    \"\"\"Provides the schema for the SummaryStatistics dataset.\n\n    Returns:\n        StructType: Schema for the SummaryStatistics dataset\n    \"\"\"\n    return parse_spark_schema(\"summary_statistics.json\")\n</code></pre>"},{"location":"python_api/dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics.pvalue_filter","title":"<code>pvalue_filter(pvalue: float) -&gt; SummaryStatistics</code>","text":"<p>Filter summary statistics based on the provided p-value threshold.</p> <p>Parameters:</p> Name Type Description Default <code>pvalue</code> <code>float</code> <p>upper limit of the p-value to be filtered upon.</p> required <p>Returns:</p> Name Type Description <code>SummaryStatistics</code> <code>SummaryStatistics</code> <p>summary statistics object containing single point associations with p-values at least as significant as the provided threshold.</p> Source code in <code>src/otg/dataset/summary_statistics.py</code> <pre><code>def pvalue_filter(self: SummaryStatistics, pvalue: float) -&gt; SummaryStatistics:\n    \"\"\"Filter summary statistics based on the provided p-value threshold.\n\n    Args:\n        pvalue (float): upper limit of the p-value to be filtered upon.\n\n    Returns:\n        SummaryStatistics: summary statistics object containing single point associations with p-values at least as significant as the provided threshold.\n    \"\"\"\n    # Converting p-value to mantissa and exponent:\n    (mantissa, exponent) = split_pvalue(pvalue)\n\n    # Applying filter:\n    df = self._df.filter(\n        (f.col(\"pValueExponent\") &lt; exponent)\n        | (\n            (f.col(\"pValueExponent\") == exponent)\n            &amp; (f.col(\"pValueMantissa\") &lt;= mantissa)\n        )\n    )\n    return SummaryStatistics(_df=df, _schema=self._schema)\n</code></pre>"},{"location":"python_api/dataset/summary_statistics/#otg.dataset.summary_statistics.SummaryStatistics.window_based_clumping","title":"<code>window_based_clumping(distance: int = 500000, gwas_significance: float = 5e-08, baseline_significance: float = 0.05, locus_collect_distance: int | None = None) -&gt; StudyLocus</code>","text":"<p>Generate study-locus from summary statistics by distance based clumping + collect locus.</p> <p>Parameters:</p> Name Type Description Default <code>distance</code> <code>int</code> <p>Distance in base pairs to be used for clumping. Defaults to 500_000.</p> <code>500000</code> <code>gwas_significance</code> <code>float</code> <p>GWAS significance threshold. Defaults to 5e-8.</p> <code>5e-08</code> <code>baseline_significance</code> <code>float</code> <p>Baseline significance threshold for inclusion in the locus. Defaults to 0.05.</p> <code>0.05</code> <code>locus_collect_distance</code> <code>int | None</code> <p>The distance to collect locus around semi-indices. If not provided, locus is not collected.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Clumped study-locus containing variants based on window.</p> Source code in <code>src/otg/dataset/summary_statistics.py</code> <pre><code>def window_based_clumping(\n    self: SummaryStatistics,\n    distance: int = 500_000,\n    gwas_significance: float = 5e-8,\n    baseline_significance: float = 0.05,\n    locus_collect_distance: int | None = None,\n) -&gt; StudyLocus:\n    \"\"\"Generate study-locus from summary statistics by distance based clumping + collect locus.\n\n    Args:\n        distance (int): Distance in base pairs to be used for clumping. Defaults to 500_000.\n        gwas_significance (float, optional): GWAS significance threshold. Defaults to 5e-8.\n        baseline_significance (float, optional): Baseline significance threshold for inclusion in the locus. Defaults to 0.05.\n        locus_collect_distance (int | None): The distance to collect locus around semi-indices. If not provided, locus is not collected.\n\n    Returns:\n        StudyLocus: Clumped study-locus containing variants based on window.\n    \"\"\"\n    return (\n        WindowBasedClumping.clump_with_locus(\n            self,\n            window_length=distance,\n            p_value_significance=gwas_significance,\n            p_value_baseline=baseline_significance,\n            locus_window_length=locus_collect_distance,\n        )\n        if locus_collect_distance\n        else WindowBasedClumping.clump(\n            self,\n            window_length=distance,\n            p_value_significance=gwas_significance,\n        )\n    )\n</code></pre>"},{"location":"python_api/dataset/summary_statistics/#schema","title":"Schema","text":"<pre><code>root\n |-- studyId: string (nullable = false)\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- position: integer (nullable = false)\n |-- beta: double (nullable = false)\n |-- sampleSize: integer (nullable = true)\n |-- pValueMantissa: float (nullable = false)\n |-- pValueExponent: integer (nullable = false)\n |-- effectAlleleFrequencyFromSource: float (nullable = true)\n |-- standardError: double (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/","title":"Variant annotation","text":""},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation","title":"<code>otg.dataset.variant_annotation.VariantAnnotation</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset with variant-level annotations.</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>@dataclass\nclass VariantAnnotation(Dataset):\n    \"\"\"Dataset with variant-level annotations.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[VariantAnnotation]) -&gt; StructType:\n        \"\"\"Provides the schema for the VariantAnnotation dataset.\n\n        Returns:\n            StructType: Schema for the VariantAnnotation dataset\n        \"\"\"\n        return parse_spark_schema(\"variant_annotation.json\")\n\n    def max_maf(self: VariantAnnotation) -&gt; Column:\n        \"\"\"Maximum minor allele frequency accross all populations.\n\n        Returns:\n            Column: Maximum minor allele frequency accross all populations.\n        \"\"\"\n        return f.array_max(\n            f.transform(\n                self.df.alleleFrequencies,\n                lambda af: f.when(\n                    af.alleleFrequency &gt; 0.5, 1 - af.alleleFrequency\n                ).otherwise(af.alleleFrequency),\n            )\n        )\n\n    def filter_by_variant_df(\n        self: VariantAnnotation, df: DataFrame\n    ) -&gt; VariantAnnotation:\n        \"\"\"Filter variant annotation dataset by a variant dataframe.\n\n        Args:\n            df (DataFrame): A dataframe of variants\n\n        Returns:\n            VariantAnnotation: A filtered variant annotation dataset\n        \"\"\"\n        self.df = self._df.join(\n            f.broadcast(df.select(\"variantId\", \"chromosome\")),\n            on=[\"variantId\", \"chromosome\"],\n            how=\"inner\",\n        )\n        return self\n\n    def get_transcript_consequence_df(\n        self: VariantAnnotation, gene_index: GeneIndex | None = None\n    ) -&gt; DataFrame:\n        \"\"\"Dataframe of exploded transcript consequences.\n\n        Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n        Args:\n            gene_index (GeneIndex | None): A gene index. Defaults to None.\n\n        Returns:\n            DataFrame: A dataframe exploded by transcript consequences with the columns variantId, chromosome, transcriptConsequence\n        \"\"\"\n        # exploding the array removes records without VEP annotation\n        transript_consequences = self.df.withColumn(\n            \"transcriptConsequence\", f.explode(\"vep.transcriptConsequences\")\n        ).select(\n            \"variantId\",\n            \"chromosome\",\n            \"position\",\n            \"transcriptConsequence\",\n            f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n        )\n        if gene_index:\n            transript_consequences = transript_consequences.join(\n                f.broadcast(gene_index.df),\n                on=[\"chromosome\", \"geneId\"],\n            )\n        return transript_consequences.persist()\n\n    def get_most_severe_vep_v2g(\n        self: VariantAnnotation,\n        vep_consequences: DataFrame,\n        gene_index: GeneIndex,\n    ) -&gt; V2G:\n        \"\"\"Creates a dataset with variant to gene assignments based on VEP's predicted consequence of the transcript.\n\n        Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n        Args:\n            vep_consequences (DataFrame): A dataframe of VEP consequences\n            gene_index (GeneIndex): A gene index to filter by. Defaults to None.\n\n        Returns:\n            V2G: High and medium severity variant to gene assignments\n        \"\"\"\n        return V2G(\n            _df=self.get_transcript_consequence_df(gene_index)\n            .select(\n                \"variantId\",\n                \"chromosome\",\n                f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n                f.explode(\"transcriptConsequence.consequenceTerms\").alias(\"label\"),\n                f.lit(\"vep\").alias(\"datatypeId\"),\n                f.lit(\"variantConsequence\").alias(\"datasourceId\"),\n            )\n            .join(\n                f.broadcast(vep_consequences),\n                on=\"label\",\n                how=\"inner\",\n            )\n            .drop(\"label\")\n            .filter(f.col(\"score\") != 0)\n            # A variant can have multiple predicted consequences on a transcript, the most severe one is selected\n            .transform(\n                lambda df: get_record_with_maximum_value(\n                    df, [\"variantId\", \"geneId\"], \"score\"\n                )\n            ),\n            _schema=V2G.get_schema(),\n        )\n\n    def get_plof_v2g(self: VariantAnnotation, gene_index: GeneIndex) -&gt; V2G:\n        \"\"\"Creates a dataset with variant to gene assignments with a flag indicating if the variant is predicted to be a loss-of-function variant by the LOFTEE algorithm.\n\n        Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n        Args:\n            gene_index (GeneIndex): A gene index to filter by.\n\n        Returns:\n            V2G: variant to gene assignments from the LOFTEE algorithm\n        \"\"\"\n        return V2G(\n            _df=(\n                self.get_transcript_consequence_df(gene_index)\n                .filter(f.col(\"transcriptConsequence.lof\").isNotNull())\n                .withColumn(\n                    \"isHighQualityPlof\",\n                    f.when(f.col(\"transcriptConsequence.lof\") == \"HC\", True).when(\n                        f.col(\"transcriptConsequence.lof\") == \"LC\", False\n                    ),\n                )\n                .withColumn(\n                    \"score\",\n                    f.when(f.col(\"isHighQualityPlof\"), 1.0).when(\n                        ~f.col(\"isHighQualityPlof\"), 0\n                    ),\n                )\n                .select(\n                    \"variantId\",\n                    \"chromosome\",\n                    \"geneId\",\n                    \"isHighQualityPlof\",\n                    f.col(\"score\"),\n                    f.lit(\"vep\").alias(\"datatypeId\"),\n                    f.lit(\"loftee\").alias(\"datasourceId\"),\n                )\n            ),\n            _schema=V2G.get_schema(),\n        )\n\n    def get_distance_to_tss(\n        self: VariantAnnotation,\n        gene_index: GeneIndex,\n        max_distance: int = 500_000,\n    ) -&gt; V2G:\n        \"\"\"Extracts variant to gene assignments for variants falling within a window of a gene's TSS.\n\n        Args:\n            gene_index (GeneIndex): A gene index to filter by.\n            max_distance (int): The maximum distance from the TSS to consider. Defaults to 500_000.\n\n        Returns:\n            V2G: variant to gene assignments with their distance to the TSS\n        \"\"\"\n        return V2G(\n            _df=(\n                self.df.alias(\"variant\")\n                .join(\n                    f.broadcast(gene_index.locations_lut()).alias(\"gene\"),\n                    on=[\n                        f.col(\"variant.chromosome\") == f.col(\"gene.chromosome\"),\n                        f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n                        &lt;= max_distance,\n                    ],\n                    how=\"inner\",\n                )\n                .withColumn(\n                    \"distance\", f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n                )\n                .withColumn(\n                    \"inverse_distance\",\n                    max_distance - f.col(\"distance\"),\n                )\n                .transform(lambda df: normalise_column(df, \"inverse_distance\", \"score\"))\n                .select(\n                    \"variantId\",\n                    f.col(\"variant.chromosome\").alias(\"chromosome\"),\n                    \"distance\",\n                    \"geneId\",\n                    \"score\",\n                    f.lit(\"distance\").alias(\"datatypeId\"),\n                    f.lit(\"canonical_tss\").alias(\"datasourceId\"),\n                )\n            ),\n            _schema=V2G.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df","title":"<code>filter_by_variant_df(df: DataFrame) -&gt; VariantAnnotation</code>","text":"<p>Filter variant annotation dataset by a variant dataframe.</p> <p>Parameters:</p> Name Type Description Default <code>df</code> <code>DataFrame</code> <p>A dataframe of variants</p> required <p>Returns:</p> Name Type Description <code>VariantAnnotation</code> <code>VariantAnnotation</code> <p>A filtered variant annotation dataset</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>def filter_by_variant_df(\n    self: VariantAnnotation, df: DataFrame\n) -&gt; VariantAnnotation:\n    \"\"\"Filter variant annotation dataset by a variant dataframe.\n\n    Args:\n        df (DataFrame): A dataframe of variants\n\n    Returns:\n        VariantAnnotation: A filtered variant annotation dataset\n    \"\"\"\n    self.df = self._df.join(\n        f.broadcast(df.select(\"variantId\", \"chromosome\")),\n        on=[\"variantId\", \"chromosome\"],\n        how=\"inner\",\n    )\n    return self\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss","title":"<code>get_distance_to_tss(gene_index: GeneIndex, max_distance: int = 500000) -&gt; V2G</code>","text":"<p>Extracts variant to gene assignments for variants falling within a window of a gene's TSS.</p> <p>Parameters:</p> Name Type Description Default <code>gene_index</code> <code>GeneIndex</code> <p>A gene index to filter by.</p> required <code>max_distance</code> <code>int</code> <p>The maximum distance from the TSS to consider. Defaults to 500_000.</p> <code>500000</code> <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>variant to gene assignments with their distance to the TSS</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>def get_distance_to_tss(\n    self: VariantAnnotation,\n    gene_index: GeneIndex,\n    max_distance: int = 500_000,\n) -&gt; V2G:\n    \"\"\"Extracts variant to gene assignments for variants falling within a window of a gene's TSS.\n\n    Args:\n        gene_index (GeneIndex): A gene index to filter by.\n        max_distance (int): The maximum distance from the TSS to consider. Defaults to 500_000.\n\n    Returns:\n        V2G: variant to gene assignments with their distance to the TSS\n    \"\"\"\n    return V2G(\n        _df=(\n            self.df.alias(\"variant\")\n            .join(\n                f.broadcast(gene_index.locations_lut()).alias(\"gene\"),\n                on=[\n                    f.col(\"variant.chromosome\") == f.col(\"gene.chromosome\"),\n                    f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n                    &lt;= max_distance,\n                ],\n                how=\"inner\",\n            )\n            .withColumn(\n                \"distance\", f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n            )\n            .withColumn(\n                \"inverse_distance\",\n                max_distance - f.col(\"distance\"),\n            )\n            .transform(lambda df: normalise_column(df, \"inverse_distance\", \"score\"))\n            .select(\n                \"variantId\",\n                f.col(\"variant.chromosome\").alias(\"chromosome\"),\n                \"distance\",\n                \"geneId\",\n                \"score\",\n                f.lit(\"distance\").alias(\"datatypeId\"),\n                f.lit(\"canonical_tss\").alias(\"datasourceId\"),\n            )\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g","title":"<code>get_most_severe_vep_v2g(vep_consequences: DataFrame, gene_index: GeneIndex) -&gt; V2G</code>","text":"<p>Creates a dataset with variant to gene assignments based on VEP's predicted consequence of the transcript.</p> <p>Optionally the trancript consequences can be reduced to the universe of a gene index.</p> <p>Parameters:</p> Name Type Description Default <code>vep_consequences</code> <code>DataFrame</code> <p>A dataframe of VEP consequences</p> required <code>gene_index</code> <code>GeneIndex</code> <p>A gene index to filter by. Defaults to None.</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>High and medium severity variant to gene assignments</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>def get_most_severe_vep_v2g(\n    self: VariantAnnotation,\n    vep_consequences: DataFrame,\n    gene_index: GeneIndex,\n) -&gt; V2G:\n    \"\"\"Creates a dataset with variant to gene assignments based on VEP's predicted consequence of the transcript.\n\n    Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n    Args:\n        vep_consequences (DataFrame): A dataframe of VEP consequences\n        gene_index (GeneIndex): A gene index to filter by. Defaults to None.\n\n    Returns:\n        V2G: High and medium severity variant to gene assignments\n    \"\"\"\n    return V2G(\n        _df=self.get_transcript_consequence_df(gene_index)\n        .select(\n            \"variantId\",\n            \"chromosome\",\n            f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n            f.explode(\"transcriptConsequence.consequenceTerms\").alias(\"label\"),\n            f.lit(\"vep\").alias(\"datatypeId\"),\n            f.lit(\"variantConsequence\").alias(\"datasourceId\"),\n        )\n        .join(\n            f.broadcast(vep_consequences),\n            on=\"label\",\n            how=\"inner\",\n        )\n        .drop(\"label\")\n        .filter(f.col(\"score\") != 0)\n        # A variant can have multiple predicted consequences on a transcript, the most severe one is selected\n        .transform(\n            lambda df: get_record_with_maximum_value(\n                df, [\"variantId\", \"geneId\"], \"score\"\n            )\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation.get_plof_v2g","title":"<code>get_plof_v2g(gene_index: GeneIndex) -&gt; V2G</code>","text":"<p>Creates a dataset with variant to gene assignments with a flag indicating if the variant is predicted to be a loss-of-function variant by the LOFTEE algorithm.</p> <p>Optionally the trancript consequences can be reduced to the universe of a gene index.</p> <p>Parameters:</p> Name Type Description Default <code>gene_index</code> <code>GeneIndex</code> <p>A gene index to filter by.</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>variant to gene assignments from the LOFTEE algorithm</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>def get_plof_v2g(self: VariantAnnotation, gene_index: GeneIndex) -&gt; V2G:\n    \"\"\"Creates a dataset with variant to gene assignments with a flag indicating if the variant is predicted to be a loss-of-function variant by the LOFTEE algorithm.\n\n    Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n    Args:\n        gene_index (GeneIndex): A gene index to filter by.\n\n    Returns:\n        V2G: variant to gene assignments from the LOFTEE algorithm\n    \"\"\"\n    return V2G(\n        _df=(\n            self.get_transcript_consequence_df(gene_index)\n            .filter(f.col(\"transcriptConsequence.lof\").isNotNull())\n            .withColumn(\n                \"isHighQualityPlof\",\n                f.when(f.col(\"transcriptConsequence.lof\") == \"HC\", True).when(\n                    f.col(\"transcriptConsequence.lof\") == \"LC\", False\n                ),\n            )\n            .withColumn(\n                \"score\",\n                f.when(f.col(\"isHighQualityPlof\"), 1.0).when(\n                    ~f.col(\"isHighQualityPlof\"), 0\n                ),\n            )\n            .select(\n                \"variantId\",\n                \"chromosome\",\n                \"geneId\",\n                \"isHighQualityPlof\",\n                f.col(\"score\"),\n                f.lit(\"vep\").alias(\"datatypeId\"),\n                f.lit(\"loftee\").alias(\"datasourceId\"),\n            )\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the VariantAnnotation dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the VariantAnnotation dataset</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[VariantAnnotation]) -&gt; StructType:\n    \"\"\"Provides the schema for the VariantAnnotation dataset.\n\n    Returns:\n        StructType: Schema for the VariantAnnotation dataset\n    \"\"\"\n    return parse_spark_schema(\"variant_annotation.json\")\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df","title":"<code>get_transcript_consequence_df(gene_index: GeneIndex | None = None) -&gt; DataFrame</code>","text":"<p>Dataframe of exploded transcript consequences.</p> <p>Optionally the trancript consequences can be reduced to the universe of a gene index.</p> <p>Parameters:</p> Name Type Description Default <code>gene_index</code> <code>GeneIndex | None</code> <p>A gene index. Defaults to None.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>A dataframe exploded by transcript consequences with the columns variantId, chromosome, transcriptConsequence</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>def get_transcript_consequence_df(\n    self: VariantAnnotation, gene_index: GeneIndex | None = None\n) -&gt; DataFrame:\n    \"\"\"Dataframe of exploded transcript consequences.\n\n    Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n    Args:\n        gene_index (GeneIndex | None): A gene index. Defaults to None.\n\n    Returns:\n        DataFrame: A dataframe exploded by transcript consequences with the columns variantId, chromosome, transcriptConsequence\n    \"\"\"\n    # exploding the array removes records without VEP annotation\n    transript_consequences = self.df.withColumn(\n        \"transcriptConsequence\", f.explode(\"vep.transcriptConsequences\")\n    ).select(\n        \"variantId\",\n        \"chromosome\",\n        \"position\",\n        \"transcriptConsequence\",\n        f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n    )\n    if gene_index:\n        transript_consequences = transript_consequences.join(\n            f.broadcast(gene_index.df),\n            on=[\"chromosome\", \"geneId\"],\n        )\n    return transript_consequences.persist()\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#otg.dataset.variant_annotation.VariantAnnotation.max_maf","title":"<code>max_maf() -&gt; Column</code>","text":"<p>Maximum minor allele frequency accross all populations.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>Maximum minor allele frequency accross all populations.</p> Source code in <code>src/otg/dataset/variant_annotation.py</code> <pre><code>def max_maf(self: VariantAnnotation) -&gt; Column:\n    \"\"\"Maximum minor allele frequency accross all populations.\n\n    Returns:\n        Column: Maximum minor allele frequency accross all populations.\n    \"\"\"\n    return f.array_max(\n        f.transform(\n            self.df.alleleFrequencies,\n            lambda af: f.when(\n                af.alleleFrequency &gt; 0.5, 1 - af.alleleFrequency\n            ).otherwise(af.alleleFrequency),\n        )\n    )\n</code></pre>"},{"location":"python_api/dataset/variant_annotation/#schema","title":"Schema","text":"<pre><code>root\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- position: integer (nullable = false)\n |-- gnomadVariantId: string (nullable = false)\n |-- referenceAllele: string (nullable = false)\n |-- alternateAllele: string (nullable = false)\n |-- chromosomeB37: string (nullable = true)\n |-- positionB37: integer (nullable = true)\n |-- alleleType: string (nullable = true)\n |-- rsIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- alleleFrequencies: array (nullable = false)\n |    |-- element: struct (containsNull = true)\n |    |    |-- populationName: string (nullable = true)\n |    |    |-- alleleFrequency: double (nullable = true)\n |-- inSilicoPredictors: struct (nullable = false)\n |    |-- cadd: struct (nullable = true)\n |    |    |-- raw: float (nullable = true)\n |    |    |-- phred: float (nullable = true)\n |    |-- revelMax: double (nullable = true)\n |    |-- spliceaiDsMax: float (nullable = true)\n |    |-- pangolinLargestDs: double (nullable = true)\n |    |-- phylop: double (nullable = true)\n |    |-- siftMax: double (nullable = true)\n |    |-- polyphenMax: double (nullable = true)\n |-- vep: struct (nullable = false)\n |    |-- mostSevereConsequence: string (nullable = true)\n |    |-- transcriptConsequences: array (nullable = true)\n |    |    |-- element: struct (containsNull = true)\n |    |    |    |-- aminoAcids: string (nullable = true)\n |    |    |    |-- consequenceTerms: array (nullable = true)\n |    |    |    |    |-- element: string (containsNull = true)\n |    |    |    |-- geneId: string (nullable = true)\n |    |    |    |-- lof: string (nullable = true)\n</code></pre>"},{"location":"python_api/dataset/variant_index/","title":"Variant index","text":""},{"location":"python_api/dataset/variant_index/#otg.dataset.variant_index.VariantIndex","title":"<code>otg.dataset.variant_index.VariantIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Variant index dataset.</p> <p>Variant index dataset is the result of intersecting the variant annotation dataset with the variants with V2D available information.</p> Source code in <code>src/otg/dataset/variant_index.py</code> <pre><code>@dataclass\nclass VariantIndex(Dataset):\n    \"\"\"Variant index dataset.\n\n    Variant index dataset is the result of intersecting the variant annotation dataset with the variants with V2D available information.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[VariantIndex]) -&gt; StructType:\n        \"\"\"Provides the schema for the VariantIndex dataset.\n\n        Returns:\n            StructType: Schema for the VariantIndex dataset\n        \"\"\"\n        return parse_spark_schema(\"variant_index.json\")\n\n    @classmethod\n    def from_variant_annotation(\n        cls: type[VariantIndex],\n        variant_annotation: VariantAnnotation,\n        study_locus: StudyLocus,\n    ) -&gt; VariantIndex:\n        \"\"\"Initialise VariantIndex from pre-existing variant annotation dataset.\n\n        Args:\n            variant_annotation (VariantAnnotation): Variant annotation dataset\n            study_locus (StudyLocus): Study locus dataset with the variants to intersect with the variant annotation dataset\n\n        Returns:\n            VariantIndex: Variant index dataset\n        \"\"\"\n        unchanged_cols = [\n            \"variantId\",\n            \"chromosome\",\n            \"position\",\n            \"referenceAllele\",\n            \"alternateAllele\",\n            \"chromosomeB37\",\n            \"positionB37\",\n            \"alleleType\",\n            \"alleleFrequencies\",\n            \"inSilicoPredictors\",\n        ]\n        va_slimmed = variant_annotation.filter_by_variant_df(\n            study_locus.unique_variants_in_locus()\n        )\n        return cls(\n            _df=(\n                va_slimmed.df.select(\n                    *unchanged_cols,\n                    f.col(\"vep.mostSevereConsequence\").alias(\"mostSevereConsequence\"),\n                    # filters/rsid are arrays that can be empty, in this case we convert them to null\n                    nullify_empty_array(f.col(\"rsIds\")).alias(\"rsIds\"),\n                )\n                .repartition(400, \"chromosome\")\n                .sortWithinPartitions(\"chromosome\", \"position\")\n            ),\n            _schema=cls.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/dataset/variant_index/#otg.dataset.variant_index.VariantIndex.from_variant_annotation","title":"<code>from_variant_annotation(variant_annotation: VariantAnnotation, study_locus: StudyLocus) -&gt; VariantIndex</code>  <code>classmethod</code>","text":"<p>Initialise VariantIndex from pre-existing variant annotation dataset.</p> <p>Parameters:</p> Name Type Description Default <code>variant_annotation</code> <code>VariantAnnotation</code> <p>Variant annotation dataset</p> required <code>study_locus</code> <code>StudyLocus</code> <p>Study locus dataset with the variants to intersect with the variant annotation dataset</p> required <p>Returns:</p> Name Type Description <code>VariantIndex</code> <code>VariantIndex</code> <p>Variant index dataset</p> Source code in <code>src/otg/dataset/variant_index.py</code> <pre><code>@classmethod\ndef from_variant_annotation(\n    cls: type[VariantIndex],\n    variant_annotation: VariantAnnotation,\n    study_locus: StudyLocus,\n) -&gt; VariantIndex:\n    \"\"\"Initialise VariantIndex from pre-existing variant annotation dataset.\n\n    Args:\n        variant_annotation (VariantAnnotation): Variant annotation dataset\n        study_locus (StudyLocus): Study locus dataset with the variants to intersect with the variant annotation dataset\n\n    Returns:\n        VariantIndex: Variant index dataset\n    \"\"\"\n    unchanged_cols = [\n        \"variantId\",\n        \"chromosome\",\n        \"position\",\n        \"referenceAllele\",\n        \"alternateAllele\",\n        \"chromosomeB37\",\n        \"positionB37\",\n        \"alleleType\",\n        \"alleleFrequencies\",\n        \"inSilicoPredictors\",\n    ]\n    va_slimmed = variant_annotation.filter_by_variant_df(\n        study_locus.unique_variants_in_locus()\n    )\n    return cls(\n        _df=(\n            va_slimmed.df.select(\n                *unchanged_cols,\n                f.col(\"vep.mostSevereConsequence\").alias(\"mostSevereConsequence\"),\n                # filters/rsid are arrays that can be empty, in this case we convert them to null\n                nullify_empty_array(f.col(\"rsIds\")).alias(\"rsIds\"),\n            )\n            .repartition(400, \"chromosome\")\n            .sortWithinPartitions(\"chromosome\", \"position\")\n        ),\n        _schema=cls.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/dataset/variant_index/#otg.dataset.variant_index.VariantIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the VariantIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the VariantIndex dataset</p> Source code in <code>src/otg/dataset/variant_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[VariantIndex]) -&gt; StructType:\n    \"\"\"Provides the schema for the VariantIndex dataset.\n\n    Returns:\n        StructType: Schema for the VariantIndex dataset\n    \"\"\"\n    return parse_spark_schema(\"variant_index.json\")\n</code></pre>"},{"location":"python_api/dataset/variant_index/#schema","title":"Schema","text":"<pre><code>root\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- position: integer (nullable = false)\n |-- referenceAllele: string (nullable = false)\n |-- alternateAllele: string (nullable = false)\n |-- chromosomeB37: string (nullable = true)\n |-- positionB37: integer (nullable = true)\n |-- alleleType: string (nullable = false)\n |-- alleleFrequencies: array (nullable = false)\n |    |-- element: struct (containsNull = true)\n |    |    |-- populationName: string (nullable = true)\n |    |    |-- alleleFrequency: double (nullable = true)\n |-- inSilicoPredictors: struct (nullable = false)\n |    |-- cadd: struct (nullable = true)\n |    |    |-- raw: float (nullable = true)\n |    |    |-- phred: float (nullable = true)\n |    |-- revelMax: double (nullable = true)\n |    |-- spliceaiDsMax: float (nullable = true)\n |    |-- pangolinLargestDs: double (nullable = true)\n |    |-- phylop: double (nullable = true)\n |    |-- siftMax: double (nullable = true)\n |    |-- polyphenMax: double (nullable = true)\n |-- mostSevereConsequence: string (nullable = true)\n |-- rsIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n</code></pre>"},{"location":"python_api/dataset/variant_to_gene/","title":"Variant-to-gene","text":""},{"location":"python_api/dataset/variant_to_gene/#otg.dataset.v2g.V2G","title":"<code>otg.dataset.v2g.V2G</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Variant-to-gene (V2G) evidence dataset.</p> <p>A variant-to-gene (V2G) evidence is understood as any piece of evidence that supports the association of a variant with a likely causal gene. The evidence can sometimes be context-specific and refer to specific <code>biofeatures</code> (e.g. cell types)</p> Source code in <code>src/otg/dataset/v2g.py</code> <pre><code>@dataclass\nclass V2G(Dataset):\n    \"\"\"Variant-to-gene (V2G) evidence dataset.\n\n    A variant-to-gene (V2G) evidence is understood as any piece of evidence that supports the association of a variant with a likely causal gene. The evidence can sometimes be context-specific and refer to specific `biofeatures` (e.g. cell types)\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[V2G]) -&gt; StructType:\n        \"\"\"Provides the schema for the V2G dataset.\n\n        Returns:\n            StructType: Schema for the V2G dataset\n        \"\"\"\n        return parse_spark_schema(\"v2g.json\")\n\n    def filter_by_genes(self: V2G, genes: GeneIndex) -&gt; V2G:\n        \"\"\"Filter V2G dataset by genes.\n\n        Args:\n            genes (GeneIndex): Gene index dataset to filter by\n\n        Returns:\n            V2G: V2G dataset filtered by genes\n        \"\"\"\n        self.df = self._df.join(genes.df.select(\"geneId\"), on=\"geneId\", how=\"inner\")\n        return self\n\n    def extract_distance_tss_minimum(self: V2G) -&gt; None:\n        \"\"\"Extract minimum distance to TSS.\"\"\"\n        self.df = self._df.filter(f.col(\"distance\")).withColumn(\n            \"distanceTssMinimum\",\n            f.expr(\"min(distTss) OVER (PARTITION BY studyLocusId)\"),\n        )\n</code></pre>"},{"location":"python_api/dataset/variant_to_gene/#otg.dataset.v2g.V2G.extract_distance_tss_minimum","title":"<code>extract_distance_tss_minimum() -&gt; None</code>","text":"<p>Extract minimum distance to TSS.</p> Source code in <code>src/otg/dataset/v2g.py</code> <pre><code>def extract_distance_tss_minimum(self: V2G) -&gt; None:\n    \"\"\"Extract minimum distance to TSS.\"\"\"\n    self.df = self._df.filter(f.col(\"distance\")).withColumn(\n        \"distanceTssMinimum\",\n        f.expr(\"min(distTss) OVER (PARTITION BY studyLocusId)\"),\n    )\n</code></pre>"},{"location":"python_api/dataset/variant_to_gene/#otg.dataset.v2g.V2G.filter_by_genes","title":"<code>filter_by_genes(genes: GeneIndex) -&gt; V2G</code>","text":"<p>Filter V2G dataset by genes.</p> <p>Parameters:</p> Name Type Description Default <code>genes</code> <code>GeneIndex</code> <p>Gene index dataset to filter by</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>V2G dataset filtered by genes</p> Source code in <code>src/otg/dataset/v2g.py</code> <pre><code>def filter_by_genes(self: V2G, genes: GeneIndex) -&gt; V2G:\n    \"\"\"Filter V2G dataset by genes.\n\n    Args:\n        genes (GeneIndex): Gene index dataset to filter by\n\n    Returns:\n        V2G: V2G dataset filtered by genes\n    \"\"\"\n    self.df = self._df.join(genes.df.select(\"geneId\"), on=\"geneId\", how=\"inner\")\n    return self\n</code></pre>"},{"location":"python_api/dataset/variant_to_gene/#otg.dataset.v2g.V2G.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the V2G dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the V2G dataset</p> Source code in <code>src/otg/dataset/v2g.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[V2G]) -&gt; StructType:\n    \"\"\"Provides the schema for the V2G dataset.\n\n    Returns:\n        StructType: Schema for the V2G dataset\n    \"\"\"\n    return parse_spark_schema(\"v2g.json\")\n</code></pre>"},{"location":"python_api/dataset/variant_to_gene/#schema","title":"Schema","text":"<pre><code>root\n |-- geneId: string (nullable = false)\n |-- variantId: string (nullable = false)\n |-- distance: long (nullable = true)\n |-- chromosome: string (nullable = false)\n |-- datatypeId: string (nullable = false)\n |-- datasourceId: string (nullable = false)\n |-- score: double (nullable = true)\n |-- resourceScore: double (nullable = true)\n |-- pmid: string (nullable = true)\n |-- biofeature: string (nullable = true)\n |-- variantFunctionalConsequenceId: string (nullable = true)\n |-- isHighQualityPlof: boolean (nullable = true)\n</code></pre>"},{"location":"python_api/datasource/_datasource/","title":"Data Source","text":"<p>TBC</p>"},{"location":"python_api/datasource/eqtl_catalogue/study_index/","title":"Study Index","text":""},{"location":"python_api/datasource/eqtl_catalogue/study_index/#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex","title":"<code>otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex</code>","text":"<p>Study index dataset from eQTL Catalogue.</p> Source code in <code>src/otg/datasource/eqtl_catalogue/study_index.py</code> <pre><code>class EqtlCatalogueStudyIndex:\n    \"\"\"Study index dataset from eQTL Catalogue.\"\"\"\n\n    @staticmethod\n    def _all_attributes() -&gt; List[Column]:\n        \"\"\"A helper function to return all study index attribute expressions.\n\n        Returns:\n            List[Column]: all study index attribute expressions.\n        \"\"\"\n        study_attributes = [\n            # Project ID, example: \"GTEx_V8\".\n            f.col(\"study\").alias(\"projectId\"),\n            # Partial study ID, example: \"GTEx_V8_Adipose_Subcutaneous\". This ID will be converted to final only when\n            # summary statistics are parsed, because it must also include a gene ID.\n            f.concat(f.col(\"study\"), f.lit(\"_\"), f.col(\"qtl_group\")).alias(\"studyId\"),\n            # Summary stats location.\n            f.col(\"ftp_path\").alias(\"summarystatsLocation\"),\n            # Constant value fields.\n            f.lit(True).alias(\"hasSumstats\"),\n            f.lit(\"eqtl\").alias(\"studyType\"),\n        ]\n        tissue_attributes = [\n            # Human readable tissue label, example: \"Adipose - Subcutaneous\".\n            f.col(\"tissue_label\").alias(\"traitFromSource\"),\n            # Ontology identifier for the tissue, for example: \"UBERON:0001157\".\n            f.array(\n                f.regexp_replace(\n                    f.regexp_replace(\n                        f.col(\"tissue_ontology_id\"),\n                        \"UBER_\",\n                        \"UBERON_\",\n                    ),\n                    \"_\",\n                    \":\",\n                )\n            ).alias(\"traitFromSourceMappedIds\"),\n        ]\n        sample_attributes = [\n            f.lit(838).cast(\"long\").alias(\"nSamples\"),\n            f.lit(\"838 (281 females and 557 males)\").alias(\"initialSampleSize\"),\n            f.array(\n                f.struct(\n                    f.lit(715).cast(\"long\").alias(\"sampleSize\"),\n                    f.lit(\"European American\").alias(\"ancestry\"),\n                ),\n                f.struct(\n                    f.lit(103).cast(\"long\").alias(\"sampleSize\"),\n                    f.lit(\"African American\").alias(\"ancestry\"),\n                ),\n                f.struct(\n                    f.lit(12).cast(\"long\").alias(\"sampleSize\"),\n                    f.lit(\"Asian American\").alias(\"ancestry\"),\n                ),\n                f.struct(\n                    f.lit(16).cast(\"long\").alias(\"sampleSize\"),\n                    f.lit(\"Hispanic or Latino\").alias(\"ancestry\"),\n                ),\n            ).alias(\"discoverySamples\"),\n        ]\n        publication_attributes = [\n            f.lit(\"32913098\").alias(\"pubmedId\"),\n            f.lit(\n                \"The GTEx Consortium atlas of genetic regulatory effects across human tissues\"\n            ).alias(\"publicationTitle\"),\n            f.lit(\"GTEx Consortium\").alias(\"publicationFirstAuthor\"),\n            f.lit(\"2020-09-11\").alias(\"publicationDate\"),\n            f.lit(\"Science\").alias(\"publicationJournal\"),\n        ]\n        return (\n            study_attributes\n            + tissue_attributes\n            + sample_attributes\n            + publication_attributes\n        )\n\n    @classmethod\n    def from_source(\n        cls: type[EqtlCatalogueStudyIndex],\n        eqtl_studies: DataFrame,\n    ) -&gt; StudyIndex:\n        \"\"\"Ingest study level metadata from eQTL Catalogue.\n\n        Args:\n            eqtl_studies (DataFrame): ingested but unprocessed eQTL Catalogue studies.\n\n        Returns:\n            StudyIndex: preliminary processed study index for eQTL Catalogue studies.\n        \"\"\"\n        return StudyIndex(\n            _df=eqtl_studies.select(*cls._all_attributes()).withColumn(\n                \"ldPopulationStructure\",\n                StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n            ),\n            _schema=StudyIndex.get_schema(),\n        )\n\n    @classmethod\n    def add_gene_id_column(\n        cls: type[EqtlCatalogueStudyIndex],\n        study_index_df: DataFrame,\n        summary_stats_df: DataFrame,\n    ) -&gt; StudyIndex:\n        \"\"\"Add a geneId column to the study index and explode.\n\n        While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for\n        an expression of a _particular gene_ in a particular study.  At this stage we have a study index with partial\n        study IDs like \"PROJECT_QTLGROUP\", and a summary statistics object with full study IDs like\n        \"PROJECT_QTLGROUP_GENEID\", so we need to perform a merge and explosion to obtain our final study index.\n\n        Args:\n            study_index_df (DataFrame): preliminary study index for eQTL Catalogue studies.\n            summary_stats_df (DataFrame): summary statistics dataframe for eQTL Catalogue data.\n\n        Returns:\n            StudyIndex: final study index for eQTL Catalogue studies.\n        \"\"\"\n        partial_to_full_study_id = (\n            summary_stats_df.select(f.col(\"studyId\"))\n            .distinct()\n            .select(\n                f.col(\"studyId\").alias(\"fullStudyId\"),  # PROJECT_QTLGROUP_GENEID\n                f.regexp_extract(f.col(\"studyId\"), r\"(.*)_[\\_]+\", 1).alias(\n                    \"studyId\"\n                ),  # PROJECT_QTLGROUP\n            )\n            .groupBy(\"studyId\")\n            .agg(f.collect_list(\"fullStudyId\").alias(\"fullStudyIdList\"))\n        )\n        study_index_df = (\n            study_index_df.join(partial_to_full_study_id, \"studyId\", \"inner\")\n            .withColumn(\"fullStudyId\", f.explode(\"fullStudyIdList\"))\n            .drop(\"fullStudyIdList\")\n            .withColumn(\"geneId\", f.regexp_extract(f.col(\"studyId\"), r\".*_([\\_]+)\", 1))\n            .drop(\"fullStudyId\")\n        )\n        return StudyIndex(_df=study_index_df, _schema=StudyIndex.get_schema())\n</code></pre>"},{"location":"python_api/datasource/eqtl_catalogue/study_index/#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_id_column","title":"<code>add_gene_id_column(study_index_df: DataFrame, summary_stats_df: DataFrame) -&gt; StudyIndex</code>  <code>classmethod</code>","text":"<p>Add a geneId column to the study index and explode.</p> <p>While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for an expression of a particular gene in a particular study.  At this stage we have a study index with partial study IDs like \"PROJECT_QTLGROUP\", and a summary statistics object with full study IDs like \"PROJECT_QTLGROUP_GENEID\", so we need to perform a merge and explosion to obtain our final study index.</p> <p>Parameters:</p> Name Type Description Default <code>study_index_df</code> <code>DataFrame</code> <p>preliminary study index for eQTL Catalogue studies.</p> required <code>summary_stats_df</code> <code>DataFrame</code> <p>summary statistics dataframe for eQTL Catalogue data.</p> required <p>Returns:</p> Name Type Description <code>StudyIndex</code> <code>StudyIndex</code> <p>final study index for eQTL Catalogue studies.</p> Source code in <code>src/otg/datasource/eqtl_catalogue/study_index.py</code> <pre><code>@classmethod\ndef add_gene_id_column(\n    cls: type[EqtlCatalogueStudyIndex],\n    study_index_df: DataFrame,\n    summary_stats_df: DataFrame,\n) -&gt; StudyIndex:\n    \"\"\"Add a geneId column to the study index and explode.\n\n    While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for\n    an expression of a _particular gene_ in a particular study.  At this stage we have a study index with partial\n    study IDs like \"PROJECT_QTLGROUP\", and a summary statistics object with full study IDs like\n    \"PROJECT_QTLGROUP_GENEID\", so we need to perform a merge and explosion to obtain our final study index.\n\n    Args:\n        study_index_df (DataFrame): preliminary study index for eQTL Catalogue studies.\n        summary_stats_df (DataFrame): summary statistics dataframe for eQTL Catalogue data.\n\n    Returns:\n        StudyIndex: final study index for eQTL Catalogue studies.\n    \"\"\"\n    partial_to_full_study_id = (\n        summary_stats_df.select(f.col(\"studyId\"))\n        .distinct()\n        .select(\n            f.col(\"studyId\").alias(\"fullStudyId\"),  # PROJECT_QTLGROUP_GENEID\n            f.regexp_extract(f.col(\"studyId\"), r\"(.*)_[\\_]+\", 1).alias(\n                \"studyId\"\n            ),  # PROJECT_QTLGROUP\n        )\n        .groupBy(\"studyId\")\n        .agg(f.collect_list(\"fullStudyId\").alias(\"fullStudyIdList\"))\n    )\n    study_index_df = (\n        study_index_df.join(partial_to_full_study_id, \"studyId\", \"inner\")\n        .withColumn(\"fullStudyId\", f.explode(\"fullStudyIdList\"))\n        .drop(\"fullStudyIdList\")\n        .withColumn(\"geneId\", f.regexp_extract(f.col(\"studyId\"), r\".*_([\\_]+)\", 1))\n        .drop(\"fullStudyId\")\n    )\n    return StudyIndex(_df=study_index_df, _schema=StudyIndex.get_schema())\n</code></pre>"},{"location":"python_api/datasource/eqtl_catalogue/study_index/#otg.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source","title":"<code>from_source(eqtl_studies: DataFrame) -&gt; StudyIndex</code>  <code>classmethod</code>","text":"<p>Ingest study level metadata from eQTL Catalogue.</p> <p>Parameters:</p> Name Type Description Default <code>eqtl_studies</code> <code>DataFrame</code> <p>ingested but unprocessed eQTL Catalogue studies.</p> required <p>Returns:</p> Name Type Description <code>StudyIndex</code> <code>StudyIndex</code> <p>preliminary processed study index for eQTL Catalogue studies.</p> Source code in <code>src/otg/datasource/eqtl_catalogue/study_index.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[EqtlCatalogueStudyIndex],\n    eqtl_studies: DataFrame,\n) -&gt; StudyIndex:\n    \"\"\"Ingest study level metadata from eQTL Catalogue.\n\n    Args:\n        eqtl_studies (DataFrame): ingested but unprocessed eQTL Catalogue studies.\n\n    Returns:\n        StudyIndex: preliminary processed study index for eQTL Catalogue studies.\n    \"\"\"\n    return StudyIndex(\n        _df=eqtl_studies.select(*cls._all_attributes()).withColumn(\n            \"ldPopulationStructure\",\n            StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n        ),\n        _schema=StudyIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/eqtl_catalogue/summary_stats/","title":"Summary Stats","text":""},{"location":"python_api/datasource/eqtl_catalogue/summary_stats/#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats","title":"<code>otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats</code>  <code>dataclass</code>","text":"<p>Summary statistics dataset for eQTL Catalogue.</p> Source code in <code>src/otg/datasource/eqtl_catalogue/summary_stats.py</code> <pre><code>@dataclass\nclass EqtlCatalogueSummaryStats:\n    \"\"\"Summary statistics dataset for eQTL Catalogue.\"\"\"\n\n    @staticmethod\n    def _full_study_id_regexp() -&gt; Column:\n        \"\"\"Constructs a full study ID from the URI.\n\n        Returns:\n            Column: expression to extract a full study ID from the URI.\n        \"\"\"\n        # Example of a URI which is used for parsing:\n        # \"gs://genetics_etl_python_playground/input/preprocess/eqtl_catalogue/imported/GTEx_V8/ge/Adipose_Subcutaneous.tsv.gz\".\n\n        # Regular expession to extract project ID from URI.  Example: \"GTEx_V8\".\n        _project_id = f.regexp_extract(\n            f.input_file_name(),\n            r\"imported/([^/]+)/.*\",\n            1,\n        )\n        # Regular expression to extract QTL group from URI.  Example: \"Adipose_Subcutaneous\".\n        _qtl_group = f.regexp_extract(f.input_file_name(), r\"([^/]+)\\.tsv\\.gz\", 1)\n        # Extracting gene ID from the column.  Example: \"ENSG00000225630\".\n        _gene_id = f.col(\"gene_id\")\n\n        # We can now construct the full study ID based on all fields.\n        # Example: \"GTEx_V8_Adipose_Subcutaneous_ENSG00000225630\".\n        return f.concat(_project_id, f.lit(\"_\"), _qtl_group, f.lit(\"_\"), _gene_id)\n\n    @classmethod\n    def from_source(\n        cls: type[EqtlCatalogueSummaryStats],\n        summary_stats_df: DataFrame,\n    ) -&gt; SummaryStatistics:\n        \"\"\"Ingests all summary stats for all eQTL Catalogue studies.\n\n        Args:\n            summary_stats_df (DataFrame): an ingested but unprocessed summary statistics dataframe from eQTL Catalogue.\n\n        Returns:\n            SummaryStatistics: a processed summary statistics dataframe for eQTL Catalogue.\n        \"\"\"\n        processed_summary_stats_df = (\n            summary_stats_df.select(\n                # Construct study ID from the appropriate columns.\n                cls._full_study_id_regexp().alias(\"studyId\"),\n                # Add variant information.\n                f.concat_ws(\n                    \"_\",\n                    f.col(\"chromosome\"),\n                    f.col(\"position\"),\n                    f.col(\"ref\"),\n                    f.col(\"alt\"),\n                ).alias(\"variantId\"),\n                f.col(\"chromosome\"),\n                f.col(\"position\").cast(t.IntegerType()),\n                # Parse p-value into mantissa and exponent.\n                *parse_pvalue(f.col(\"pvalue\")),\n                # Add beta, standard error, and allele frequency information.\n                f.col(\"beta\").cast(\"double\"),\n                f.col(\"se\").cast(\"double\").alias(\"standardError\"),\n                f.col(\"maf\").cast(\"float\").alias(\"effectAlleleFrequencyFromSource\"),\n            )\n            # Drop rows which don't have proper position or beta value.\n            .filter(\n                f.col(\"position\").cast(t.IntegerType()).isNotNull()\n                &amp; (f.col(\"beta\") != 0)\n            )\n        )\n\n        # Initialise a summary statistics object.\n        return SummaryStatistics(\n            _df=processed_summary_stats_df,\n            _schema=SummaryStatistics.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/eqtl_catalogue/summary_stats/#otg.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source","title":"<code>from_source(summary_stats_df: DataFrame) -&gt; SummaryStatistics</code>  <code>classmethod</code>","text":"<p>Ingests all summary stats for all eQTL Catalogue studies.</p> <p>Parameters:</p> Name Type Description Default <code>summary_stats_df</code> <code>DataFrame</code> <p>an ingested but unprocessed summary statistics dataframe from eQTL Catalogue.</p> required <p>Returns:</p> Name Type Description <code>SummaryStatistics</code> <code>SummaryStatistics</code> <p>a processed summary statistics dataframe for eQTL Catalogue.</p> Source code in <code>src/otg/datasource/eqtl_catalogue/summary_stats.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[EqtlCatalogueSummaryStats],\n    summary_stats_df: DataFrame,\n) -&gt; SummaryStatistics:\n    \"\"\"Ingests all summary stats for all eQTL Catalogue studies.\n\n    Args:\n        summary_stats_df (DataFrame): an ingested but unprocessed summary statistics dataframe from eQTL Catalogue.\n\n    Returns:\n        SummaryStatistics: a processed summary statistics dataframe for eQTL Catalogue.\n    \"\"\"\n    processed_summary_stats_df = (\n        summary_stats_df.select(\n            # Construct study ID from the appropriate columns.\n            cls._full_study_id_regexp().alias(\"studyId\"),\n            # Add variant information.\n            f.concat_ws(\n                \"_\",\n                f.col(\"chromosome\"),\n                f.col(\"position\"),\n                f.col(\"ref\"),\n                f.col(\"alt\"),\n            ).alias(\"variantId\"),\n            f.col(\"chromosome\"),\n            f.col(\"position\").cast(t.IntegerType()),\n            # Parse p-value into mantissa and exponent.\n            *parse_pvalue(f.col(\"pvalue\")),\n            # Add beta, standard error, and allele frequency information.\n            f.col(\"beta\").cast(\"double\"),\n            f.col(\"se\").cast(\"double\").alias(\"standardError\"),\n            f.col(\"maf\").cast(\"float\").alias(\"effectAlleleFrequencyFromSource\"),\n        )\n        # Drop rows which don't have proper position or beta value.\n        .filter(\n            f.col(\"position\").cast(t.IntegerType()).isNotNull()\n            &amp; (f.col(\"beta\") != 0)\n        )\n    )\n\n    # Initialise a summary statistics object.\n    return SummaryStatistics(\n        _df=processed_summary_stats_df,\n        _schema=SummaryStatistics.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/finngen/_finngen/","title":"FinnGen","text":"<p>FinnGen is a research project in genomics and personalized medicine. It is large public-private partnership that has collected and analysed genome and health data from 500,000 Finnish biobank donors to understand the genetic basis of diseases. FinnGen is a now expanding into understanding the progression and biological mechanisms of diseases. FinnGen provides a world-class resource for further breakthroughs in disease prevention, diagnosis, and treatment and a outlook into our genetic make-up.</p>"},{"location":"python_api/datasource/finngen/study_index/","title":"Study Index","text":""},{"location":"python_api/datasource/finngen/study_index/#otg.datasource.finngen.study_index.FinnGenStudyIndex","title":"<code>otg.datasource.finngen.study_index.FinnGenStudyIndex</code>","text":"<p>Study index dataset from FinnGen.</p> <p>The following information is aggregated/extracted:</p> <ul> <li>Study ID in the special format (FINNGEN_R9_*)</li> <li>Trait name (for example, Amoebiasis)</li> <li>Number of cases and controls</li> <li>Link to the summary statistics location</li> </ul> <p>Some fields are also populated as constants, such as study type and the initial sample size.</p> Source code in <code>src/otg/datasource/finngen/study_index.py</code> <pre><code>class FinnGenStudyIndex:\n    \"\"\"Study index dataset from FinnGen.\n\n    The following information is aggregated/extracted:\n\n    - Study ID in the special format (FINNGEN_R9_*)\n    - Trait name (for example, Amoebiasis)\n    - Number of cases and controls\n    - Link to the summary statistics location\n\n    Some fields are also populated as constants, such as study type and the initial sample size.\n    \"\"\"\n\n    finngen_phenotype_table_url: str = \"https://r9.finngen.fi/api/phenos\"\n    finngen_release_prefix: str = \"FINNGEN_R9\"\n    finngen_summary_stats_url_prefix: str = (\n        \"gs://finngen-public-data-r9/summary_stats/finngen_R9_\"\n    )\n    finngen_summary_stats_url_suffix: str = \".gz\"\n\n    @classmethod\n    def from_source(\n        cls: type[FinnGenStudyIndex],\n        spark: SparkSession,\n    ) -&gt; StudyIndex:\n        \"\"\"This function ingests study level metadata from FinnGen.\n\n        Args:\n            spark (SparkSession): Spark session object.\n\n        Returns:\n            StudyIndex: Parsed and annotated FinnGen study table.\n        \"\"\"\n        json_data = urlopen(cls.finngen_phenotype_table_url).read().decode(\"utf-8\")\n        rdd = spark.sparkContext.parallelize([json_data])\n        raw_df = spark.read.json(rdd)\n        return StudyIndex(\n            _df=raw_df.select(\n                f.concat(\n                    f.lit(f\"{cls.finngen_release_prefix}_\"), f.col(\"phenocode\")\n                ).alias(\"studyId\"),\n                f.col(\"phenostring\").alias(\"traitFromSource\"),\n                f.col(\"num_cases\").alias(\"nCases\"),\n                f.col(\"num_controls\").alias(\"nControls\"),\n                (f.col(\"num_cases\") + f.col(\"num_controls\")).alias(\"nSamples\"),\n                f.lit(cls.finngen_release_prefix).alias(\"projectId\"),\n                f.lit(\"gwas\").alias(\"studyType\"),\n                f.lit(True).alias(\"hasSumstats\"),\n                f.lit(\"377,277 (210,870 females and 166,407 males)\").alias(\n                    \"initialSampleSize\"\n                ),\n                f.array(\n                    f.struct(\n                        f.lit(377277).cast(\"long\").alias(\"sampleSize\"),\n                        f.lit(\"Finnish\").alias(\"ancestry\"),\n                    )\n                ).alias(\"discoverySamples\"),\n                # Cohort label is consistent with GWAS Catalog curation.\n                f.array(f.lit(\"FinnGen\")).alias(\"cohorts\"),\n                f.concat(\n                    f.lit(cls.finngen_summary_stats_url_prefix),\n                    f.col(\"phenocode\"),\n                    f.lit(cls.finngen_summary_stats_url_suffix),\n                ).alias(\"summarystatsLocation\"),\n            ).withColumn(\n                \"ldPopulationStructure\",\n                StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n            ),\n            _schema=StudyIndex.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/finngen/study_index/#otg.datasource.finngen.study_index.FinnGenStudyIndex.from_source","title":"<code>from_source(spark: SparkSession) -&gt; StudyIndex</code>  <code>classmethod</code>","text":"<p>This function ingests study level metadata from FinnGen.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session object.</p> required <p>Returns:</p> Name Type Description <code>StudyIndex</code> <code>StudyIndex</code> <p>Parsed and annotated FinnGen study table.</p> Source code in <code>src/otg/datasource/finngen/study_index.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[FinnGenStudyIndex],\n    spark: SparkSession,\n) -&gt; StudyIndex:\n    \"\"\"This function ingests study level metadata from FinnGen.\n\n    Args:\n        spark (SparkSession): Spark session object.\n\n    Returns:\n        StudyIndex: Parsed and annotated FinnGen study table.\n    \"\"\"\n    json_data = urlopen(cls.finngen_phenotype_table_url).read().decode(\"utf-8\")\n    rdd = spark.sparkContext.parallelize([json_data])\n    raw_df = spark.read.json(rdd)\n    return StudyIndex(\n        _df=raw_df.select(\n            f.concat(\n                f.lit(f\"{cls.finngen_release_prefix}_\"), f.col(\"phenocode\")\n            ).alias(\"studyId\"),\n            f.col(\"phenostring\").alias(\"traitFromSource\"),\n            f.col(\"num_cases\").alias(\"nCases\"),\n            f.col(\"num_controls\").alias(\"nControls\"),\n            (f.col(\"num_cases\") + f.col(\"num_controls\")).alias(\"nSamples\"),\n            f.lit(cls.finngen_release_prefix).alias(\"projectId\"),\n            f.lit(\"gwas\").alias(\"studyType\"),\n            f.lit(True).alias(\"hasSumstats\"),\n            f.lit(\"377,277 (210,870 females and 166,407 males)\").alias(\n                \"initialSampleSize\"\n            ),\n            f.array(\n                f.struct(\n                    f.lit(377277).cast(\"long\").alias(\"sampleSize\"),\n                    f.lit(\"Finnish\").alias(\"ancestry\"),\n                )\n            ).alias(\"discoverySamples\"),\n            # Cohort label is consistent with GWAS Catalog curation.\n            f.array(f.lit(\"FinnGen\")).alias(\"cohorts\"),\n            f.concat(\n                f.lit(cls.finngen_summary_stats_url_prefix),\n                f.col(\"phenocode\"),\n                f.lit(cls.finngen_summary_stats_url_suffix),\n            ).alias(\"summarystatsLocation\"),\n        ).withColumn(\n            \"ldPopulationStructure\",\n            StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n        ),\n        _schema=StudyIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/gnomad/_gnomad/","title":"GnomAD","text":""},{"location":"python_api/datasource/gnomad/gnomad_ld/","title":"LD Matrix","text":""},{"location":"python_api/datasource/gnomad/gnomad_ld/#otg.datasource.gnomad.ld.GnomADLDMatrix","title":"<code>otg.datasource.gnomad.ld.GnomADLDMatrix</code>  <code>dataclass</code>","text":"<p>Toolset ot interact with GnomAD LD dataset (version: r2.1.1).</p> <p>Datasets are accessed in Hail's native format, as provided by the GnomAD consortium.</p> <p>Attributes:</p> Name Type Description <code>ld_matrix_template</code> <code>str</code> <p>Template for the LD matrix path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm\".</p> <code>ld_index_raw_template</code> <code>str</code> <p>Template for the LD index path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht\".</p> <code>grch37_to_grch38_chain_path</code> <code>str</code> <p>Path to the chain file used to lift over the coordinates. Defaults to \"gs://hail-common/references/grch37_to_grch38.over.chain.gz\".</p> <code>ld_populations</code> <code>list[str]</code> <p>List of populations to use to build the LDIndex. Defaults to [\"afr\", \"amr\", \"asj\", \"eas\", \"fin\", \"nfe\", \"nwe\", \"seu\"].</p> Source code in <code>src/otg/datasource/gnomad/ld.py</code> <pre><code>@dataclass\nclass GnomADLDMatrix:\n    \"\"\"Toolset ot interact with GnomAD LD dataset (version: r2.1.1).\n\n    Datasets are accessed in Hail's native format, as provided by the [GnomAD consortium](https://gnomad.broadinstitute.org/downloads/#v2-linkage-disequilibrium).\n\n    Attributes:\n        ld_matrix_template (str): Template for the LD matrix path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm\".\n        ld_index_raw_template (str): Template for the LD index path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht\".\n        grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates. Defaults to \"gs://hail-common/references/grch37_to_grch38.over.chain.gz\".\n        ld_populations (list[str]): List of populations to use to build the LDIndex. Defaults to [\"afr\", \"amr\", \"asj\", \"eas\", \"fin\", \"nfe\", \"nwe\", \"seu\"].\n    \"\"\"\n\n    ld_matrix_template: str = \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm\"\n    ld_index_raw_template: str = \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht\"\n    grch37_to_grch38_chain_path: str = (\n        \"gs://hail-common/references/grch37_to_grch38.over.chain.gz\"\n    )\n    ld_populations: list[str] = field(\n        default_factory=lambda: [\n            \"afr\",  # African-American\n            \"amr\",  # American Admixed/Latino\n            \"asj\",  # Ashkenazi Jewish\n            \"eas\",  # East Asian\n            \"fin\",  # Finnish\n            \"nfe\",  # Non-Finnish European\n            \"nwe\",  # Northwestern European\n            \"seu\",  # Southeastern European\n        ]\n    )\n\n    @staticmethod\n    def _aggregate_ld_index_across_populations(\n        unaggregated_ld_index: DataFrame,\n    ) -&gt; DataFrame:\n        \"\"\"Aggregate LDIndex across populations.\n\n        Args:\n            unaggregated_ld_index (DataFrame): Unaggregate LDIndex index dataframe  each row is a variant pair in a population\n\n        Returns:\n            DataFrame: Aggregated LDIndex index dataframe  each row is a variant with the LD set across populations\n\n        Examples:\n            &gt;&gt;&gt; data = [(\"1.0\", \"var1\", \"X\", \"var1\", \"pop1\"), (\"1.0\", \"X\", \"var2\", \"var2\", \"pop1\"),\n            ...         (\"0.5\", \"var1\", \"X\", \"var2\", \"pop1\"), (\"0.5\", \"var1\", \"X\", \"var2\", \"pop2\"),\n            ...         (\"0.5\", \"var2\", \"X\", \"var1\", \"pop1\"), (\"0.5\", \"X\", \"var2\", \"var1\", \"pop2\")]\n            &gt;&gt;&gt; df = spark.createDataFrame(data, [\"r\", \"variantId\", \"chromosome\", \"tagvariantId\", \"population\"])\n            &gt;&gt;&gt; GnomADLDMatrix._aggregate_ld_index_across_populations(df).printSchema()\n            root\n             |-- variantId: string (nullable = true)\n             |-- chromosome: string (nullable = true)\n             |-- ldSet: array (nullable = false)\n             |    |-- element: struct (containsNull = false)\n             |    |    |-- tagVariantId: string (nullable = true)\n             |    |    |-- rValues: array (nullable = false)\n             |    |    |    |-- element: struct (containsNull = false)\n             |    |    |    |    |-- population: string (nullable = true)\n             |    |    |    |    |-- r: string (nullable = true)\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        return (\n            unaggregated_ld_index\n            # First level of aggregation: get r/population for each variant/tagVariant pair\n            .withColumn(\"r_pop_struct\", f.struct(\"population\", \"r\"))\n            .groupBy(\"chromosome\", \"variantId\", \"tagVariantId\")\n            .agg(\n                f.collect_set(\"r_pop_struct\").alias(\"rValues\"),\n            )\n            # Second level of aggregation: get r/population for each variant\n            .withColumn(\"r_pop_tag_struct\", f.struct(\"tagVariantId\", \"rValues\"))\n            .groupBy(\"variantId\", \"chromosome\")\n            .agg(\n                f.collect_set(\"r_pop_tag_struct\").alias(\"ldSet\"),\n            )\n        )\n\n    @staticmethod\n    def _convert_ld_matrix_to_table(\n        block_matrix: BlockMatrix, min_r2: float\n    ) -&gt; DataFrame:\n        \"\"\"Convert LD matrix to table.\n\n        Args:\n            block_matrix (BlockMatrix): LD matrix\n            min_r2 (float): Minimum r2 value to keep in the table\n\n        Returns:\n            DataFrame: LD matrix as a Spark DataFrame\n        \"\"\"\n        table = block_matrix.entries(keyed=False)\n        return (\n            table.filter(hl.abs(table.entry) &gt;= min_r2**0.5)\n            .to_spark()\n            .withColumnRenamed(\"entry\", \"r\")\n        )\n\n    @staticmethod\n    def _create_ldindex_for_population(\n        population_id: str,\n        ld_matrix_path: str,\n        ld_index_raw_path: str,\n        grch37_to_grch38_chain_path: str,\n        min_r2: float,\n    ) -&gt; DataFrame:\n        \"\"\"Create LDIndex for a specific population.\n\n        Args:\n            population_id (str): Population ID\n            ld_matrix_path (str): Path to the LD matrix\n            ld_index_raw_path (str): Path to the LD index\n            grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates\n            min_r2 (float): Minimum r2 value to keep in the table\n\n        Returns:\n            DataFrame: LDIndex for a specific population\n        \"\"\"\n        # Prepare LD Block matrix\n        ld_matrix = GnomADLDMatrix._convert_ld_matrix_to_table(\n            BlockMatrix.read(ld_matrix_path), min_r2\n        )\n\n        # Prepare table with variant indices\n        ld_index = GnomADLDMatrix._process_variant_indices(\n            hl.read_table(ld_index_raw_path),\n            grch37_to_grch38_chain_path,\n        )\n\n        return GnomADLDMatrix._resolve_variant_indices(ld_index, ld_matrix).select(\n            \"*\",\n            f.lit(population_id).alias(\"population\"),\n        )\n\n    @staticmethod\n    def _process_variant_indices(\n        ld_index_raw: hl.Table, grch37_to_grch38_chain_path: str\n    ) -&gt; DataFrame:\n        \"\"\"Creates a look up table between variants and their coordinates in the LD Matrix.\n\n        !!! info \"Gnomad's LD Matrix and Index are based on GRCh37 coordinates. This function will lift over the coordinates to GRCh38 to build the lookup table.\"\n\n        Args:\n            ld_index_raw (hl.Table): LD index table from GnomAD\n            grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates\n\n        Returns:\n            DataFrame: Look up table between variants in build hg38 and their coordinates in the LD Matrix\n        \"\"\"\n        ld_index_38 = _liftover_loci(\n            ld_index_raw, grch37_to_grch38_chain_path, \"GRCh38\"\n        )\n\n        return (\n            ld_index_38.to_spark()\n            # Filter out variants where the liftover failed\n            .filter(f.col(\"`locus_GRCh38.position`\").isNotNull())\n            .withColumn(\n                \"chromosome\", f.regexp_replace(\"`locus_GRCh38.contig`\", \"chr\", \"\")\n            )\n            .withColumn(\n                \"position\",\n                convert_gnomad_position_to_ensembl(\n                    f.col(\"`locus_GRCh38.position`\"),\n                    f.col(\"`alleles`\").getItem(0),\n                    f.col(\"`alleles`\").getItem(1),\n                ),\n            )\n            .select(\n                \"chromosome\",\n                \"position\",\n                f.concat_ws(\n                    \"_\",\n                    f.col(\"chromosome\"),\n                    f.col(\"position\"),\n                    f.col(\"`alleles`\").getItem(0),\n                    f.col(\"`alleles`\").getItem(1),\n                ).alias(\"variantId\"),\n                f.col(\"idx\"),\n            )\n            # Filter out ambiguous liftover results: multiple indices for the same variant\n            .withColumn(\"count\", f.count(\"*\").over(Window.partitionBy([\"variantId\"])))\n            .filter(f.col(\"count\") == 1)\n            .drop(\"count\")\n        )\n\n    @staticmethod\n    def _resolve_variant_indices(\n        ld_index: DataFrame, ld_matrix: DataFrame\n    ) -&gt; DataFrame:\n        \"\"\"Resolve the `i` and `j` indices of the block matrix to variant IDs (build 38).\n\n        Args:\n            ld_index (DataFrame): Dataframe with resolved variant indices\n            ld_matrix (DataFrame): Dataframe with the filtered LD matrix\n\n        Returns:\n            DataFrame: Dataframe with variant IDs instead of `i` and `j` indices\n        \"\"\"\n        ld_index_i = ld_index.selectExpr(\n            \"idx as i\", \"variantId as variantId_i\", \"chromosome\"\n        )\n        ld_index_j = ld_index.selectExpr(\"idx as j\", \"variantId as variantId_j\")\n        return (\n            ld_matrix.join(ld_index_i, on=\"i\", how=\"inner\")\n            .join(ld_index_j, on=\"j\", how=\"inner\")\n            .drop(\"i\", \"j\")\n        )\n\n    @staticmethod\n    def _transpose_ld_matrix(ld_matrix: DataFrame) -&gt; DataFrame:\n        \"\"\"Transpose LD matrix to a square matrix format.\n\n        Args:\n            ld_matrix (DataFrame): Triangular LD matrix converted to a Spark DataFrame\n\n        Returns:\n            DataFrame: Square LD matrix without diagonal duplicates\n\n        Examples:\n            &gt;&gt;&gt; df = spark.createDataFrame(\n            ...     [\n            ...         (1, 1, 1.0, \"1\", \"AFR\"),\n            ...         (1, 2, 0.5, \"1\", \"AFR\"),\n            ...         (2, 2, 1.0, \"1\", \"AFR\"),\n            ...     ],\n            ...     [\"variantId_i\", \"variantId_j\", \"r\", \"chromosome\", \"population\"],\n            ... )\n            &gt;&gt;&gt; GnomADLDMatrix._transpose_ld_matrix(df).show()\n            +-----------+-----------+---+----------+----------+\n            |variantId_i|variantId_j|  r|chromosome|population|\n            +-----------+-----------+---+----------+----------+\n            |          1|          2|0.5|         1|       AFR|\n            |          1|          1|1.0|         1|       AFR|\n            |          2|          1|0.5|         1|       AFR|\n            |          2|          2|1.0|         1|       AFR|\n            +-----------+-----------+---+----------+----------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        ld_matrix_transposed = ld_matrix.selectExpr(\n            \"variantId_i as variantId_j\",\n            \"variantId_j as variantId_i\",\n            \"r\",\n            \"chromosome\",\n            \"population\",\n        )\n        return ld_matrix.filter(\n            f.col(\"variantId_i\") != f.col(\"variantId_j\")\n        ).unionByName(ld_matrix_transposed)\n\n    def as_ld_index(\n        self: GnomADLDMatrix,\n        min_r2: float,\n    ) -&gt; LDIndex:\n        \"\"\"Create LDIndex dataset aggregating the LD information across a set of populations.\n\n        **The basic steps to generate the LDIndex are:**\n\n        1. Convert LD matrix to a Spark DataFrame.\n        2. Resolve the matrix indices to variant IDs by lifting over the coordinates to GRCh38.\n        3. Aggregate the LD information across populations.\n\n        Args:\n            min_r2 (float): Minimum r2 value to keep in the table\n\n        Returns:\n            LDIndex: LDIndex dataset\n        \"\"\"\n        ld_indices_unaggregated = []\n        for pop in self.ld_populations:\n            try:\n                ld_matrix_path = self.ld_matrix_template.format(POP=pop)\n                ld_index_raw_path = self.ld_index_raw_template.format(POP=pop)\n                pop_ld_index = self._create_ldindex_for_population(\n                    pop,\n                    ld_matrix_path,\n                    ld_index_raw_path.format(pop),\n                    self.grch37_to_grch38_chain_path,\n                    min_r2,\n                )\n                ld_indices_unaggregated.append(pop_ld_index)\n            except Exception as e:\n                print(f\"Failed to create LDIndex for population {pop}: {e}\")  # noqa: T201\n                sys.exit(1)\n\n        ld_index_unaggregated = (\n            GnomADLDMatrix._transpose_ld_matrix(\n                reduce(lambda df1, df2: df1.unionByName(df2), ld_indices_unaggregated)\n            )\n            .withColumnRenamed(\"variantId_i\", \"variantId\")\n            .withColumnRenamed(\"variantId_j\", \"tagVariantId\")\n        )\n        return LDIndex(\n            _df=self._aggregate_ld_index_across_populations(ld_index_unaggregated),\n            _schema=LDIndex.get_schema(),\n        )\n\n    def get_ld_variants(\n        self: GnomADLDMatrix,\n        gnomad_ancestry: str,\n        chromosome: str,\n        start: int,\n        end: int,\n    ) -&gt; DataFrame | None:\n        \"\"\"Return melted LD table with resolved variant id based on ancestry and genomic location.\n\n        Args:\n            gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe`\n            chromosome (str): chromosome label\n            start (int): window upper bound\n            end (int): window lower bound\n\n        Returns:\n            DataFrame | None: LD table with resolved variant id based on ancestry and genomic location\n        \"\"\"\n        # Extracting locus:\n        ld_index_df = (\n            self._process_variant_indices(\n                hl.read_table(self.ld_index_raw_template.format(POP=gnomad_ancestry)),\n                self.grch37_to_grch38_chain_path,\n            )\n            .filter(\n                (f.col(\"chromosome\") == chromosome)\n                &amp; (f.col(\"position\") &gt;= start)\n                &amp; (f.col(\"position\") &lt;= end)\n            )\n            .select(\"chromosome\", \"position\", \"variantId\", \"idx\")\n            .persist()\n        )\n\n        if ld_index_df.limit(1).count() == 0:\n            # If the returned slice from the ld index is empty, return None\n            return None\n\n        # Compute start and end indices\n        start_index = get_value_from_row(\n            get_top_ranked_in_window(\n                ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").asc())\n            ).collect()[0],\n            \"idx\",\n        )\n        end_index = get_value_from_row(\n            get_top_ranked_in_window(\n                ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").desc())\n            ).collect()[0],\n            \"idx\",\n        )\n\n        return self._extract_square_matrix(\n            ld_index_df, gnomad_ancestry, start_index, end_index\n        )\n\n    def _extract_square_matrix(\n        self: GnomADLDMatrix,\n        ld_index_df: DataFrame,\n        gnomad_ancestry: str,\n        start_index: int,\n        end_index: int,\n    ) -&gt; DataFrame:\n        \"\"\"Return LD square matrix for a region where coordinates are normalised.\n\n        Args:\n            ld_index_df (DataFrame): Look up table between a variantId and its index in the LD matrix\n            gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe`\n            start_index (int): start index of the slice\n            end_index (int): end index of the slice\n\n        Returns:\n            DataFrame: square LD matrix resolved to variants.\n        \"\"\"\n        return (\n            self.get_ld_matrix_slice(\n                gnomad_ancestry, start_index=start_index, end_index=end_index\n            )\n            .join(\n                ld_index_df.select(\n                    f.col(\"idx\").alias(\"idx_i\"),\n                    f.col(\"variantId\").alias(\"variantId_i\"),\n                ),\n                on=\"idx_i\",\n                how=\"inner\",\n            )\n            .join(\n                ld_index_df.select(\n                    f.col(\"idx\").alias(\"idx_j\"),\n                    f.col(\"variantId\").alias(\"variantId_j\"),\n                ),\n                on=\"idx_j\",\n                how=\"inner\",\n            )\n            .select(\"variantId_i\", \"variantId_j\", \"r\")\n        )\n\n    def get_ld_matrix_slice(\n        self: GnomADLDMatrix,\n        gnomad_ancestry: str,\n        start_index: int,\n        end_index: int,\n    ) -&gt; DataFrame:\n        \"\"\"Extract a slice of the LD matrix based on the provided ancestry and stop and end indices.\n\n        - The half matrix is completed into a full square.\n        - The returned indices are adjusted based on the start index.\n\n        Args:\n            gnomad_ancestry (str): LD population label eg. `nfe`\n            start_index (int): start index of the slice\n            end_index (int): end index of the slice\n\n        Returns:\n            DataFrame: square slice of the LD matrix melted as dataframe with idx_i, idx_j and r columns\n        \"\"\"\n        # Extracting block matrix slice:\n        half_matrix = BlockMatrix.read(\n            self.ld_matrix_template.format(POP=gnomad_ancestry)\n        ).filter(range(start_index, end_index + 1), range(start_index, end_index + 1))\n\n        # Return converted Dataframe:\n        return (\n            (half_matrix + half_matrix.T)\n            .entries()\n            .to_spark()\n            .select(\n                (f.col(\"i\") + start_index).alias(\"idx_i\"),\n                (f.col(\"j\") + start_index).alias(\"idx_j\"),\n                f.when(f.col(\"i\") == f.col(\"j\"), f.col(\"entry\") / 2)\n                .otherwise(f.col(\"entry\"))\n                .alias(\"r\"),\n            )\n        )\n</code></pre>"},{"location":"python_api/datasource/gnomad/gnomad_ld/#otg.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index","title":"<code>as_ld_index(min_r2: float) -&gt; LDIndex</code>","text":"<p>Create LDIndex dataset aggregating the LD information across a set of populations.</p> <p>The basic steps to generate the LDIndex are:</p> <ol> <li>Convert LD matrix to a Spark DataFrame.</li> <li>Resolve the matrix indices to variant IDs by lifting over the coordinates to GRCh38.</li> <li>Aggregate the LD information across populations.</li> </ol> <p>Parameters:</p> Name Type Description Default <code>min_r2</code> <code>float</code> <p>Minimum r2 value to keep in the table</p> required <p>Returns:</p> Name Type Description <code>LDIndex</code> <code>LDIndex</code> <p>LDIndex dataset</p> Source code in <code>src/otg/datasource/gnomad/ld.py</code> <pre><code>def as_ld_index(\n    self: GnomADLDMatrix,\n    min_r2: float,\n) -&gt; LDIndex:\n    \"\"\"Create LDIndex dataset aggregating the LD information across a set of populations.\n\n    **The basic steps to generate the LDIndex are:**\n\n    1. Convert LD matrix to a Spark DataFrame.\n    2. Resolve the matrix indices to variant IDs by lifting over the coordinates to GRCh38.\n    3. Aggregate the LD information across populations.\n\n    Args:\n        min_r2 (float): Minimum r2 value to keep in the table\n\n    Returns:\n        LDIndex: LDIndex dataset\n    \"\"\"\n    ld_indices_unaggregated = []\n    for pop in self.ld_populations:\n        try:\n            ld_matrix_path = self.ld_matrix_template.format(POP=pop)\n            ld_index_raw_path = self.ld_index_raw_template.format(POP=pop)\n            pop_ld_index = self._create_ldindex_for_population(\n                pop,\n                ld_matrix_path,\n                ld_index_raw_path.format(pop),\n                self.grch37_to_grch38_chain_path,\n                min_r2,\n            )\n            ld_indices_unaggregated.append(pop_ld_index)\n        except Exception as e:\n            print(f\"Failed to create LDIndex for population {pop}: {e}\")  # noqa: T201\n            sys.exit(1)\n\n    ld_index_unaggregated = (\n        GnomADLDMatrix._transpose_ld_matrix(\n            reduce(lambda df1, df2: df1.unionByName(df2), ld_indices_unaggregated)\n        )\n        .withColumnRenamed(\"variantId_i\", \"variantId\")\n        .withColumnRenamed(\"variantId_j\", \"tagVariantId\")\n    )\n    return LDIndex(\n        _df=self._aggregate_ld_index_across_populations(ld_index_unaggregated),\n        _schema=LDIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/gnomad/gnomad_ld/#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice","title":"<code>get_ld_matrix_slice(gnomad_ancestry: str, start_index: int, end_index: int) -&gt; DataFrame</code>","text":"<p>Extract a slice of the LD matrix based on the provided ancestry and stop and end indices.</p> <ul> <li>The half matrix is completed into a full square.</li> <li>The returned indices are adjusted based on the start index.</li> </ul> <p>Parameters:</p> Name Type Description Default <code>gnomad_ancestry</code> <code>str</code> <p>LD population label eg. <code>nfe</code></p> required <code>start_index</code> <code>int</code> <p>start index of the slice</p> required <code>end_index</code> <code>int</code> <p>end index of the slice</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>square slice of the LD matrix melted as dataframe with idx_i, idx_j and r columns</p> Source code in <code>src/otg/datasource/gnomad/ld.py</code> <pre><code>def get_ld_matrix_slice(\n    self: GnomADLDMatrix,\n    gnomad_ancestry: str,\n    start_index: int,\n    end_index: int,\n) -&gt; DataFrame:\n    \"\"\"Extract a slice of the LD matrix based on the provided ancestry and stop and end indices.\n\n    - The half matrix is completed into a full square.\n    - The returned indices are adjusted based on the start index.\n\n    Args:\n        gnomad_ancestry (str): LD population label eg. `nfe`\n        start_index (int): start index of the slice\n        end_index (int): end index of the slice\n\n    Returns:\n        DataFrame: square slice of the LD matrix melted as dataframe with idx_i, idx_j and r columns\n    \"\"\"\n    # Extracting block matrix slice:\n    half_matrix = BlockMatrix.read(\n        self.ld_matrix_template.format(POP=gnomad_ancestry)\n    ).filter(range(start_index, end_index + 1), range(start_index, end_index + 1))\n\n    # Return converted Dataframe:\n    return (\n        (half_matrix + half_matrix.T)\n        .entries()\n        .to_spark()\n        .select(\n            (f.col(\"i\") + start_index).alias(\"idx_i\"),\n            (f.col(\"j\") + start_index).alias(\"idx_j\"),\n            f.when(f.col(\"i\") == f.col(\"j\"), f.col(\"entry\") / 2)\n            .otherwise(f.col(\"entry\"))\n            .alias(\"r\"),\n        )\n    )\n</code></pre>"},{"location":"python_api/datasource/gnomad/gnomad_ld/#otg.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants","title":"<code>get_ld_variants(gnomad_ancestry: str, chromosome: str, start: int, end: int) -&gt; DataFrame | None</code>","text":"<p>Return melted LD table with resolved variant id based on ancestry and genomic location.</p> <p>Parameters:</p> Name Type Description Default <code>gnomad_ancestry</code> <code>str</code> <p>GnomAD major ancestry label eg. <code>nfe</code></p> required <code>chromosome</code> <code>str</code> <p>chromosome label</p> required <code>start</code> <code>int</code> <p>window upper bound</p> required <code>end</code> <code>int</code> <p>window lower bound</p> required <p>Returns:</p> Type Description <code>DataFrame | None</code> <p>DataFrame | None: LD table with resolved variant id based on ancestry and genomic location</p> Source code in <code>src/otg/datasource/gnomad/ld.py</code> <pre><code>def get_ld_variants(\n    self: GnomADLDMatrix,\n    gnomad_ancestry: str,\n    chromosome: str,\n    start: int,\n    end: int,\n) -&gt; DataFrame | None:\n    \"\"\"Return melted LD table with resolved variant id based on ancestry and genomic location.\n\n    Args:\n        gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe`\n        chromosome (str): chromosome label\n        start (int): window upper bound\n        end (int): window lower bound\n\n    Returns:\n        DataFrame | None: LD table with resolved variant id based on ancestry and genomic location\n    \"\"\"\n    # Extracting locus:\n    ld_index_df = (\n        self._process_variant_indices(\n            hl.read_table(self.ld_index_raw_template.format(POP=gnomad_ancestry)),\n            self.grch37_to_grch38_chain_path,\n        )\n        .filter(\n            (f.col(\"chromosome\") == chromosome)\n            &amp; (f.col(\"position\") &gt;= start)\n            &amp; (f.col(\"position\") &lt;= end)\n        )\n        .select(\"chromosome\", \"position\", \"variantId\", \"idx\")\n        .persist()\n    )\n\n    if ld_index_df.limit(1).count() == 0:\n        # If the returned slice from the ld index is empty, return None\n        return None\n\n    # Compute start and end indices\n    start_index = get_value_from_row(\n        get_top_ranked_in_window(\n            ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").asc())\n        ).collect()[0],\n        \"idx\",\n    )\n    end_index = get_value_from_row(\n        get_top_ranked_in_window(\n            ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").desc())\n        ).collect()[0],\n        \"idx\",\n    )\n\n    return self._extract_square_matrix(\n        ld_index_df, gnomad_ancestry, start_index, end_index\n    )\n</code></pre>"},{"location":"python_api/datasource/gnomad/gnomad_variants/","title":"Variants","text":""},{"location":"python_api/datasource/gnomad/gnomad_variants/#otg.datasource.gnomad.variants.GnomADVariants","title":"<code>otg.datasource.gnomad.variants.GnomADVariants</code>  <code>dataclass</code>","text":"<p>GnomAD variants included in the GnomAD genomes dataset.</p> <p>Attributes:</p> Name Type Description <code>gnomad_genomes</code> <code>str</code> <p>Path to gnomAD genomes hail table. Defaults to gnomAD's 4.0 release.</p> <code>chain_hail_38_37</code> <code>str</code> <p>Path to GRCh38 to GRCh37 chain file. Defaults to Hail's chain file.</p> <code>populations</code> <code>list[str]</code> <p>List of populations to include. Defaults to all populations.</p> Source code in <code>src/otg/datasource/gnomad/variants.py</code> <pre><code>@dataclass\nclass GnomADVariants:\n    \"\"\"GnomAD variants included in the GnomAD genomes dataset.\n\n    Attributes:\n        gnomad_genomes (str): Path to gnomAD genomes hail table. Defaults to gnomAD's 4.0 release.\n        chain_hail_38_37 (str): Path to GRCh38 to GRCh37 chain file. Defaults to Hail's chain file.\n        populations (list[str]): List of populations to include. Defaults to all populations.\n    \"\"\"\n\n    gnomad_genomes: str = \"gs://gcp-public-data--gnomad/release/4.0/ht/genomes/gnomad.genomes.v4.0.sites.ht/\"\n    chain_hail_38_37: str = \"gs://hail-common/references/grch38_to_grch37.over.chain.gz\"\n    populations: list[str] = field(\n        default_factory=lambda: [\n            \"afr\",  # African-American\n            \"amr\",  # American Admixed/Latino\n            \"ami\",  # Amish ancestry\n            \"asj\",  # Ashkenazi Jewish\n            \"eas\",  # East Asian\n            \"fin\",  # Finnish\n            \"nfe\",  # Non-Finnish European\n            \"mid\",  # Middle Eastern\n            \"sas\",  # South Asian\n            \"remaining\",  # Other\n        ]\n    )\n\n    @staticmethod\n    def _convert_gnomad_position_to_ensembl_hail(\n        position: Int32Expression,\n        reference: StringExpression,\n        alternate: StringExpression,\n    ) -&gt; Int32Expression:\n        \"\"\"Convert GnomAD variant position to Ensembl variant position in hail table.\n\n        For indels (the reference or alternate allele is longer than 1), then adding 1 to the position, for SNPs, the position is unchanged.\n        More info about the problem: https://www.biostars.org/p/84686/\n\n        Args:\n            position (Int32Expression): Position of the variant in the GnomAD genome.\n            reference (StringExpression): The reference allele.\n            alternate (StringExpression): The alternate allele\n\n        Returns:\n            Int32Expression: The position of the variant according to Ensembl genome.\n        \"\"\"\n        return hl.if_else(\n            (reference.length() &gt; 1) | (alternate.length() &gt; 1), position + 1, position\n        )\n\n    def as_variant_annotation(self: GnomADVariants) -&gt; VariantAnnotation:\n        \"\"\"Generate variant annotation dataset from gnomAD.\n\n        Some relevant modifications to the original dataset are:\n\n        1. The transcript consequences features provided by VEP are filtered to only refer to the Ensembl canonical transcript.\n        2. Genome coordinates are liftovered from GRCh38 to GRCh37 to keep as annotation.\n        3. Field names are converted to camel case to follow the convention.\n\n        Returns:\n            VariantAnnotation: Variant annotation dataset\n        \"\"\"\n        # Load variants dataset\n        ht = hl.read_table(\n            self.gnomad_genomes,\n            _load_refs=False,\n        )\n\n        # Liftover\n        grch37 = hl.get_reference(\"GRCh37\")\n        grch38 = hl.get_reference(\"GRCh38\")\n        grch38.add_liftover(self.chain_hail_38_37, grch37)\n\n        # Drop non biallelic variants\n        ht = ht.filter(ht.alleles.length() == 2)\n        # Liftover\n        ht = ht.annotate(locus_GRCh37=hl.liftover(ht.locus, \"GRCh37\"))\n        # Select relevant fields and nested records to create class\n        return VariantAnnotation(\n            _df=(\n                ht.select(\n                    gnomadVariantId=hl.str(\"-\").join(\n                        [\n                            ht.locus.contig.replace(\"chr\", \"\"),\n                            hl.str(ht.locus.position),\n                            ht.alleles[0],\n                            ht.alleles[1],\n                        ]\n                    ),\n                    chromosome=ht.locus.contig.replace(\"chr\", \"\"),\n                    position=GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                        ht.locus.position, ht.alleles[0], ht.alleles[1]\n                    ),\n                    variantId=hl.str(\"_\").join(\n                        [\n                            ht.locus.contig.replace(\"chr\", \"\"),\n                            hl.str(\n                                GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                                    ht.locus.position, ht.alleles[0], ht.alleles[1]\n                                )\n                            ),\n                            ht.alleles[0],\n                            ht.alleles[1],\n                        ]\n                    ),\n                    chromosomeB37=ht.locus_GRCh37.contig.replace(\"chr\", \"\"),\n                    positionB37=ht.locus_GRCh37.position,\n                    referenceAllele=ht.alleles[0],\n                    alternateAllele=ht.alleles[1],\n                    rsIds=ht.rsid,\n                    alleleType=ht.allele_info.allele_type,\n                    alleleFrequencies=hl.set(\n                        [f\"{pop}_adj\" for pop in self.populations]\n                    ).map(\n                        lambda p: hl.struct(\n                            populationName=p,\n                            alleleFrequency=ht.freq[ht.globals.freq_index_dict[p]].AF,\n                        )\n                    ),\n                    vep=hl.struct(\n                        mostSevereConsequence=ht.vep.most_severe_consequence,\n                        transcriptConsequences=hl.map(\n                            lambda x: hl.struct(\n                                aminoAcids=x.amino_acids,\n                                consequenceTerms=x.consequence_terms,\n                                geneId=x.gene_id,\n                                lof=x.lof,\n                            ),\n                            # Only keeping canonical transcripts\n                            ht.vep.transcript_consequences.filter(\n                                lambda x: (x.canonical == 1)\n                                &amp; (x.gene_symbol_source == \"HGNC\")\n                            ),\n                        ),\n                    ),\n                    inSilicoPredictors=hl.struct(\n                        cadd=hl.struct(\n                            phred=ht.in_silico_predictors.cadd.phred,\n                            raw=ht.in_silico_predictors.cadd.raw_score,\n                        ),\n                        revelMax=ht.in_silico_predictors.revel_max,\n                        spliceaiDsMax=ht.in_silico_predictors.spliceai_ds_max,\n                        pangolinLargestDs=ht.in_silico_predictors.pangolin_largest_ds,\n                        phylop=ht.in_silico_predictors.phylop,\n                        siftMax=ht.in_silico_predictors.sift_max,\n                        polyphenMax=ht.in_silico_predictors.polyphen_max,\n                    ),\n                )\n                .key_by(\"chromosome\", \"position\")\n                .drop(\"locus\", \"alleles\")\n                .select_globals()\n                .to_spark(flatten=False)\n            ),\n            _schema=VariantAnnotation.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/gnomad/gnomad_variants/#otg.datasource.gnomad.variants.GnomADVariants.as_variant_annotation","title":"<code>as_variant_annotation() -&gt; VariantAnnotation</code>","text":"<p>Generate variant annotation dataset from gnomAD.</p> <p>Some relevant modifications to the original dataset are:</p> <ol> <li>The transcript consequences features provided by VEP are filtered to only refer to the Ensembl canonical transcript.</li> <li>Genome coordinates are liftovered from GRCh38 to GRCh37 to keep as annotation.</li> <li>Field names are converted to camel case to follow the convention.</li> </ol> <p>Returns:</p> Name Type Description <code>VariantAnnotation</code> <code>VariantAnnotation</code> <p>Variant annotation dataset</p> Source code in <code>src/otg/datasource/gnomad/variants.py</code> <pre><code>def as_variant_annotation(self: GnomADVariants) -&gt; VariantAnnotation:\n    \"\"\"Generate variant annotation dataset from gnomAD.\n\n    Some relevant modifications to the original dataset are:\n\n    1. The transcript consequences features provided by VEP are filtered to only refer to the Ensembl canonical transcript.\n    2. Genome coordinates are liftovered from GRCh38 to GRCh37 to keep as annotation.\n    3. Field names are converted to camel case to follow the convention.\n\n    Returns:\n        VariantAnnotation: Variant annotation dataset\n    \"\"\"\n    # Load variants dataset\n    ht = hl.read_table(\n        self.gnomad_genomes,\n        _load_refs=False,\n    )\n\n    # Liftover\n    grch37 = hl.get_reference(\"GRCh37\")\n    grch38 = hl.get_reference(\"GRCh38\")\n    grch38.add_liftover(self.chain_hail_38_37, grch37)\n\n    # Drop non biallelic variants\n    ht = ht.filter(ht.alleles.length() == 2)\n    # Liftover\n    ht = ht.annotate(locus_GRCh37=hl.liftover(ht.locus, \"GRCh37\"))\n    # Select relevant fields and nested records to create class\n    return VariantAnnotation(\n        _df=(\n            ht.select(\n                gnomadVariantId=hl.str(\"-\").join(\n                    [\n                        ht.locus.contig.replace(\"chr\", \"\"),\n                        hl.str(ht.locus.position),\n                        ht.alleles[0],\n                        ht.alleles[1],\n                    ]\n                ),\n                chromosome=ht.locus.contig.replace(\"chr\", \"\"),\n                position=GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                    ht.locus.position, ht.alleles[0], ht.alleles[1]\n                ),\n                variantId=hl.str(\"_\").join(\n                    [\n                        ht.locus.contig.replace(\"chr\", \"\"),\n                        hl.str(\n                            GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                                ht.locus.position, ht.alleles[0], ht.alleles[1]\n                            )\n                        ),\n                        ht.alleles[0],\n                        ht.alleles[1],\n                    ]\n                ),\n                chromosomeB37=ht.locus_GRCh37.contig.replace(\"chr\", \"\"),\n                positionB37=ht.locus_GRCh37.position,\n                referenceAllele=ht.alleles[0],\n                alternateAllele=ht.alleles[1],\n                rsIds=ht.rsid,\n                alleleType=ht.allele_info.allele_type,\n                alleleFrequencies=hl.set(\n                    [f\"{pop}_adj\" for pop in self.populations]\n                ).map(\n                    lambda p: hl.struct(\n                        populationName=p,\n                        alleleFrequency=ht.freq[ht.globals.freq_index_dict[p]].AF,\n                    )\n                ),\n                vep=hl.struct(\n                    mostSevereConsequence=ht.vep.most_severe_consequence,\n                    transcriptConsequences=hl.map(\n                        lambda x: hl.struct(\n                            aminoAcids=x.amino_acids,\n                            consequenceTerms=x.consequence_terms,\n                            geneId=x.gene_id,\n                            lof=x.lof,\n                        ),\n                        # Only keeping canonical transcripts\n                        ht.vep.transcript_consequences.filter(\n                            lambda x: (x.canonical == 1)\n                            &amp; (x.gene_symbol_source == \"HGNC\")\n                        ),\n                    ),\n                ),\n                inSilicoPredictors=hl.struct(\n                    cadd=hl.struct(\n                        phred=ht.in_silico_predictors.cadd.phred,\n                        raw=ht.in_silico_predictors.cadd.raw_score,\n                    ),\n                    revelMax=ht.in_silico_predictors.revel_max,\n                    spliceaiDsMax=ht.in_silico_predictors.spliceai_ds_max,\n                    pangolinLargestDs=ht.in_silico_predictors.pangolin_largest_ds,\n                    phylop=ht.in_silico_predictors.phylop,\n                    siftMax=ht.in_silico_predictors.sift_max,\n                    polyphenMax=ht.in_silico_predictors.polyphen_max,\n                ),\n            )\n            .key_by(\"chromosome\", \"position\")\n            .drop(\"locus\", \"alleles\")\n            .select_globals()\n            .to_spark(flatten=False)\n        ),\n        _schema=VariantAnnotation.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/_gwas_catalog/","title":"GWAS Catalog","text":"GWAS Catalog"},{"location":"python_api/datasource/gwas_catalog/associations/","title":"Associations","text":""},{"location":"python_api/datasource/gwas_catalog/associations/#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser","title":"<code>otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser</code>  <code>dataclass</code>","text":"<p>GWAS Catalog curated associations parser.</p> Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code> <pre><code>@dataclass\nclass GWASCatalogCuratedAssociationsParser:\n    \"\"\"GWAS Catalog curated associations parser.\"\"\"\n\n    @staticmethod\n    def _parse_pvalue(pvalue: Column) -&gt; tuple[Column, Column]:\n        \"\"\"Parse p-value column.\n\n        Args:\n            pvalue (Column): p-value [string]\n\n        Returns:\n            tuple[Column, Column]: p-value mantissa and exponent\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [(\"1.0\"), (\"0.5\"), (\"1E-20\"), (\"3E-3\"), (\"1E-1000\")]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StringType())\n            &gt;&gt;&gt; df.select('value',*GWASCatalogCuratedAssociationsParser._parse_pvalue(f.col('value'))).show()\n            +-------+--------------+--------------+\n            |  value|pValueMantissa|pValueExponent|\n            +-------+--------------+--------------+\n            |    1.0|           1.0|             1|\n            |    0.5|           0.5|             1|\n            |  1E-20|           1.0|           -20|\n            |   3E-3|           3.0|            -3|\n            |1E-1000|           1.0|         -1000|\n            +-------+--------------+--------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        split = f.split(pvalue, \"E\")\n        return split.getItem(0).cast(\"float\").alias(\"pValueMantissa\"), f.coalesce(\n            split.getItem(1).cast(\"integer\"), f.lit(1)\n        ).alias(\"pValueExponent\")\n\n    @staticmethod\n    def _normalise_pvaluetext(p_value_text: Column) -&gt; Column:\n        \"\"\"Normalised p-value text column to a standardised format.\n\n        For cases where there is no mapping, the value is set to null.\n\n        Args:\n            p_value_text (Column): `pValueText` column from GWASCatalog\n\n        Returns:\n            Column: Array column after using GWAS Catalog mappings. There might be multiple mappings for a single p-value text.\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [(\"European Ancestry\"), (\"African ancestry\"), (\"Alzheimer\u2019s Disease\"), (\"(progression)\"), (\"\"), (None)]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StringType())\n            &gt;&gt;&gt; df.withColumn('normalised', GWASCatalogCuratedAssociationsParser._normalise_pvaluetext(f.col('value'))).show()\n            +-------------------+----------+\n            |              value|normalised|\n            +-------------------+----------+\n            |  European Ancestry|      [EA]|\n            |   African ancestry|      [AA]|\n            |Alzheimer\u2019s Disease|      [AD]|\n            |      (progression)|      null|\n            |                   |      null|\n            |               null|      null|\n            +-------------------+----------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # GWAS Catalog to p-value mapping\n        json_dict = json.loads(\n            pkg_resources.read_text(data, \"gwas_pValueText_map.json\", encoding=\"utf-8\")\n        )\n        map_expr = f.create_map(*[f.lit(x) for x in chain(*json_dict.items())])\n\n        splitted_col = f.split(f.regexp_replace(p_value_text, r\"[\\(\\)]\", \"\"), \",\")\n        mapped_col = f.transform(splitted_col, lambda x: map_expr[x])\n        return f.when(f.forall(mapped_col, lambda x: x.isNull()), None).otherwise(\n            mapped_col\n        )\n\n    @staticmethod\n    def _normalise_risk_allele(risk_allele: Column) -&gt; Column:\n        \"\"\"Normalised risk allele column to a standardised format.\n\n        If multiple risk alleles are present, the first one is returned.\n\n        Args:\n            risk_allele (Column): `riskAllele` column from GWASCatalog\n\n        Returns:\n            Column: mapped using GWAS Catalog mapping\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [(\"rs1234-A-G\"), (\"rs1234-A\"), (\"rs1234-A; rs1235-G\")]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StringType())\n            &gt;&gt;&gt; df.withColumn('normalised', GWASCatalogCuratedAssociationsParser._normalise_risk_allele(f.col('value'))).show()\n            +------------------+----------+\n            |             value|normalised|\n            +------------------+----------+\n            |        rs1234-A-G|         A|\n            |          rs1234-A|         A|\n            |rs1234-A; rs1235-G|         A|\n            +------------------+----------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # GWAS Catalog to risk allele mapping\n        return f.split(f.split(risk_allele, \"; \").getItem(0), \"-\").getItem(1)\n\n    @staticmethod\n    def _collect_rsids(\n        snp_id: Column, snp_id_current: Column, risk_allele: Column\n    ) -&gt; Column:\n        \"\"\"It takes three columns, and returns an array of distinct values from those columns.\n\n        Args:\n            snp_id (Column): The original snp id from the GWAS catalog.\n            snp_id_current (Column): The current snp id field is just a number at the moment (stored as a string). Adding 'rs' prefix if looks good.\n            risk_allele (Column): The risk allele for the SNP.\n\n        Returns:\n            Column: An array of distinct values.\n        \"\"\"\n        # The current snp id field is just a number at the moment (stored as a string). Adding 'rs' prefix if looks good.\n        snp_id_current = f.when(\n            snp_id_current.rlike(\"^[0-9]*$\"),\n            f.format_string(\"rs%s\", snp_id_current),\n        )\n        # Cleaning risk allele:\n        risk_allele = f.split(risk_allele, \"-\").getItem(0)\n\n        # Collecting all values:\n        return f.array_distinct(f.array(snp_id, snp_id_current, risk_allele))\n\n    @staticmethod\n    def _map_to_variant_annotation_variants(\n        gwas_associations: DataFrame, variant_annotation: VariantAnnotation\n    ) -&gt; DataFrame:\n        \"\"\"Add variant metadata in associations.\n\n        Args:\n            gwas_associations (DataFrame): raw GWAS Catalog associations\n            variant_annotation (VariantAnnotation): variant annotation dataset\n\n        Returns:\n            DataFrame: GWAS Catalog associations data including `variantId`, `referenceAllele`,\n            `alternateAllele`, `chromosome`, `position` with variant metadata\n        \"\"\"\n        # Subset of GWAS Catalog associations required for resolving variant IDs:\n        gwas_associations_subset = gwas_associations.select(\n            \"studyLocusId\",\n            f.col(\"CHR_ID\").alias(\"chromosome\"),\n            f.col(\"CHR_POS\").cast(IntegerType()).alias(\"position\"),\n            # List of all SNPs associated with the variant\n            GWASCatalogCuratedAssociationsParser._collect_rsids(\n                f.split(f.col(\"SNPS\"), \"; \").getItem(0),\n                f.col(\"SNP_ID_CURRENT\"),\n                f.split(f.col(\"STRONGEST SNP-RISK ALLELE\"), \"; \").getItem(0),\n            ).alias(\"rsIdsGwasCatalog\"),\n            GWASCatalogCuratedAssociationsParser._normalise_risk_allele(\n                f.col(\"STRONGEST SNP-RISK ALLELE\")\n            ).alias(\"riskAllele\"),\n        )\n\n        # Subset of variant annotation required for GWAS Catalog annotations:\n        va_subset = variant_annotation.df.select(\n            \"variantId\",\n            \"chromosome\",\n            \"position\",\n            f.col(\"rsIds\").alias(\"rsIdsGnomad\"),\n            \"referenceAllele\",\n            \"alternateAllele\",\n            \"alleleFrequencies\",\n            variant_annotation.max_maf().alias(\"maxMaf\"),\n        ).join(\n            f.broadcast(\n                gwas_associations_subset.select(\"chromosome\", \"position\").distinct()\n            ),\n            on=[\"chromosome\", \"position\"],\n            how=\"inner\",\n        )\n\n        # Semi-resolved ids (still contains duplicates when conclusion was not possible to make\n        # based on rsIds or allele concordance)\n        filtered_associations = (\n            gwas_associations_subset.join(\n                f.broadcast(va_subset),\n                on=[\"chromosome\", \"position\"],\n                how=\"left\",\n            )\n            .withColumn(\n                \"rsIdFilter\",\n                GWASCatalogCuratedAssociationsParser._flag_mappings_to_retain(\n                    f.col(\"studyLocusId\"),\n                    GWASCatalogCuratedAssociationsParser._compare_rsids(\n                        f.col(\"rsIdsGnomad\"), f.col(\"rsIdsGwasCatalog\")\n                    ),\n                ),\n            )\n            .withColumn(\n                \"concordanceFilter\",\n                GWASCatalogCuratedAssociationsParser._flag_mappings_to_retain(\n                    f.col(\"studyLocusId\"),\n                    GWASCatalogCuratedAssociationsParser._check_concordance(\n                        f.col(\"riskAllele\"),\n                        f.col(\"referenceAllele\"),\n                        f.col(\"alternateAllele\"),\n                    ),\n                ),\n            )\n            .filter(\n                # Filter out rows where GWAS Catalog rsId does not match with GnomAD rsId,\n                # but there is corresponding variant for the same association\n                f.col(\"rsIdFilter\")\n                # or filter out rows where GWAS Catalog alleles are not concordant with GnomAD alleles,\n                # but there is corresponding variant for the same association\n                | f.col(\"concordanceFilter\")\n            )\n        )\n\n        # Keep only highest maxMaf variant per studyLocusId\n        fully_mapped_associations = get_record_with_maximum_value(\n            filtered_associations, grouping_col=\"studyLocusId\", sorting_col=\"maxMaf\"\n        ).select(\n            \"studyLocusId\",\n            \"variantId\",\n            \"referenceAllele\",\n            \"alternateAllele\",\n            \"chromosome\",\n            \"position\",\n        )\n\n        return gwas_associations.join(\n            fully_mapped_associations, on=\"studyLocusId\", how=\"left\"\n        )\n\n    @staticmethod\n    def _compare_rsids(gnomad: Column, gwas: Column) -&gt; Column:\n        \"\"\"If the intersection of the two arrays is greater than 0, return True, otherwise return False.\n\n        Args:\n            gnomad (Column): rsids from gnomad\n            gwas (Column): rsids from the GWAS Catalog\n\n        Returns:\n            Column: A boolean column that is true if the GnomAD rsIDs can be found in the GWAS rsIDs.\n\n        Examples:\n            &gt;&gt;&gt; d = [\n            ...    (1, [\"rs123\", \"rs523\"], [\"rs123\"]),\n            ...    (2, [], [\"rs123\"]),\n            ...    (3, [\"rs123\", \"rs523\"], []),\n            ...    (4, [], []),\n            ... ]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, ['associationId', 'gnomad', 'gwas'])\n            &gt;&gt;&gt; df.withColumn(\"rsid_matches\", GWASCatalogCuratedAssociationsParser._compare_rsids(f.col(\"gnomad\"),f.col('gwas'))).show()\n            +-------------+--------------+-------+------------+\n            |associationId|        gnomad|   gwas|rsid_matches|\n            +-------------+--------------+-------+------------+\n            |            1|[rs123, rs523]|[rs123]|        true|\n            |            2|            []|[rs123]|       false|\n            |            3|[rs123, rs523]|     []|       false|\n            |            4|            []|     []|       false|\n            +-------------+--------------+-------+------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return f.when(f.size(f.array_intersect(gnomad, gwas)) &gt; 0, True).otherwise(\n            False\n        )\n\n    @staticmethod\n    def _flag_mappings_to_retain(\n        association_id: Column, filter_column: Column\n    ) -&gt; Column:\n        \"\"\"Flagging mappings to drop for each association.\n\n        Some associations have multiple mappings. Some has matching rsId others don't. We only\n        want to drop the non-matching mappings, when a matching is available for the given association.\n        This logic can be generalised for other measures eg. allele concordance.\n\n        Args:\n            association_id (Column): association identifier column\n            filter_column (Column): boolean col indicating to keep a mapping\n\n        Returns:\n            Column: A column with a boolean value.\n\n        Examples:\n        &gt;&gt;&gt; d = [\n        ...    (1, False),\n        ...    (1, False),\n        ...    (2, False),\n        ...    (2, True),\n        ...    (3, True),\n        ...    (3, True),\n        ... ]\n        &gt;&gt;&gt; df = spark.createDataFrame(d, ['associationId', 'filter'])\n        &gt;&gt;&gt; df.withColumn(\"isConcordant\", GWASCatalogCuratedAssociationsParser._flag_mappings_to_retain(f.col(\"associationId\"),f.col('filter'))).show()\n        +-------------+------+------------+\n        |associationId|filter|isConcordant|\n        +-------------+------+------------+\n        |            1| false|        true|\n        |            1| false|        true|\n        |            2| false|       false|\n        |            2|  true|        true|\n        |            3|  true|        true|\n        |            3|  true|        true|\n        +-------------+------+------------+\n        &lt;BLANKLINE&gt;\n\n        \"\"\"\n        w = Window.partitionBy(association_id)\n\n        # Generating a boolean column informing if the filter column contains true anywhere for the association:\n        aggregated_filter = f.when(\n            f.array_contains(f.collect_set(filter_column).over(w), True), True\n        ).otherwise(False)\n\n        # Generate a filter column:\n        return f.when(aggregated_filter &amp; (~filter_column), False).otherwise(True)\n\n    @staticmethod\n    def _check_concordance(\n        risk_allele: Column, reference_allele: Column, alternate_allele: Column\n    ) -&gt; Column:\n        \"\"\"A function to check if the risk allele is concordant with the alt or ref allele.\n\n        If the risk allele is the same as the reference or alternate allele, or if the reverse complement of\n        the risk allele is the same as the reference or alternate allele, then the allele is concordant.\n        If no mapping is available (ref/alt is null), the function returns True.\n\n        Args:\n            risk_allele (Column): The allele that is associated with the risk of the disease.\n            reference_allele (Column): The reference allele from the GWAS catalog\n            alternate_allele (Column): The alternate allele of the variant.\n\n        Returns:\n            Column: A boolean column that is True if the risk allele is the same as the reference or alternate allele,\n            or if the reverse complement of the risk allele is the same as the reference or alternate allele.\n\n        Examples:\n            &gt;&gt;&gt; d = [\n            ...     ('A', 'A', 'G'),\n            ...     ('A', 'T', 'G'),\n            ...     ('A', 'C', 'G'),\n            ...     ('A', 'A', '?'),\n            ...     (None, None, 'A'),\n            ... ]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, ['riskAllele', 'referenceAllele', 'alternateAllele'])\n            &gt;&gt;&gt; df.withColumn(\"isConcordant\", GWASCatalogCuratedAssociationsParser._check_concordance(f.col(\"riskAllele\"),f.col('referenceAllele'), f.col('alternateAllele'))).show()\n            +----------+---------------+---------------+------------+\n            |riskAllele|referenceAllele|alternateAllele|isConcordant|\n            +----------+---------------+---------------+------------+\n            |         A|              A|              G|        true|\n            |         A|              T|              G|        true|\n            |         A|              C|              G|       false|\n            |         A|              A|              ?|        true|\n            |      null|           null|              A|        true|\n            +----------+---------------+---------------+------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # Calculating the reverse complement of the risk allele:\n        risk_allele_reverse_complement = f.when(\n            risk_allele.rlike(r\"^[ACTG]+$\"),\n            f.reverse(f.translate(risk_allele, \"ACTG\", \"TGAC\")),\n        ).otherwise(risk_allele)\n\n        # OK, is the risk allele or the reverse complent is the same as the mapped alleles:\n        return (\n            f.when(\n                (risk_allele == reference_allele) | (risk_allele == alternate_allele),\n                True,\n            )\n            # If risk allele is found on the negative strand:\n            .when(\n                (risk_allele_reverse_complement == reference_allele)\n                | (risk_allele_reverse_complement == alternate_allele),\n                True,\n            )\n            # If risk allele is ambiguous, still accepted: &lt; This condition could be reconsidered\n            .when(risk_allele == \"?\", True)\n            # If the association could not be mapped we keep it:\n            .when(reference_allele.isNull(), True)\n            # Allele is discordant:\n            .otherwise(False)\n        )\n\n    @staticmethod\n    def _get_reverse_complement(allele_col: Column) -&gt; Column:\n        \"\"\"A function to return the reverse complement of an allele column.\n\n        It takes a string and returns the reverse complement of that string if it's a DNA sequence,\n        otherwise it returns the original string. Assumes alleles in upper case.\n\n        Args:\n            allele_col (Column): The column containing the allele to reverse complement.\n\n        Returns:\n            Column: A column that is the reverse complement of the allele column.\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"allele\": 'A'}, {\"allele\": 'T'},{\"allele\": 'G'}, {\"allele\": 'C'},{\"allele\": 'AC'}, {\"allele\": 'GTaatc'},{\"allele\": '?'}, {\"allele\": None}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"revcom_allele\", GWASCatalogCuratedAssociationsParser._get_reverse_complement(f.col(\"allele\"))).show()\n            +------+-------------+\n            |allele|revcom_allele|\n            +------+-------------+\n            |     A|            T|\n            |     T|            A|\n            |     G|            C|\n            |     C|            G|\n            |    AC|           GT|\n            |GTaatc|       GATTAC|\n            |     ?|            ?|\n            |  null|         null|\n            +------+-------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        allele_col = f.upper(allele_col)\n        return f.when(\n            allele_col.rlike(\"[ACTG]+\"),\n            f.reverse(f.translate(allele_col, \"ACTG\", \"TGAC\")),\n        ).otherwise(allele_col)\n\n    @staticmethod\n    def _effect_needs_harmonisation(\n        risk_allele: Column, reference_allele: Column\n    ) -&gt; Column:\n        \"\"\"A function to check if the effect allele needs to be harmonised.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Effect allele column\n\n        Returns:\n            Column: A boolean column indicating if the effect allele needs to be harmonised.\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"risk\": 'A', \"reference\": 'A'}, {\"risk\": 'A', \"reference\": 'T'}, {\"risk\": 'AT', \"reference\": 'TA'}, {\"risk\": 'AT', \"reference\": 'AT'}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"needs_harmonisation\", GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(f.col(\"risk\"), f.col(\"reference\"))).show()\n            +---------+----+-------------------+\n            |reference|risk|needs_harmonisation|\n            +---------+----+-------------------+\n            |        A|   A|               true|\n            |        T|   A|               true|\n            |       TA|  AT|              false|\n            |       AT|  AT|               true|\n            +---------+----+-------------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return (risk_allele == reference_allele) | (\n            risk_allele\n            == GWASCatalogCuratedAssociationsParser._get_reverse_complement(\n                reference_allele\n            )\n        )\n\n    @staticmethod\n    def _are_alleles_palindromic(\n        reference_allele: Column, alternate_allele: Column\n    ) -&gt; Column:\n        \"\"\"A function to check if the alleles are palindromic.\n\n        Args:\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n\n        Returns:\n            Column: A boolean column indicating if the alleles are palindromic.\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"reference\": 'A', \"alternate\": 'T'}, {\"reference\": 'AT', \"alternate\": 'AG'}, {\"reference\": 'AT', \"alternate\": 'AT'}, {\"reference\": 'CATATG', \"alternate\": 'CATATG'}, {\"reference\": '-', \"alternate\": None}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"is_palindromic\", GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(f.col(\"reference\"), f.col(\"alternate\"))).show()\n            +---------+---------+--------------+\n            |alternate|reference|is_palindromic|\n            +---------+---------+--------------+\n            |        T|        A|          true|\n            |       AG|       AT|         false|\n            |       AT|       AT|          true|\n            |   CATATG|   CATATG|          true|\n            |     null|        -|         false|\n            +---------+---------+--------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        revcomp = GWASCatalogCuratedAssociationsParser._get_reverse_complement(\n            alternate_allele\n        )\n        return (\n            f.when(reference_allele == revcomp, True)\n            .when(revcomp.isNull(), False)\n            .otherwise(False)\n        )\n\n    @staticmethod\n    def _harmonise_beta(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n    ) -&gt; Column:\n        \"\"\"A function to extract the beta value from the effect size and confidence interval.\n\n        If the confidence interval contains the word \"increase\" or \"decrease\" it indicates, we are dealing with betas.\n        If it's \"increase\" and the effect size needs to be harmonized, then multiply the effect size by -1\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n\n        Returns:\n            Column: A column containing the beta value.\n        \"\"\"\n        return (\n            f.when(\n                GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(\n                    reference_allele, alternate_allele\n                ),\n                None,\n            )\n            .when(\n                (\n                    GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(\n                        risk_allele, reference_allele\n                    )\n                    &amp; confidence_interval.contains(\"increase\")\n                )\n                | (\n                    ~GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(\n                        risk_allele, reference_allele\n                    )\n                    &amp; confidence_interval.contains(\"decrease\")\n                ),\n                -effect_size,\n            )\n            .otherwise(effect_size)\n            .cast(DoubleType())\n        )\n\n    @staticmethod\n    def _harmonise_beta_ci(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n        p_value: Column,\n        direction: str,\n    ) -&gt; Column:\n        \"\"\"Calculating confidence intervals for beta values.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n            p_value (Column): GWAS Catalog p-value column\n            direction (str): This is the direction of the confidence interval. It can be either \"upper\" or \"lower\".\n\n        Returns:\n            Column: The upper and lower bounds of the confidence interval for the beta coefficient.\n        \"\"\"\n        zscore_95 = f.lit(1.96)\n        beta = GWASCatalogCuratedAssociationsParser._harmonise_beta(\n            risk_allele,\n            reference_allele,\n            alternate_allele,\n            effect_size,\n            confidence_interval,\n        )\n        zscore = pvalue_to_zscore(p_value)\n        return (\n            f.when(f.lit(direction) == \"upper\", beta + f.abs(zscore_95 * beta) / zscore)\n            .when(f.lit(direction) == \"lower\", beta - f.abs(zscore_95 * beta) / zscore)\n            .otherwise(None)\n        )\n\n    @staticmethod\n    def _harmonise_odds_ratio(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n    ) -&gt; Column:\n        \"\"\"Harmonizing odds ratio.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n\n        Returns:\n            Column: A column with the odds ratio, or 1/odds_ratio if harmonization required.\n        \"\"\"\n        return (\n            f.when(\n                GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(\n                    reference_allele, alternate_allele\n                ),\n                None,\n            )\n            .when(\n                (\n                    GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(\n                        risk_allele, reference_allele\n                    )\n                    &amp; ~confidence_interval.rlike(\"|\".join([\"decrease\", \"increase\"]))\n                ),\n                1 / effect_size,\n            )\n            .otherwise(effect_size)\n            .cast(DoubleType())\n        )\n\n    @staticmethod\n    def _harmonise_odds_ratio_ci(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n        p_value: Column,\n        direction: str,\n    ) -&gt; Column:\n        \"\"\"Calculating confidence intervals for beta values.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n            p_value (Column): GWAS Catalog p-value column\n            direction (str): This is the direction of the confidence interval. It can be either \"upper\" or \"lower\".\n\n        Returns:\n            Column: The upper and lower bounds of the 95% confidence interval for the odds ratio.\n        \"\"\"\n        zscore_95 = f.lit(1.96)\n        odds_ratio = GWASCatalogCuratedAssociationsParser._harmonise_odds_ratio(\n            risk_allele,\n            reference_allele,\n            alternate_allele,\n            effect_size,\n            confidence_interval,\n        )\n        odds_ratio_estimate = f.log(odds_ratio)\n        zscore = pvalue_to_zscore(p_value)\n        odds_ratio_se = odds_ratio_estimate / zscore\n        return f.when(\n            f.lit(direction) == \"upper\",\n            f.exp(odds_ratio_estimate + f.abs(zscore_95 * odds_ratio_se)),\n        ).when(\n            f.lit(direction) == \"lower\",\n            f.exp(odds_ratio_estimate - f.abs(zscore_95 * odds_ratio_se)),\n        )\n\n    @staticmethod\n    def _concatenate_substudy_description(\n        association_trait: Column, pvalue_text: Column, mapped_trait_uri: Column\n    ) -&gt; Column:\n        \"\"\"Substudy description parsing. Complex string containing metadata about the substudy (e.g. QTL, specific EFO, etc.).\n\n        Args:\n            association_trait (Column): GWAS Catalog association trait column\n            pvalue_text (Column): GWAS Catalog p-value text column\n            mapped_trait_uri (Column): GWAS Catalog mapped trait URI column\n\n        Returns:\n            Column: A column with the substudy description in the shape trait|pvaluetext1_pvaluetext2|EFO1_EFO2.\n\n        Examples:\n        &gt;&gt;&gt; df = spark.createDataFrame([\n        ...    (\"Height\", \"http://www.ebi.ac.uk/efo/EFO_0000001,http://www.ebi.ac.uk/efo/EFO_0000002\", \"European Ancestry\"),\n        ...    (\"Schizophrenia\", \"http://www.ebi.ac.uk/efo/MONDO_0005090\", None)],\n        ...    [\"association_trait\", \"mapped_trait_uri\", \"pvalue_text\"]\n        ... )\n        &gt;&gt;&gt; df.withColumn('substudy_description', GWASCatalogCuratedAssociationsParser._concatenate_substudy_description(df.association_trait, df.pvalue_text, df.mapped_trait_uri)).show(truncate=False)\n        +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+\n        |association_trait|mapped_trait_uri                                                         |pvalue_text      |substudy_description                      |\n        +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+\n        |Height           |http://www.ebi.ac.uk/efo/EFO_0000001,http://www.ebi.ac.uk/efo/EFO_0000002|European Ancestry|Height|EA|EFO_0000001/EFO_0000002         |\n        |Schizophrenia    |http://www.ebi.ac.uk/efo/MONDO_0005090                                   |null             |Schizophrenia|no_pvalue_text|MONDO_0005090|\n        +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+\n        &lt;BLANKLINE&gt;\n        \"\"\"\n        p_value_text = f.coalesce(\n            GWASCatalogCuratedAssociationsParser._normalise_pvaluetext(pvalue_text),\n            f.array(f.lit(\"no_pvalue_text\")),\n        )\n        return f.concat_ws(\n            \"|\",\n            association_trait,\n            f.concat_ws(\n                \"/\",\n                p_value_text,\n            ),\n            f.concat_ws(\n                \"/\",\n                parse_efos(mapped_trait_uri),\n            ),\n        )\n\n    @staticmethod\n    def _qc_all(\n        qc: Column,\n        chromosome: Column,\n        position: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        strongest_snp_risk_allele: Column,\n        p_value_mantissa: Column,\n        p_value_exponent: Column,\n        p_value_cutoff: float,\n    ) -&gt; Column:\n        \"\"\"Flag associations that fail any QC.\n\n        Args:\n            qc (Column): QC column\n            chromosome (Column): Chromosome column\n            position (Column): Position column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            strongest_snp_risk_allele (Column): Strongest SNP risk allele column\n            p_value_mantissa (Column): P-value mantissa column\n            p_value_exponent (Column): P-value exponent column\n            p_value_cutoff (float): P-value cutoff\n\n        Returns:\n            Column: Updated QC column with flag.\n        \"\"\"\n        qc = GWASCatalogCuratedAssociationsParser._qc_variant_interactions(\n            qc, strongest_snp_risk_allele\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_subsignificant_associations(\n            qc, p_value_mantissa, p_value_exponent, p_value_cutoff\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_genomic_location(\n            qc, chromosome, position\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_variant_inconsistencies(\n            qc, chromosome, position, strongest_snp_risk_allele\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_unmapped_variants(\n            qc, alternate_allele\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_palindromic_alleles(\n            qc, reference_allele, alternate_allele\n        )\n        return qc\n\n    @staticmethod\n    def _qc_variant_interactions(\n        qc: Column, strongest_snp_risk_allele: Column\n    ) -&gt; Column:\n        \"\"\"Flag associations based on variant x variant interactions.\n\n        Args:\n            qc (Column): QC column\n            strongest_snp_risk_allele (Column): Column with the strongest SNP risk allele\n\n        Returns:\n            Column: Updated QC column with flag.\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            strongest_snp_risk_allele.contains(\";\"),\n            StudyLocusQualityCheck.COMPOSITE_FLAG,\n        )\n\n    @staticmethod\n    def _qc_subsignificant_associations(\n        qc: Column,\n        p_value_mantissa: Column,\n        p_value_exponent: Column,\n        pvalue_cutoff: float,\n    ) -&gt; Column:\n        \"\"\"Flag associations below significant threshold.\n\n        Args:\n            qc (Column): QC column\n            p_value_mantissa (Column): P-value mantissa column\n            p_value_exponent (Column): P-value exponent column\n            pvalue_cutoff (float): association p-value cut-off\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Examples:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [{'qc': None, 'p_value_mantissa': 1, 'p_value_exponent': -7}, {'qc': None, 'p_value_mantissa': 1, 'p_value_exponent': -8}, {'qc': None, 'p_value_mantissa': 5, 'p_value_exponent': -8}, {'qc': None, 'p_value_mantissa': 1, 'p_value_exponent': -9}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StructType([t.StructField('qc', t.ArrayType(t.StringType()), True), t.StructField('p_value_mantissa', t.IntegerType()), t.StructField('p_value_exponent', t.IntegerType())]))\n            &gt;&gt;&gt; df.withColumn('qc', GWASCatalogCuratedAssociationsParser._qc_subsignificant_associations(f.col(\"qc\"), f.col(\"p_value_mantissa\"), f.col(\"p_value_exponent\"), 5e-8)).show(truncate = False)\n            +------------------------+----------------+----------------+\n            |qc                      |p_value_mantissa|p_value_exponent|\n            +------------------------+----------------+----------------+\n            |[Subsignificant p-value]|1               |-7              |\n            |[]                      |1               |-8              |\n            |[]                      |5               |-8              |\n            |[]                      |1               |-9              |\n            +------------------------+----------------+----------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            calculate_neglog_pvalue(p_value_mantissa, p_value_exponent)\n            &lt; f.lit(-np.log10(pvalue_cutoff)),\n            StudyLocusQualityCheck.SUBSIGNIFICANT_FLAG,\n        )\n\n    @staticmethod\n    def _qc_genomic_location(\n        qc: Column, chromosome: Column, position: Column\n    ) -&gt; Column:\n        \"\"\"Flag associations without genomic location in GWAS Catalog.\n\n        Args:\n            qc (Column): QC column\n            chromosome (Column): Chromosome column in GWAS Catalog\n            position (Column): Position column in GWAS Catalog\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Examples:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [{'qc': None, 'chromosome': None, 'position': None}, {'qc': None, 'chromosome': '1', 'position': None}, {'qc': None, 'chromosome': None, 'position': 1}, {'qc': None, 'chromosome': '1', 'position': 1}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, schema=t.StructType([t.StructField('qc', t.ArrayType(t.StringType()), True), t.StructField('chromosome', t.StringType()), t.StructField('position', t.IntegerType())]))\n            &gt;&gt;&gt; df.withColumn('qc', GWASCatalogCuratedAssociationsParser._qc_genomic_location(df.qc, df.chromosome, df.position)).show(truncate=False)\n            +----------------------------+----------+--------+\n            |qc                          |chromosome|position|\n            +----------------------------+----------+--------+\n            |[Incomplete genomic mapping]|null      |null    |\n            |[Incomplete genomic mapping]|1         |null    |\n            |[Incomplete genomic mapping]|null      |1       |\n            |[]                          |1         |1       |\n            +----------------------------+----------+--------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            position.isNull() | chromosome.isNull(),\n            StudyLocusQualityCheck.NO_GENOMIC_LOCATION_FLAG,\n        )\n\n    @staticmethod\n    def _qc_variant_inconsistencies(\n        qc: Column,\n        chromosome: Column,\n        position: Column,\n        strongest_snp_risk_allele: Column,\n    ) -&gt; Column:\n        \"\"\"Flag associations with inconsistencies in the variant annotation.\n\n        Args:\n            qc (Column): QC column\n            chromosome (Column): Chromosome column in GWAS Catalog\n            position (Column): Position column in GWAS Catalog\n            strongest_snp_risk_allele (Column): Strongest SNP risk allele column in GWAS Catalog\n\n        Returns:\n            Column: Updated QC column with flag.\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            # Number of chromosomes does not correspond to the number of positions:\n            (f.size(f.split(chromosome, \";\")) != f.size(f.split(position, \";\")))\n            # Number of chromosome values different from riskAllele values:\n            | (\n                f.size(f.split(chromosome, \";\"))\n                != f.size(f.split(strongest_snp_risk_allele, \";\"))\n            ),\n            StudyLocusQualityCheck.INCONSISTENCY_FLAG,\n        )\n\n    @staticmethod\n    def _qc_unmapped_variants(qc: Column, alternate_allele: Column) -&gt; Column:\n        \"\"\"Flag associations with variants not mapped to variantAnnotation.\n\n        Args:\n            qc (Column): QC column\n            alternate_allele (Column): alternate allele\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [{'alternate_allele': 'A', 'qc': None}, {'alternate_allele': None, 'qc': None}]\n            &gt;&gt;&gt; schema = t.StructType([t.StructField('alternate_allele', t.StringType(), True), t.StructField('qc', t.ArrayType(t.StringType()), True)])\n            &gt;&gt;&gt; df = spark.createDataFrame(data=d, schema=schema)\n            &gt;&gt;&gt; df.withColumn(\"new_qc\", GWASCatalogCuratedAssociationsParser._qc_unmapped_variants(f.col(\"qc\"), f.col(\"alternate_allele\"))).show()\n            +----------------+----+--------------------+\n            |alternate_allele|  qc|              new_qc|\n            +----------------+----+--------------------+\n            |               A|null|                  []|\n            |            null|null|[No mapping in Gn...|\n            +----------------+----+--------------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            alternate_allele.isNull(),\n            StudyLocusQualityCheck.NON_MAPPED_VARIANT_FLAG,\n        )\n\n    @staticmethod\n    def _qc_palindromic_alleles(\n        qc: Column, reference_allele: Column, alternate_allele: Column\n    ) -&gt; Column:\n        \"\"\"Flag associations with palindromic variants which effects can not be harmonised.\n\n        Args:\n            qc (Column): QC column\n            reference_allele (Column): reference allele\n            alternate_allele (Column): alternate allele\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; schema = t.StructType([t.StructField('reference_allele', t.StringType(), True), t.StructField('alternate_allele', t.StringType(), True), t.StructField('qc', t.ArrayType(t.StringType()), True)])\n            &gt;&gt;&gt; d = [{'reference_allele': 'A', 'alternate_allele': 'T', 'qc': None}, {'reference_allele': 'AT', 'alternate_allele': 'TA', 'qc': None}, {'reference_allele': 'AT', 'alternate_allele': 'AT', 'qc': None}]\n            &gt;&gt;&gt; df = spark.createDataFrame(data=d, schema=schema)\n            &gt;&gt;&gt; df.withColumn(\"qc\", GWASCatalogCuratedAssociationsParser._qc_palindromic_alleles(f.col(\"qc\"), f.col(\"reference_allele\"), f.col(\"alternate_allele\"))).show(truncate=False)\n            +----------------+----------------+---------------------------------------+\n            |reference_allele|alternate_allele|qc                                     |\n            +----------------+----------------+---------------------------------------+\n            |A               |T               |[Palindrome alleles - cannot harmonize]|\n            |AT              |TA              |[]                                     |\n            |AT              |AT              |[Palindrome alleles - cannot harmonize]|\n            +----------------+----------------+---------------------------------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(\n                reference_allele, alternate_allele\n            ),\n            StudyLocusQualityCheck.PALINDROMIC_ALLELE_FLAG,\n        )\n\n    @classmethod\n    def from_source(\n        cls: type[GWASCatalogCuratedAssociationsParser],\n        gwas_associations: DataFrame,\n        variant_annotation: VariantAnnotation,\n        pvalue_threshold: float = 5e-8,\n    ) -&gt; StudyLocusGWASCatalog:\n        \"\"\"Read GWASCatalog associations.\n\n        It reads the GWAS Catalog association dataset, selects and renames columns, casts columns, and\n        applies some pre-defined filters on the data:\n\n        Args:\n            gwas_associations (DataFrame): GWAS Catalog raw associations dataset\n            variant_annotation (VariantAnnotation): Variant annotation dataset\n            pvalue_threshold (float): P-value threshold for flagging associations\n\n        Returns:\n            StudyLocusGWASCatalog: GWASCatalogAssociations dataset\n        \"\"\"\n        return StudyLocusGWASCatalog(\n            _df=gwas_associations.withColumn(\n                \"studyLocusId\", f.monotonically_increasing_id().cast(LongType())\n            )\n            .transform(\n                # Map/harmonise variants to variant annotation dataset:\n                # This function adds columns: variantId, referenceAllele, alternateAllele, chromosome, position\n                lambda df: GWASCatalogCuratedAssociationsParser._map_to_variant_annotation_variants(\n                    df, variant_annotation\n                )\n            )\n            .withColumn(\n                # Perform all quality control checks:\n                \"qualityControls\",\n                GWASCatalogCuratedAssociationsParser._qc_all(\n                    f.array().alias(\"qualityControls\"),\n                    f.col(\"CHR_ID\"),\n                    f.col(\"CHR_POS\").cast(IntegerType()),\n                    f.col(\"referenceAllele\"),\n                    f.col(\"alternateAllele\"),\n                    f.col(\"STRONGEST SNP-RISK ALLELE\"),\n                    *GWASCatalogCuratedAssociationsParser._parse_pvalue(\n                        f.col(\"P-VALUE\")\n                    ),\n                    pvalue_threshold,\n                ),\n            )\n            .select(\n                # INSIDE STUDY-LOCUS SCHEMA:\n                \"studyLocusId\",\n                \"variantId\",\n                # Mapped genomic location of the variant (; separated list)\n                \"chromosome\",\n                \"position\",\n                f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n                # beta value of the association\n                GWASCatalogCuratedAssociationsParser._harmonise_beta(\n                    GWASCatalogCuratedAssociationsParser._normalise_risk_allele(\n                        f.col(\"STRONGEST SNP-RISK ALLELE\")\n                    ),\n                    f.col(\"referenceAllele\"),\n                    f.col(\"alternateAllele\"),\n                    f.col(\"OR or BETA\"),\n                    f.col(\"95% CI (TEXT)\"),\n                ).alias(\"beta\"),\n                # p-value of the association, string: split into exponent and mantissa.\n                *GWASCatalogCuratedAssociationsParser._parse_pvalue(f.col(\"P-VALUE\")),\n                # Capturing phenotype granularity at the association level\n                GWASCatalogCuratedAssociationsParser._concatenate_substudy_description(\n                    f.col(\"DISEASE/TRAIT\"),\n                    f.col(\"P-VALUE (TEXT)\"),\n                    f.col(\"MAPPED_TRAIT_URI\"),\n                ).alias(\"subStudyDescription\"),\n                # Quality controls (array of strings)\n                \"qualityControls\",\n            ),\n            _schema=StudyLocusGWASCatalog.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/associations/#otg.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source","title":"<code>from_source(gwas_associations: DataFrame, variant_annotation: VariantAnnotation, pvalue_threshold: float = 5e-08) -&gt; StudyLocusGWASCatalog</code>  <code>classmethod</code>","text":"<p>Read GWASCatalog associations.</p> <p>It reads the GWAS Catalog association dataset, selects and renames columns, casts columns, and applies some pre-defined filters on the data:</p> <p>Parameters:</p> Name Type Description Default <code>gwas_associations</code> <code>DataFrame</code> <p>GWAS Catalog raw associations dataset</p> required <code>variant_annotation</code> <code>VariantAnnotation</code> <p>Variant annotation dataset</p> required <code>pvalue_threshold</code> <code>float</code> <p>P-value threshold for flagging associations</p> <code>5e-08</code> <p>Returns:</p> Name Type Description <code>StudyLocusGWASCatalog</code> <code>StudyLocusGWASCatalog</code> <p>GWASCatalogAssociations dataset</p> Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[GWASCatalogCuratedAssociationsParser],\n    gwas_associations: DataFrame,\n    variant_annotation: VariantAnnotation,\n    pvalue_threshold: float = 5e-8,\n) -&gt; StudyLocusGWASCatalog:\n    \"\"\"Read GWASCatalog associations.\n\n    It reads the GWAS Catalog association dataset, selects and renames columns, casts columns, and\n    applies some pre-defined filters on the data:\n\n    Args:\n        gwas_associations (DataFrame): GWAS Catalog raw associations dataset\n        variant_annotation (VariantAnnotation): Variant annotation dataset\n        pvalue_threshold (float): P-value threshold for flagging associations\n\n    Returns:\n        StudyLocusGWASCatalog: GWASCatalogAssociations dataset\n    \"\"\"\n    return StudyLocusGWASCatalog(\n        _df=gwas_associations.withColumn(\n            \"studyLocusId\", f.monotonically_increasing_id().cast(LongType())\n        )\n        .transform(\n            # Map/harmonise variants to variant annotation dataset:\n            # This function adds columns: variantId, referenceAllele, alternateAllele, chromosome, position\n            lambda df: GWASCatalogCuratedAssociationsParser._map_to_variant_annotation_variants(\n                df, variant_annotation\n            )\n        )\n        .withColumn(\n            # Perform all quality control checks:\n            \"qualityControls\",\n            GWASCatalogCuratedAssociationsParser._qc_all(\n                f.array().alias(\"qualityControls\"),\n                f.col(\"CHR_ID\"),\n                f.col(\"CHR_POS\").cast(IntegerType()),\n                f.col(\"referenceAllele\"),\n                f.col(\"alternateAllele\"),\n                f.col(\"STRONGEST SNP-RISK ALLELE\"),\n                *GWASCatalogCuratedAssociationsParser._parse_pvalue(\n                    f.col(\"P-VALUE\")\n                ),\n                pvalue_threshold,\n            ),\n        )\n        .select(\n            # INSIDE STUDY-LOCUS SCHEMA:\n            \"studyLocusId\",\n            \"variantId\",\n            # Mapped genomic location of the variant (; separated list)\n            \"chromosome\",\n            \"position\",\n            f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n            # beta value of the association\n            GWASCatalogCuratedAssociationsParser._harmonise_beta(\n                GWASCatalogCuratedAssociationsParser._normalise_risk_allele(\n                    f.col(\"STRONGEST SNP-RISK ALLELE\")\n                ),\n                f.col(\"referenceAllele\"),\n                f.col(\"alternateAllele\"),\n                f.col(\"OR or BETA\"),\n                f.col(\"95% CI (TEXT)\"),\n            ).alias(\"beta\"),\n            # p-value of the association, string: split into exponent and mantissa.\n            *GWASCatalogCuratedAssociationsParser._parse_pvalue(f.col(\"P-VALUE\")),\n            # Capturing phenotype granularity at the association level\n            GWASCatalogCuratedAssociationsParser._concatenate_substudy_description(\n                f.col(\"DISEASE/TRAIT\"),\n                f.col(\"P-VALUE (TEXT)\"),\n                f.col(\"MAPPED_TRAIT_URI\"),\n            ).alias(\"subStudyDescription\"),\n            # Quality controls (array of strings)\n            \"qualityControls\",\n        ),\n        _schema=StudyLocusGWASCatalog.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/associations/#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog","title":"<code>otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog</code>  <code>dataclass</code>","text":"<p>             Bases: <code>StudyLocus</code></p> <p>Study locus Dataset for GWAS Catalog curated associations.</p> <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p> Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code> <pre><code>@dataclass\nclass StudyLocusGWASCatalog(StudyLocus):\n    \"\"\"Study locus Dataset for GWAS Catalog curated associations.\n\n    A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.\n    \"\"\"\n\n    def update_study_id(\n        self: StudyLocusGWASCatalog, study_annotation: DataFrame\n    ) -&gt; StudyLocusGWASCatalog:\n        \"\"\"Update final studyId and studyLocusId with a dataframe containing study annotation.\n\n        Args:\n            study_annotation (DataFrame): Dataframe containing `updatedStudyId` and key columns `studyId` and `subStudyDescription`.\n\n        Returns:\n            StudyLocusGWASCatalog: Updated study locus with new `studyId` and `studyLocusId`.\n        \"\"\"\n        self.df = (\n            self._df.join(\n                study_annotation, on=[\"studyId\", \"subStudyDescription\"], how=\"left\"\n            )\n            .withColumn(\"studyId\", f.coalesce(\"updatedStudyId\", \"studyId\"))\n            .drop(\"subStudyDescription\", \"updatedStudyId\")\n        ).withColumn(\n            \"studyLocusId\",\n            StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n        )\n        return self\n\n    def qc_ambiguous_study(self: StudyLocusGWASCatalog) -&gt; StudyLocusGWASCatalog:\n        \"\"\"Flag associations with variants that can not be unambiguously associated with one study.\n\n        Returns:\n            StudyLocusGWASCatalog: Updated study locus.\n        \"\"\"\n        assoc_ambiguity_window = Window.partitionBy(\n            f.col(\"studyId\"), f.col(\"variantId\")\n        )\n\n        self._df.withColumn(\n            \"qualityControls\",\n            StudyLocus.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.count(f.col(\"variantId\")).over(assoc_ambiguity_window) &gt; 1,\n                StudyLocusQualityCheck.AMBIGUOUS_STUDY,\n            ),\n        )\n        return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/associations/#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study","title":"<code>qc_ambiguous_study() -&gt; StudyLocusGWASCatalog</code>","text":"<p>Flag associations with variants that can not be unambiguously associated with one study.</p> <p>Returns:</p> Name Type Description <code>StudyLocusGWASCatalog</code> <code>StudyLocusGWASCatalog</code> <p>Updated study locus.</p> Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code> <pre><code>def qc_ambiguous_study(self: StudyLocusGWASCatalog) -&gt; StudyLocusGWASCatalog:\n    \"\"\"Flag associations with variants that can not be unambiguously associated with one study.\n\n    Returns:\n        StudyLocusGWASCatalog: Updated study locus.\n    \"\"\"\n    assoc_ambiguity_window = Window.partitionBy(\n        f.col(\"studyId\"), f.col(\"variantId\")\n    )\n\n    self._df.withColumn(\n        \"qualityControls\",\n        StudyLocus.update_quality_flag(\n            f.col(\"qualityControls\"),\n            f.count(f.col(\"variantId\")).over(assoc_ambiguity_window) &gt; 1,\n            StudyLocusQualityCheck.AMBIGUOUS_STUDY,\n        ),\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/associations/#otg.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id","title":"<code>update_study_id(study_annotation: DataFrame) -&gt; StudyLocusGWASCatalog</code>","text":"<p>Update final studyId and studyLocusId with a dataframe containing study annotation.</p> <p>Parameters:</p> Name Type Description Default <code>study_annotation</code> <code>DataFrame</code> <p>Dataframe containing <code>updatedStudyId</code> and key columns <code>studyId</code> and <code>subStudyDescription</code>.</p> required <p>Returns:</p> Name Type Description <code>StudyLocusGWASCatalog</code> <code>StudyLocusGWASCatalog</code> <p>Updated study locus with new <code>studyId</code> and <code>studyLocusId</code>.</p> Source code in <code>src/otg/datasource/gwas_catalog/associations.py</code> <pre><code>def update_study_id(\n    self: StudyLocusGWASCatalog, study_annotation: DataFrame\n) -&gt; StudyLocusGWASCatalog:\n    \"\"\"Update final studyId and studyLocusId with a dataframe containing study annotation.\n\n    Args:\n        study_annotation (DataFrame): Dataframe containing `updatedStudyId` and key columns `studyId` and `subStudyDescription`.\n\n    Returns:\n        StudyLocusGWASCatalog: Updated study locus with new `studyId` and `studyLocusId`.\n    \"\"\"\n    self.df = (\n        self._df.join(\n            study_annotation, on=[\"studyId\", \"subStudyDescription\"], how=\"left\"\n        )\n        .withColumn(\"studyId\", f.coalesce(\"updatedStudyId\", \"studyId\"))\n        .drop(\"subStudyDescription\", \"updatedStudyId\")\n    ).withColumn(\n        \"studyLocusId\",\n        StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/","title":"Study Index","text":""},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser","title":"<code>otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser</code>  <code>dataclass</code>","text":"<p>GWAS Catalog study index parser.</p> <p>The following information is harmonised from the GWAS Catalog:</p> <ul> <li>All publication related information retained.</li> <li>Mapped measured and background traits parsed.</li> <li>Flagged if harmonized summary statistics datasets available.</li> <li>If available, the ftp path to these files presented.</li> <li>Ancestries from the discovery and replication stages are structured with sample counts.</li> <li>Case/control counts extracted.</li> <li>The number of samples with European ancestry extracted.</li> </ul> Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>@dataclass\nclass StudyIndexGWASCatalogParser:\n    \"\"\"GWAS Catalog study index parser.\n\n    The following information is harmonised from the GWAS Catalog:\n\n    - All publication related information retained.\n    - Mapped measured and background traits parsed.\n    - Flagged if harmonized summary statistics datasets available.\n    - If available, the ftp path to these files presented.\n    - Ancestries from the discovery and replication stages are structured with sample counts.\n    - Case/control counts extracted.\n    - The number of samples with European ancestry extracted.\n\n    \"\"\"\n\n    @staticmethod\n    def _parse_discovery_samples(discovery_samples: Column) -&gt; Column:\n        \"\"\"Parse discovery sample sizes from GWAS Catalog.\n\n        This is a curated field. From publication sometimes it is not clear how the samples were split\n        across the reported ancestries. In such cases we are assuming the ancestries were evenly presented\n        and the total sample size is split:\n\n        [\"European, African\", 100] -&gt; [\"European, 50], [\"African\", 50]\n\n        Args:\n            discovery_samples (Column): Raw discovery sample sizes\n\n        Returns:\n            Column: Parsed and de-duplicated list of discovery ancestries with sample size.\n\n        Examples:\n            &gt;&gt;&gt; data = [('s1', \"European\", 10), ('s1', \"African\", 10), ('s2', \"European, African, Asian\", 100), ('s2', \"European\", 50)]\n            &gt;&gt;&gt; df = (\n            ...    spark.createDataFrame(data, ['studyId', 'ancestry', 'sampleSize'])\n            ...    .groupBy('studyId')\n            ...    .agg(\n            ...        f.collect_set(\n            ...            f.struct('ancestry', 'sampleSize')\n            ...        ).alias('discoverySampleSize')\n            ...    )\n            ...    .orderBy('studyId')\n            ...    .withColumn('discoverySampleSize', StudyIndexGWASCatalogParser._parse_discovery_samples(f.col('discoverySampleSize')))\n            ...    .select('discoverySampleSize')\n            ...    .show(truncate=False)\n            ... )\n            +--------------------------------------------+\n            |discoverySampleSize                         |\n            +--------------------------------------------+\n            |[{African, 10}, {European, 10}]             |\n            |[{European, 83}, {African, 33}, {Asian, 33}]|\n            +--------------------------------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        # To initialize return objects for aggregate functions, schema has to be definied:\n        schema = t.ArrayType(\n            t.StructType(\n                [\n                    t.StructField(\"ancestry\", t.StringType(), True),\n                    t.StructField(\"sampleSize\", t.IntegerType(), True),\n                ]\n            )\n        )\n\n        # Splitting comma separated ancestries:\n        exploded_ancestries = f.transform(\n            discovery_samples,\n            lambda sample: f.split(sample.ancestry, r\",\\s(?![^()]*\\))\"),\n        )\n\n        # Initialize discoverySample object from unique list of ancestries:\n        unique_ancestries = f.transform(\n            f.aggregate(\n                exploded_ancestries,\n                f.array().cast(t.ArrayType(t.StringType())),\n                lambda x, y: f.array_union(x, y),\n                f.array_distinct,\n            ),\n            lambda ancestry: f.struct(\n                ancestry.alias(\"ancestry\"),\n                f.lit(0).cast(t.LongType()).alias(\"sampleSize\"),\n            ),\n        )\n\n        # Computing sample sizes for ancestries when splitting is needed:\n        resolved_sample_count = f.transform(\n            f.arrays_zip(\n                f.transform(exploded_ancestries, lambda pop: f.size(pop)).alias(\n                    \"pop_size\"\n                ),\n                f.transform(discovery_samples, lambda pop: pop.sampleSize).alias(\n                    \"pop_count\"\n                ),\n            ),\n            lambda pop: (pop.pop_count / pop.pop_size).cast(t.IntegerType()),\n        )\n\n        # Flattening out ancestries with sample sizes:\n        parsed_sample_size = f.aggregate(\n            f.transform(\n                f.arrays_zip(\n                    exploded_ancestries.alias(\"ancestries\"),\n                    resolved_sample_count.alias(\"sample_count\"),\n                ),\n                StudyIndexGWASCatalogParser._merge_ancestries_and_counts,\n            ),\n            f.array().cast(schema),\n            lambda x, y: f.array_union(x, y),\n        )\n\n        # Normalize ancestries:\n        return f.aggregate(\n            parsed_sample_size,\n            unique_ancestries,\n            StudyIndexGWASCatalogParser._normalize_ancestries,\n        )\n\n    @staticmethod\n    def _normalize_ancestries(merged: Column, ancestry: Column) -&gt; Column:\n        \"\"\"Normalize ancestries from a list of structs.\n\n        As some ancestry label might be repeated with different sample counts,\n        these counts need to be collected.\n\n        Args:\n            merged (Column): Resulting list of struct with unique ancestries.\n            ancestry (Column): One ancestry object coming from raw.\n\n        Returns:\n            Column: Unique list of ancestries with the sample counts.\n        \"\"\"\n        # Iterating over the list of unique ancestries and adding the sample size if label matches:\n        return f.transform(\n            merged,\n            lambda a: f.when(\n                a.ancestry == ancestry.ancestry,\n                f.struct(\n                    a.ancestry.alias(\"ancestry\"),\n                    (a.sampleSize + ancestry.sampleSize)\n                    .cast(t.LongType())\n                    .alias(\"sampleSize\"),\n                ),\n            ).otherwise(a),\n        )\n\n    @staticmethod\n    def _merge_ancestries_and_counts(ancestry_group: Column) -&gt; Column:\n        \"\"\"Merge ancestries with sample sizes.\n\n        After splitting ancestry annotations, all resulting ancestries needs to be assigned\n        with the proper sample size.\n\n        Args:\n            ancestry_group (Column): Each element is a struct with `sample_count` (int) and `ancestries` (list)\n\n        Returns:\n            Column: a list of structs with `ancestry` and `sampleSize` fields.\n\n        Examples:\n            &gt;&gt;&gt; data = [(12, ['African', 'European']),(12, ['African'])]\n            &gt;&gt;&gt; (\n            ...     spark.createDataFrame(data, ['sample_count', 'ancestries'])\n            ...     .select(StudyIndexGWASCatalogParser._merge_ancestries_and_counts(f.struct('sample_count', 'ancestries')).alias('test'))\n            ...     .show(truncate=False)\n            ... )\n            +-------------------------------+\n            |test                           |\n            +-------------------------------+\n            |[{African, 12}, {European, 12}]|\n            |[{African, 12}]                |\n            +-------------------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        # Extract sample size for the ancestry group:\n        count = ancestry_group.sample_count\n\n        # We need to loop through the ancestries:\n        return f.transform(\n            ancestry_group.ancestries,\n            lambda ancestry: f.struct(\n                ancestry.alias(\"ancestry\"),\n                count.alias(\"sampleSize\"),\n            ),\n        )\n\n    @staticmethod\n    def parse_cohorts(raw_cohort: Column) -&gt; Column:\n        \"\"\"Return a list of unique cohort labels from pipe separated list if provided.\n\n        Args:\n            raw_cohort (Column): Cohort list column, where labels are separated by `|` sign.\n\n        Returns:\n            Column: an array colun with string elements.\n\n        Examples:\n        &gt;&gt;&gt; data = [('BioME|CaPS|Estonia|FHS|UKB|GERA|GERA|GERA',),(None,),]\n        &gt;&gt;&gt; spark.createDataFrame(data, ['cohorts']).select(StudyIndexGWASCatalogParser.parse_cohorts(f.col('cohorts')).alias('parsedCohorts')).show(truncate=False)\n        +--------------------------------------+\n        |parsedCohorts                         |\n        +--------------------------------------+\n        |[BioME, CaPS, Estonia, FHS, UKB, GERA]|\n        |[null]                                |\n        +--------------------------------------+\n        &lt;BLANKLINE&gt;\n        \"\"\"\n        return f.when(\n            (raw_cohort.isNull()) | (raw_cohort == \"\"),\n            f.array(f.lit(None).cast(t.StringType())),\n        ).otherwise(f.array_distinct(f.split(raw_cohort, r\"\\|\")))\n\n    @classmethod\n    def _parse_study_table(\n        cls: type[StudyIndexGWASCatalogParser], catalog_studies: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Harmonise GWASCatalog study table with `StudyIndex` schema.\n\n        Args:\n            catalog_studies (DataFrame): GWAS Catalog study table\n\n        Returns:\n            StudyIndexGWASCatalog: Parsed and annotated GWAS Catalog study table.\n        \"\"\"\n        return StudyIndexGWASCatalog(\n            _df=catalog_studies.select(\n                f.coalesce(\n                    f.col(\"STUDY ACCESSION\"), f.monotonically_increasing_id()\n                ).alias(\"studyId\"),\n                f.lit(\"GCST\").alias(\"projectId\"),\n                f.lit(\"gwas\").alias(\"studyType\"),\n                f.col(\"PUBMED ID\").alias(\"pubmedId\"),\n                f.col(\"FIRST AUTHOR\").alias(\"publicationFirstAuthor\"),\n                f.col(\"DATE\").alias(\"publicationDate\"),\n                f.col(\"JOURNAL\").alias(\"publicationJournal\"),\n                f.col(\"STUDY\").alias(\"publicationTitle\"),\n                f.coalesce(f.col(\"DISEASE/TRAIT\"), f.lit(\"Unreported\")).alias(\n                    \"traitFromSource\"\n                ),\n                f.col(\"INITIAL SAMPLE SIZE\").alias(\"initialSampleSize\"),\n                parse_efos(f.col(\"MAPPED_TRAIT_URI\")).alias(\"traitFromSourceMappedIds\"),\n                parse_efos(f.col(\"MAPPED BACKGROUND TRAIT URI\")).alias(\n                    \"backgroundTraitFromSourceMappedIds\"\n                ),\n            ),\n            _schema=StudyIndexGWASCatalog.get_schema(),\n        )\n\n    @classmethod\n    def from_source(\n        cls: type[StudyIndexGWASCatalogParser],\n        catalog_studies: DataFrame,\n        ancestry_file: DataFrame,\n        sumstats_lut: DataFrame,\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Ingests study level metadata from the GWAS Catalog.\n\n        Args:\n            catalog_studies (DataFrame): GWAS Catalog raw study table\n            ancestry_file (DataFrame): GWAS Catalog ancestry table.\n            sumstats_lut (DataFrame): GWAS Catalog summary statistics list.\n\n        Returns:\n            StudyIndexGWASCatalog: Parsed and annotated GWAS Catalog study table.\n        \"\"\"\n        # Read GWAS Catalogue raw data\n        return (\n            cls._parse_study_table(catalog_studies)\n            .annotate_ancestries(ancestry_file)\n            .annotate_sumstats_info(sumstats_lut)\n            .annotate_discovery_sample_sizes()\n        )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source","title":"<code>from_source(catalog_studies: DataFrame, ancestry_file: DataFrame, sumstats_lut: DataFrame) -&gt; StudyIndexGWASCatalog</code>  <code>classmethod</code>","text":"<p>Ingests study level metadata from the GWAS Catalog.</p> <p>Parameters:</p> Name Type Description Default <code>catalog_studies</code> <code>DataFrame</code> <p>GWAS Catalog raw study table</p> required <code>ancestry_file</code> <code>DataFrame</code> <p>GWAS Catalog ancestry table.</p> required <code>sumstats_lut</code> <code>DataFrame</code> <p>GWAS Catalog summary statistics list.</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Parsed and annotated GWAS Catalog study table.</p> Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[StudyIndexGWASCatalogParser],\n    catalog_studies: DataFrame,\n    ancestry_file: DataFrame,\n    sumstats_lut: DataFrame,\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Ingests study level metadata from the GWAS Catalog.\n\n    Args:\n        catalog_studies (DataFrame): GWAS Catalog raw study table\n        ancestry_file (DataFrame): GWAS Catalog ancestry table.\n        sumstats_lut (DataFrame): GWAS Catalog summary statistics list.\n\n    Returns:\n        StudyIndexGWASCatalog: Parsed and annotated GWAS Catalog study table.\n    \"\"\"\n    # Read GWAS Catalogue raw data\n    return (\n        cls._parse_study_table(catalog_studies)\n        .annotate_ancestries(ancestry_file)\n        .annotate_sumstats_info(sumstats_lut)\n        .annotate_discovery_sample_sizes()\n    )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts","title":"<code>parse_cohorts(raw_cohort: Column) -&gt; Column</code>  <code>staticmethod</code>","text":"<p>Return a list of unique cohort labels from pipe separated list if provided.</p> <p>Parameters:</p> Name Type Description Default <code>raw_cohort</code> <code>Column</code> <p>Cohort list column, where labels are separated by <code>|</code> sign.</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>an array colun with string elements.</p> <p>Examples:</p> <p>data = [('BioME|CaPS|Estonia|FHS|UKB|GERA|GERA|GERA',),(None,),] spark.createDataFrame(data, ['cohorts']).select(StudyIndexGWASCatalogParser.parse_cohorts(f.col('cohorts')).alias('parsedCohorts')).show(truncate=False) +--------------------------------------+ |parsedCohorts                         | +--------------------------------------+ |[BioME, CaPS, Estonia, FHS, UKB, GERA]| |[null]                                | +--------------------------------------+  Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>@staticmethod\ndef parse_cohorts(raw_cohort: Column) -&gt; Column:\n    \"\"\"Return a list of unique cohort labels from pipe separated list if provided.\n\n    Args:\n        raw_cohort (Column): Cohort list column, where labels are separated by `|` sign.\n\n    Returns:\n        Column: an array colun with string elements.\n\n    Examples:\n    &gt;&gt;&gt; data = [('BioME|CaPS|Estonia|FHS|UKB|GERA|GERA|GERA',),(None,),]\n    &gt;&gt;&gt; spark.createDataFrame(data, ['cohorts']).select(StudyIndexGWASCatalogParser.parse_cohorts(f.col('cohorts')).alias('parsedCohorts')).show(truncate=False)\n    +--------------------------------------+\n    |parsedCohorts                         |\n    +--------------------------------------+\n    |[BioME, CaPS, Estonia, FHS, UKB, GERA]|\n    |[null]                                |\n    +--------------------------------------+\n    &lt;BLANKLINE&gt;\n    \"\"\"\n    return f.when(\n        (raw_cohort.isNull()) | (raw_cohort == \"\"),\n        f.array(f.lit(None).cast(t.StringType())),\n    ).otherwise(f.array_distinct(f.split(raw_cohort, r\"\\|\")))\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog","title":"<code>otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog</code>  <code>dataclass</code>","text":"<p>             Bases: <code>StudyIndex</code></p> <p>Study index dataset from GWAS Catalog.</p> <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p> Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>@dataclass\nclass StudyIndexGWASCatalog(StudyIndex):\n    \"\"\"Study index dataset from GWAS Catalog.\n\n    A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.\n    \"\"\"\n\n    def update_study_id(\n        self: StudyIndexGWASCatalog, study_annotation: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Update studyId with a dataframe containing study.\n\n        Args:\n            study_annotation (DataFrame): Dataframe containing `updatedStudyId`, `traitFromSource`, `traitFromSourceMappedIds` and key column `studyId`.\n\n        Returns:\n            StudyIndexGWASCatalog: Updated study table.\n        \"\"\"\n        self.df = (\n            self._df.join(\n                study_annotation.select(\n                    *[\n                        f.col(c).alias(f\"updated{c}\")\n                        if c not in [\"studyId\", \"updatedStudyId\"]\n                        else f.col(c)\n                        for c in study_annotation.columns\n                    ]\n                ),\n                on=\"studyId\",\n                how=\"left\",\n            )\n            .withColumn(\n                \"studyId\",\n                f.coalesce(f.col(\"updatedStudyId\"), f.col(\"studyId\")),\n            )\n            .withColumn(\n                \"traitFromSource\",\n                f.coalesce(f.col(\"updatedtraitFromSource\"), f.col(\"traitFromSource\")),\n            )\n            .withColumn(\n                \"traitFromSourceMappedIds\",\n                f.coalesce(\n                    f.col(\"updatedtraitFromSourceMappedIds\"),\n                    f.col(\"traitFromSourceMappedIds\"),\n                ),\n            )\n            .select(self._df.columns)\n        )\n\n        return self\n\n    def annotate_ancestries(\n        self: StudyIndexGWASCatalog, ancestry_lut: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Extracting sample sizes and ancestry information.\n\n        This function parses the ancestry data. Also get counts for the europeans in the same\n        discovery stage.\n\n        Args:\n            ancestry_lut (DataFrame): Ancestry table as downloaded from the GWAS Catalog\n\n        Returns:\n            StudyIndexGWASCatalog: Slimmed and cleaned version of the ancestry annotation.\n        \"\"\"\n        from otg.datasource.gwas_catalog.study_index import (\n            StudyIndexGWASCatalogParser as GWASCatalogStudyIndexParser,\n        )\n\n        ancestry = (\n            ancestry_lut\n            # Convert column headers to camelcase:\n            .transform(\n                lambda df: df.select(\n                    *[f.expr(column2camel_case(x)) for x in df.columns]\n                )\n            ).withColumnRenamed(\n                \"studyAccession\", \"studyId\"\n            )  # studyId has not been split yet\n        )\n\n        # Parsing cohort information:\n        cohorts = ancestry_lut.select(\n            f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n            GWASCatalogStudyIndexParser.parse_cohorts(f.col(\"COHORT(S)\")).alias(\n                \"cohorts\"\n            ),\n        ).distinct()\n\n        # Get a high resolution dataset on experimental stage:\n        ancestry_stages = (\n            ancestry.groupBy(\"studyId\")\n            .pivot(\"stage\")\n            .agg(\n                f.collect_set(\n                    f.struct(\n                        f.col(\"broadAncestralCategory\").alias(\"ancestry\"),\n                        f.col(\"numberOfIndividuals\")\n                        .cast(t.LongType())\n                        .alias(\"sampleSize\"),\n                    )\n                )\n            )\n            .withColumn(\n                \"discoverySamples\",\n                GWASCatalogStudyIndexParser._parse_discovery_samples(f.col(\"initial\")),\n            )\n            .withColumnRenamed(\"replication\", \"replicationSamples\")\n            # Mapping discovery stage ancestries to LD reference:\n            .withColumn(\n                \"ldPopulationStructure\",\n                self.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n            )\n            .drop(\"initial\")\n            .persist()\n        )\n\n        # Generate information on the ancestry composition of the discovery stage, and calculate\n        # the proportion of the Europeans:\n        europeans_deconvoluted = (\n            ancestry\n            # Focus on discovery stage:\n            .filter(f.col(\"stage\") == \"initial\")\n            # Sorting ancestries if European:\n            .withColumn(\n                \"ancestryFlag\",\n                # Excluding finnish:\n                f.when(\n                    f.col(\"initialSampleDescription\").contains(\"Finnish\"),\n                    f.lit(\"other\"),\n                )\n                # Excluding Icelandic population:\n                .when(\n                    f.col(\"initialSampleDescription\").contains(\"Icelandic\"),\n                    f.lit(\"other\"),\n                )\n                # Including European ancestry:\n                .when(f.col(\"broadAncestralCategory\") == \"European\", f.lit(\"european\"))\n                # Exclude all other population:\n                .otherwise(\"other\"),\n            )\n            # Grouping by study accession and initial sample description:\n            .groupBy(\"studyId\")\n            .pivot(\"ancestryFlag\")\n            .agg(\n                # Summarizing sample sizes for all ancestries:\n                f.sum(f.col(\"numberOfIndividuals\"))\n            )\n            # Do arithmetics to make sure we have the right proportion of european in the set:\n            .withColumn(\n                \"initialSampleCountEuropean\",\n                f.when(f.col(\"european\").isNull(), f.lit(0)).otherwise(\n                    f.col(\"european\")\n                ),\n            )\n            .withColumn(\n                \"initialSampleCountOther\",\n                f.when(f.col(\"other\").isNull(), f.lit(0)).otherwise(f.col(\"other\")),\n            )\n            .withColumn(\n                \"initialSampleCount\",\n                f.col(\"initialSampleCountEuropean\") + f.col(\"other\"),\n            )\n            .drop(\n                \"european\",\n                \"other\",\n                \"initialSampleCount\",\n                \"initialSampleCountEuropean\",\n                \"initialSampleCountOther\",\n            )\n        )\n\n        parsed_ancestry_lut = ancestry_stages.join(\n            europeans_deconvoluted, on=\"studyId\", how=\"outer\"\n        )\n\n        self.df = self.df.join(parsed_ancestry_lut, on=\"studyId\", how=\"left\").join(\n            cohorts, on=\"studyId\", how=\"left\"\n        )\n        return self\n\n    def annotate_sumstats_info(\n        self: StudyIndexGWASCatalog, sumstats_lut: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Annotate summary stat locations.\n\n        Args:\n            sumstats_lut (DataFrame): listing GWAS Catalog summary stats paths\n\n        Returns:\n            StudyIndexGWASCatalog: including `summarystatsLocation` and `hasSumstats` columns\n        \"\"\"\n        gwas_sumstats_base_uri = (\n            \"ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/\"\n        )\n\n        parsed_sumstats_lut = sumstats_lut.withColumn(\n            \"summarystatsLocation\",\n            f.concat(\n                f.lit(gwas_sumstats_base_uri),\n                f.regexp_replace(f.col(\"_c0\"), r\"^\\.\\/\", \"\"),\n            ),\n        ).select(\n            f.regexp_extract(f.col(\"summarystatsLocation\"), r\"\\/(GCST\\d+)\\/\", 1).alias(\n                \"studyId\"\n            ),\n            \"summarystatsLocation\",\n            f.lit(True).alias(\"hasSumstats\"),\n        )\n\n        self.df = (\n            self.df.drop(\"hasSumstats\")\n            .join(parsed_sumstats_lut, on=\"studyId\", how=\"left\")\n            .withColumn(\"hasSumstats\", f.coalesce(f.col(\"hasSumstats\"), f.lit(False)))\n        )\n        return self\n\n    def annotate_discovery_sample_sizes(\n        self: StudyIndexGWASCatalog,\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Extract the sample size of the discovery stage of the study as annotated in the GWAS Catalog.\n\n        For some studies that measure quantitative traits, nCases and nControls can't be extracted. Therefore, we assume these are 0.\n\n        Returns:\n            StudyIndexGWASCatalog: object with columns `nCases`, `nControls`, and `nSamples` per `studyId` correctly extracted.\n        \"\"\"\n        sample_size_lut = (\n            self.df.select(\n                \"studyId\",\n                f.explode_outer(f.split(f.col(\"initialSampleSize\"), r\",\\s+\")).alias(\n                    \"samples\"\n                ),\n            )\n            # Extracting the sample size from the string:\n            .withColumn(\n                \"sampleSize\",\n                f.regexp_extract(\n                    f.regexp_replace(f.col(\"samples\"), \",\", \"\"), r\"[0-9,]+\", 0\n                ).cast(t.IntegerType()),\n            )\n            .select(\n                \"studyId\",\n                \"sampleSize\",\n                f.when(f.col(\"samples\").contains(\"cases\"), f.col(\"sampleSize\"))\n                .otherwise(f.lit(0))\n                .alias(\"nCases\"),\n                f.when(f.col(\"samples\").contains(\"controls\"), f.col(\"sampleSize\"))\n                .otherwise(f.lit(0))\n                .alias(\"nControls\"),\n            )\n            # Aggregating sample sizes for all ancestries:\n            .groupBy(\"studyId\")  # studyId has not been split yet\n            .agg(\n                f.sum(\"nCases\").alias(\"nCases\"),\n                f.sum(\"nControls\").alias(\"nControls\"),\n                f.sum(\"sampleSize\").alias(\"nSamples\"),\n            )\n        )\n        self.df = self.df.join(sample_size_lut, on=\"studyId\", how=\"left\")\n        return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries","title":"<code>annotate_ancestries(ancestry_lut: DataFrame) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Extracting sample sizes and ancestry information.</p> <p>This function parses the ancestry data. Also get counts for the europeans in the same discovery stage.</p> <p>Parameters:</p> Name Type Description Default <code>ancestry_lut</code> <code>DataFrame</code> <p>Ancestry table as downloaded from the GWAS Catalog</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Slimmed and cleaned version of the ancestry annotation.</p> Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>def annotate_ancestries(\n    self: StudyIndexGWASCatalog, ancestry_lut: DataFrame\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Extracting sample sizes and ancestry information.\n\n    This function parses the ancestry data. Also get counts for the europeans in the same\n    discovery stage.\n\n    Args:\n        ancestry_lut (DataFrame): Ancestry table as downloaded from the GWAS Catalog\n\n    Returns:\n        StudyIndexGWASCatalog: Slimmed and cleaned version of the ancestry annotation.\n    \"\"\"\n    from otg.datasource.gwas_catalog.study_index import (\n        StudyIndexGWASCatalogParser as GWASCatalogStudyIndexParser,\n    )\n\n    ancestry = (\n        ancestry_lut\n        # Convert column headers to camelcase:\n        .transform(\n            lambda df: df.select(\n                *[f.expr(column2camel_case(x)) for x in df.columns]\n            )\n        ).withColumnRenamed(\n            \"studyAccession\", \"studyId\"\n        )  # studyId has not been split yet\n    )\n\n    # Parsing cohort information:\n    cohorts = ancestry_lut.select(\n        f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n        GWASCatalogStudyIndexParser.parse_cohorts(f.col(\"COHORT(S)\")).alias(\n            \"cohorts\"\n        ),\n    ).distinct()\n\n    # Get a high resolution dataset on experimental stage:\n    ancestry_stages = (\n        ancestry.groupBy(\"studyId\")\n        .pivot(\"stage\")\n        .agg(\n            f.collect_set(\n                f.struct(\n                    f.col(\"broadAncestralCategory\").alias(\"ancestry\"),\n                    f.col(\"numberOfIndividuals\")\n                    .cast(t.LongType())\n                    .alias(\"sampleSize\"),\n                )\n            )\n        )\n        .withColumn(\n            \"discoverySamples\",\n            GWASCatalogStudyIndexParser._parse_discovery_samples(f.col(\"initial\")),\n        )\n        .withColumnRenamed(\"replication\", \"replicationSamples\")\n        # Mapping discovery stage ancestries to LD reference:\n        .withColumn(\n            \"ldPopulationStructure\",\n            self.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n        )\n        .drop(\"initial\")\n        .persist()\n    )\n\n    # Generate information on the ancestry composition of the discovery stage, and calculate\n    # the proportion of the Europeans:\n    europeans_deconvoluted = (\n        ancestry\n        # Focus on discovery stage:\n        .filter(f.col(\"stage\") == \"initial\")\n        # Sorting ancestries if European:\n        .withColumn(\n            \"ancestryFlag\",\n            # Excluding finnish:\n            f.when(\n                f.col(\"initialSampleDescription\").contains(\"Finnish\"),\n                f.lit(\"other\"),\n            )\n            # Excluding Icelandic population:\n            .when(\n                f.col(\"initialSampleDescription\").contains(\"Icelandic\"),\n                f.lit(\"other\"),\n            )\n            # Including European ancestry:\n            .when(f.col(\"broadAncestralCategory\") == \"European\", f.lit(\"european\"))\n            # Exclude all other population:\n            .otherwise(\"other\"),\n        )\n        # Grouping by study accession and initial sample description:\n        .groupBy(\"studyId\")\n        .pivot(\"ancestryFlag\")\n        .agg(\n            # Summarizing sample sizes for all ancestries:\n            f.sum(f.col(\"numberOfIndividuals\"))\n        )\n        # Do arithmetics to make sure we have the right proportion of european in the set:\n        .withColumn(\n            \"initialSampleCountEuropean\",\n            f.when(f.col(\"european\").isNull(), f.lit(0)).otherwise(\n                f.col(\"european\")\n            ),\n        )\n        .withColumn(\n            \"initialSampleCountOther\",\n            f.when(f.col(\"other\").isNull(), f.lit(0)).otherwise(f.col(\"other\")),\n        )\n        .withColumn(\n            \"initialSampleCount\",\n            f.col(\"initialSampleCountEuropean\") + f.col(\"other\"),\n        )\n        .drop(\n            \"european\",\n            \"other\",\n            \"initialSampleCount\",\n            \"initialSampleCountEuropean\",\n            \"initialSampleCountOther\",\n        )\n    )\n\n    parsed_ancestry_lut = ancestry_stages.join(\n        europeans_deconvoluted, on=\"studyId\", how=\"outer\"\n    )\n\n    self.df = self.df.join(parsed_ancestry_lut, on=\"studyId\", how=\"left\").join(\n        cohorts, on=\"studyId\", how=\"left\"\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes","title":"<code>annotate_discovery_sample_sizes() -&gt; StudyIndexGWASCatalog</code>","text":"<p>Extract the sample size of the discovery stage of the study as annotated in the GWAS Catalog.</p> <p>For some studies that measure quantitative traits, nCases and nControls can't be extracted. Therefore, we assume these are 0.</p> <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>object with columns <code>nCases</code>, <code>nControls</code>, and <code>nSamples</code> per <code>studyId</code> correctly extracted.</p> Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>def annotate_discovery_sample_sizes(\n    self: StudyIndexGWASCatalog,\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Extract the sample size of the discovery stage of the study as annotated in the GWAS Catalog.\n\n    For some studies that measure quantitative traits, nCases and nControls can't be extracted. Therefore, we assume these are 0.\n\n    Returns:\n        StudyIndexGWASCatalog: object with columns `nCases`, `nControls`, and `nSamples` per `studyId` correctly extracted.\n    \"\"\"\n    sample_size_lut = (\n        self.df.select(\n            \"studyId\",\n            f.explode_outer(f.split(f.col(\"initialSampleSize\"), r\",\\s+\")).alias(\n                \"samples\"\n            ),\n        )\n        # Extracting the sample size from the string:\n        .withColumn(\n            \"sampleSize\",\n            f.regexp_extract(\n                f.regexp_replace(f.col(\"samples\"), \",\", \"\"), r\"[0-9,]+\", 0\n            ).cast(t.IntegerType()),\n        )\n        .select(\n            \"studyId\",\n            \"sampleSize\",\n            f.when(f.col(\"samples\").contains(\"cases\"), f.col(\"sampleSize\"))\n            .otherwise(f.lit(0))\n            .alias(\"nCases\"),\n            f.when(f.col(\"samples\").contains(\"controls\"), f.col(\"sampleSize\"))\n            .otherwise(f.lit(0))\n            .alias(\"nControls\"),\n        )\n        # Aggregating sample sizes for all ancestries:\n        .groupBy(\"studyId\")  # studyId has not been split yet\n        .agg(\n            f.sum(\"nCases\").alias(\"nCases\"),\n            f.sum(\"nControls\").alias(\"nControls\"),\n            f.sum(\"sampleSize\").alias(\"nSamples\"),\n        )\n    )\n    self.df = self.df.join(sample_size_lut, on=\"studyId\", how=\"left\")\n    return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info","title":"<code>annotate_sumstats_info(sumstats_lut: DataFrame) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Annotate summary stat locations.</p> <p>Parameters:</p> Name Type Description Default <code>sumstats_lut</code> <code>DataFrame</code> <p>listing GWAS Catalog summary stats paths</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>including <code>summarystatsLocation</code> and <code>hasSumstats</code> columns</p> Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>def annotate_sumstats_info(\n    self: StudyIndexGWASCatalog, sumstats_lut: DataFrame\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Annotate summary stat locations.\n\n    Args:\n        sumstats_lut (DataFrame): listing GWAS Catalog summary stats paths\n\n    Returns:\n        StudyIndexGWASCatalog: including `summarystatsLocation` and `hasSumstats` columns\n    \"\"\"\n    gwas_sumstats_base_uri = (\n        \"ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/\"\n    )\n\n    parsed_sumstats_lut = sumstats_lut.withColumn(\n        \"summarystatsLocation\",\n        f.concat(\n            f.lit(gwas_sumstats_base_uri),\n            f.regexp_replace(f.col(\"_c0\"), r\"^\\.\\/\", \"\"),\n        ),\n    ).select(\n        f.regexp_extract(f.col(\"summarystatsLocation\"), r\"\\/(GCST\\d+)\\/\", 1).alias(\n            \"studyId\"\n        ),\n        \"summarystatsLocation\",\n        f.lit(True).alias(\"hasSumstats\"),\n    )\n\n    self.df = (\n        self.df.drop(\"hasSumstats\")\n        .join(parsed_sumstats_lut, on=\"studyId\", how=\"left\")\n        .withColumn(\"hasSumstats\", f.coalesce(f.col(\"hasSumstats\"), f.lit(False)))\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_index/#otg.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id","title":"<code>update_study_id(study_annotation: DataFrame) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Update studyId with a dataframe containing study.</p> <p>Parameters:</p> Name Type Description Default <code>study_annotation</code> <code>DataFrame</code> <p>Dataframe containing <code>updatedStudyId</code>, <code>traitFromSource</code>, <code>traitFromSourceMappedIds</code> and key column <code>studyId</code>.</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Updated study table.</p> Source code in <code>src/otg/datasource/gwas_catalog/study_index.py</code> <pre><code>def update_study_id(\n    self: StudyIndexGWASCatalog, study_annotation: DataFrame\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Update studyId with a dataframe containing study.\n\n    Args:\n        study_annotation (DataFrame): Dataframe containing `updatedStudyId`, `traitFromSource`, `traitFromSourceMappedIds` and key column `studyId`.\n\n    Returns:\n        StudyIndexGWASCatalog: Updated study table.\n    \"\"\"\n    self.df = (\n        self._df.join(\n            study_annotation.select(\n                *[\n                    f.col(c).alias(f\"updated{c}\")\n                    if c not in [\"studyId\", \"updatedStudyId\"]\n                    else f.col(c)\n                    for c in study_annotation.columns\n                ]\n            ),\n            on=\"studyId\",\n            how=\"left\",\n        )\n        .withColumn(\n            \"studyId\",\n            f.coalesce(f.col(\"updatedStudyId\"), f.col(\"studyId\")),\n        )\n        .withColumn(\n            \"traitFromSource\",\n            f.coalesce(f.col(\"updatedtraitFromSource\"), f.col(\"traitFromSource\")),\n        )\n        .withColumn(\n            \"traitFromSourceMappedIds\",\n            f.coalesce(\n                f.col(\"updatedtraitFromSourceMappedIds\"),\n                f.col(\"traitFromSourceMappedIds\"),\n            ),\n        )\n        .select(self._df.columns)\n    )\n\n    return self\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_splitter/","title":"Study Splitter","text":""},{"location":"python_api/datasource/gwas_catalog/study_splitter/#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter","title":"<code>otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter</code>","text":"<p>Splitting multi-trait GWAS Catalog studies.</p> Source code in <code>src/otg/datasource/gwas_catalog/study_splitter.py</code> <pre><code>class GWASCatalogStudySplitter:\n    \"\"\"Splitting multi-trait GWAS Catalog studies.\"\"\"\n\n    @staticmethod\n    def _resolve_trait(\n        study_trait: Column, association_trait: Column, p_value_text: Column\n    ) -&gt; Column:\n        \"\"\"Resolve trait names by consolidating association-level and study-level trait names.\n\n        Args:\n            study_trait (Column): Study-level trait name.\n            association_trait (Column): Association-level trait name.\n            p_value_text (Column): P-value text.\n\n        Returns:\n            Column: Resolved trait name.\n        \"\"\"\n        return (\n            f.when(\n                (p_value_text.isNotNull()) &amp; (p_value_text != (\"no_pvalue_text\")),\n                f.concat(\n                    association_trait,\n                    f.lit(\" [\"),\n                    p_value_text,\n                    f.lit(\"]\"),\n                ),\n            )\n            .when(\n                association_trait.isNotNull(),\n                association_trait,\n            )\n            .otherwise(study_trait)\n        )\n\n    @staticmethod\n    def _resolve_efo(association_efo: Column, study_efo: Column) -&gt; Column:\n        \"\"\"Resolve EFOs by consolidating association-level and study-level EFOs.\n\n        Args:\n            association_efo (Column): EFO column from the association table.\n            study_efo (Column): EFO column from the study table.\n\n        Returns:\n            Column: Consolidated EFO column.\n        \"\"\"\n        return f.coalesce(f.split(association_efo, r\"\\/\"), study_efo)\n\n    @staticmethod\n    def _resolve_study_id(study_id: Column, sub_study_description: Column) -&gt; Column:\n        \"\"\"Resolve study IDs by exploding association-level information (e.g. pvalue_text, EFO).\n\n        Args:\n            study_id (Column): Study ID column.\n            sub_study_description (Column): Sub-study description column from the association table.\n\n        Returns:\n            Column: Resolved study ID column.\n        \"\"\"\n        split_w = Window.partitionBy(study_id).orderBy(sub_study_description)\n        row_number = f.dense_rank().over(split_w)\n        substudy_count = f.approx_count_distinct(row_number).over(split_w)\n        return f.when(substudy_count == 1, study_id).otherwise(\n            f.concat_ws(\"_\", study_id, row_number)\n        )\n\n    @classmethod\n    def split(\n        cls: type[GWASCatalogStudySplitter],\n        studies: StudyIndexGWASCatalog,\n        associations: StudyLocusGWASCatalog,\n    ) -&gt; Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]:\n        \"\"\"Splitting multi-trait GWAS Catalog studies.\n\n        If assigned disease of the study and the association don't agree, we assume the study needs to be split.\n        Then disease EFOs, trait names and study ID are consolidated\n\n        Args:\n            studies (StudyIndexGWASCatalog): GWAS Catalog studies.\n            associations (StudyLocusGWASCatalog): GWAS Catalog associations.\n\n        Returns:\n            Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations.\n        \"\"\"\n        # Composite of studies and associations to resolve scattered information\n        st_ass = (\n            associations.df.join(f.broadcast(studies.df), on=\"studyId\", how=\"inner\")\n            .select(\n                \"studyId\",\n                \"subStudyDescription\",\n                cls._resolve_study_id(\n                    f.col(\"studyId\"), f.col(\"subStudyDescription\")\n                ).alias(\"updatedStudyId\"),\n                cls._resolve_trait(\n                    f.col(\"traitFromSource\"),\n                    f.split(\"subStudyDescription\", r\"\\|\").getItem(0),\n                    f.split(\"subStudyDescription\", r\"\\|\").getItem(1),\n                ).alias(\"traitFromSource\"),\n                cls._resolve_efo(\n                    f.split(\"subStudyDescription\", r\"\\|\").getItem(2),\n                    f.col(\"traitFromSourceMappedIds\"),\n                ).alias(\"traitFromSourceMappedIds\"),\n            )\n            .persist()\n        )\n\n        return (\n            studies.update_study_id(\n                st_ass.select(\n                    \"studyId\",\n                    \"updatedStudyId\",\n                    \"traitFromSource\",\n                    \"traitFromSourceMappedIds\",\n                ).distinct()\n            ),\n            associations.update_study_id(\n                st_ass.select(\n                    \"updatedStudyId\", \"studyId\", \"subStudyDescription\"\n                ).distinct()\n            ).qc_ambiguous_study(),\n        )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/study_splitter/#otg.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split","title":"<code>split(studies: StudyIndexGWASCatalog, associations: StudyLocusGWASCatalog) -&gt; Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]</code>  <code>classmethod</code>","text":"<p>Splitting multi-trait GWAS Catalog studies.</p> <p>If assigned disease of the study and the association don't agree, we assume the study needs to be split. Then disease EFOs, trait names and study ID are consolidated</p> <p>Parameters:</p> Name Type Description Default <code>studies</code> <code>StudyIndexGWASCatalog</code> <p>GWAS Catalog studies.</p> required <code>associations</code> <code>StudyLocusGWASCatalog</code> <p>GWAS Catalog associations.</p> required <p>Returns:</p> Type Description <code>Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]</code> <p>Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations.</p> Source code in <code>src/otg/datasource/gwas_catalog/study_splitter.py</code> <pre><code>@classmethod\ndef split(\n    cls: type[GWASCatalogStudySplitter],\n    studies: StudyIndexGWASCatalog,\n    associations: StudyLocusGWASCatalog,\n) -&gt; Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]:\n    \"\"\"Splitting multi-trait GWAS Catalog studies.\n\n    If assigned disease of the study and the association don't agree, we assume the study needs to be split.\n    Then disease EFOs, trait names and study ID are consolidated\n\n    Args:\n        studies (StudyIndexGWASCatalog): GWAS Catalog studies.\n        associations (StudyLocusGWASCatalog): GWAS Catalog associations.\n\n    Returns:\n        Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations.\n    \"\"\"\n    # Composite of studies and associations to resolve scattered information\n    st_ass = (\n        associations.df.join(f.broadcast(studies.df), on=\"studyId\", how=\"inner\")\n        .select(\n            \"studyId\",\n            \"subStudyDescription\",\n            cls._resolve_study_id(\n                f.col(\"studyId\"), f.col(\"subStudyDescription\")\n            ).alias(\"updatedStudyId\"),\n            cls._resolve_trait(\n                f.col(\"traitFromSource\"),\n                f.split(\"subStudyDescription\", r\"\\|\").getItem(0),\n                f.split(\"subStudyDescription\", r\"\\|\").getItem(1),\n            ).alias(\"traitFromSource\"),\n            cls._resolve_efo(\n                f.split(\"subStudyDescription\", r\"\\|\").getItem(2),\n                f.col(\"traitFromSourceMappedIds\"),\n            ).alias(\"traitFromSourceMappedIds\"),\n        )\n        .persist()\n    )\n\n    return (\n        studies.update_study_id(\n            st_ass.select(\n                \"studyId\",\n                \"updatedStudyId\",\n                \"traitFromSource\",\n                \"traitFromSourceMappedIds\",\n            ).distinct()\n        ),\n        associations.update_study_id(\n            st_ass.select(\n                \"updatedStudyId\", \"studyId\", \"subStudyDescription\"\n            ).distinct()\n        ).qc_ambiguous_study(),\n    )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/summary_statistics/","title":"Summary statistics","text":""},{"location":"python_api/datasource/gwas_catalog/summary_statistics/#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics","title":"<code>otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics</code>  <code>dataclass</code>","text":"<p>             Bases: <code>SummaryStatistics</code></p> <p>GWAS Catalog Summary Statistics reader.</p> Source code in <code>src/otg/datasource/gwas_catalog/summary_statistics.py</code> <pre><code>@dataclass\nclass GWASCatalogSummaryStatistics(SummaryStatistics):\n    \"\"\"GWAS Catalog Summary Statistics reader.\"\"\"\n\n    @classmethod\n    def from_gwas_harmonized_summary_stats(\n        cls: type[GWASCatalogSummaryStatistics],\n        spark: SparkSession,\n        sumstats_file: str,\n    ) -&gt; GWASCatalogSummaryStatistics:\n        \"\"\"Create summary statistics object from summary statistics flatfile, harmonized by the GWAS Catalog.\n\n        Things got slightly complicated given the GWAS Catalog harmonization pipelines changed recently so we had to accomodate to\n        both formats.\n\n        Args:\n            spark (SparkSession): spark session\n            sumstats_file (str): list of GWAS Catalog summary stat files, with study ids in them.\n\n        Returns:\n            GWASCatalogSummaryStatistics: Summary statistics object.\n        \"\"\"\n        sumstats_df = spark.read.csv(sumstats_file, sep=\"\\t\", header=True).withColumn(\n            # Parsing GWAS Catalog study identifier from filename:\n            \"studyId\",\n            f.lit(filename_to_study_identifier(sumstats_file)),\n        )\n\n        # Parsing variant id fields:\n        chromosome = (\n            f.col(\"hm_chrom\")\n            if \"hm_chrom\" in sumstats_df.columns\n            else f.col(\"chromosome\")\n        ).cast(t.StringType())\n        position = (\n            f.col(\"hm_pos\")\n            if \"hm_pos\" in sumstats_df.columns\n            else f.col(\"base_pair_location\")\n        ).cast(t.IntegerType())\n        ref_allele = (\n            f.col(\"hm_other_allele\")\n            if \"hm_other_allele\" in sumstats_df.columns\n            else f.col(\"other_allele\")\n        )\n        alt_allele = (\n            f.col(\"hm_effect_allele\")\n            if \"hm_effect_allele\" in sumstats_df.columns\n            else f.col(\"effect_allele\")\n        )\n\n        # Parsing p-value (get a tuple with mantissa and exponent):\n        p_value_expression = (\n            parse_pvalue(f.col(\"p_value\"))\n            if \"p_value\" in sumstats_df.columns\n            else neglog_pvalue_to_mantissa_and_exponent(f.col(\"neg_log_10_p_value\"))\n        )\n\n        # The effect allele frequency is an optional column, we have to test if it is there:\n        allele_frequency = (\n            f.col(\"effect_allele_frequency\")\n            if \"effect_allele_frequency\" in sumstats_df.columns\n            else f.lit(None)\n        ).cast(t.FloatType())\n\n        # Do we have sample size? This expression captures 99.7% of sample size columns.\n        sample_size = (f.col(\"n\") if \"n\" in sumstats_df.columns else f.lit(None)).cast(\n            t.IntegerType()\n        )\n\n        # Depending on the input, we might have beta, but the column might not be there at all also old format calls differently:\n        beta_expression = (\n            f.col(\"hm_beta\")\n            if \"hm_beta\" in sumstats_df.columns\n            else f.col(\"beta\")\n            if \"beta\" in sumstats_df.columns\n            # If no column, create one:\n            else f.lit(None)\n        ).cast(t.DoubleType())\n\n        # We might have odds ratio or hazard ratio, wich are basically the same:\n        odds_ratio_expression = (\n            f.col(\"hm_odds_ratio\")\n            if \"hm_odds_ratio\" in sumstats_df.columns\n            else f.col(\"odds_ratio\")\n            if \"odds_ratio\" in sumstats_df.columns\n            else f.col(\"hazard_ratio\")\n            if \"hazard_ratio\" in sumstats_df.columns\n            # If no column, create one:\n            else f.lit(None)\n        ).cast(t.DoubleType())\n\n        # Does the file have standard error column?\n        standard_error = (\n            f.col(\"standard_error\")\n            if \"standard_error\" in sumstats_df.columns\n            else f.lit(None)\n        ).cast(t.DoubleType())\n\n        # Processing columns of interest:\n        processed_sumstats_df = (\n            sumstats_df\n            # Dropping rows which doesn't have proper position:\n            .select(\n                \"studyId\",\n                # Adding variant identifier:\n                f.concat_ws(\n                    \"_\",\n                    chromosome,\n                    position,\n                    ref_allele,\n                    alt_allele,\n                ).alias(\"variantId\"),\n                chromosome.alias(\"chromosome\"),\n                position.alias(\"position\"),\n                # Parsing p-value mantissa and exponent:\n                *p_value_expression,\n                # Converting/calculating effect and confidence interval:\n                *convert_odds_ratio_to_beta(\n                    beta_expression,\n                    odds_ratio_expression,\n                    standard_error,\n                ),\n                allele_frequency.alias(\"effectAlleleFrequencyFromSource\"),\n                sample_size.alias(\"sampleSize\"),\n            )\n            .filter(\n                # Dropping associations where no harmonized position is available:\n                f.col(\"position\").isNotNull()\n                &amp;\n                # We are not interested in associations with zero effect:\n                (f.col(\"beta\") != 0)\n            )\n            .orderBy(f.col(\"chromosome\"), f.col(\"position\"))\n            # median study size is 200Mb, max is 2.6Gb\n            .repartition(20)\n        )\n\n        # Initializing summary statistics object:\n        return cls(\n            _df=processed_sumstats_df,\n            _schema=cls.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/gwas_catalog/summary_statistics/#otg.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats","title":"<code>from_gwas_harmonized_summary_stats(spark: SparkSession, sumstats_file: str) -&gt; GWASCatalogSummaryStatistics</code>  <code>classmethod</code>","text":"<p>Create summary statistics object from summary statistics flatfile, harmonized by the GWAS Catalog.</p> <p>Things got slightly complicated given the GWAS Catalog harmonization pipelines changed recently so we had to accomodate to both formats.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>spark session</p> required <code>sumstats_file</code> <code>str</code> <p>list of GWAS Catalog summary stat files, with study ids in them.</p> required <p>Returns:</p> Name Type Description <code>GWASCatalogSummaryStatistics</code> <code>GWASCatalogSummaryStatistics</code> <p>Summary statistics object.</p> Source code in <code>src/otg/datasource/gwas_catalog/summary_statistics.py</code> <pre><code>@classmethod\ndef from_gwas_harmonized_summary_stats(\n    cls: type[GWASCatalogSummaryStatistics],\n    spark: SparkSession,\n    sumstats_file: str,\n) -&gt; GWASCatalogSummaryStatistics:\n    \"\"\"Create summary statistics object from summary statistics flatfile, harmonized by the GWAS Catalog.\n\n    Things got slightly complicated given the GWAS Catalog harmonization pipelines changed recently so we had to accomodate to\n    both formats.\n\n    Args:\n        spark (SparkSession): spark session\n        sumstats_file (str): list of GWAS Catalog summary stat files, with study ids in them.\n\n    Returns:\n        GWASCatalogSummaryStatistics: Summary statistics object.\n    \"\"\"\n    sumstats_df = spark.read.csv(sumstats_file, sep=\"\\t\", header=True).withColumn(\n        # Parsing GWAS Catalog study identifier from filename:\n        \"studyId\",\n        f.lit(filename_to_study_identifier(sumstats_file)),\n    )\n\n    # Parsing variant id fields:\n    chromosome = (\n        f.col(\"hm_chrom\")\n        if \"hm_chrom\" in sumstats_df.columns\n        else f.col(\"chromosome\")\n    ).cast(t.StringType())\n    position = (\n        f.col(\"hm_pos\")\n        if \"hm_pos\" in sumstats_df.columns\n        else f.col(\"base_pair_location\")\n    ).cast(t.IntegerType())\n    ref_allele = (\n        f.col(\"hm_other_allele\")\n        if \"hm_other_allele\" in sumstats_df.columns\n        else f.col(\"other_allele\")\n    )\n    alt_allele = (\n        f.col(\"hm_effect_allele\")\n        if \"hm_effect_allele\" in sumstats_df.columns\n        else f.col(\"effect_allele\")\n    )\n\n    # Parsing p-value (get a tuple with mantissa and exponent):\n    p_value_expression = (\n        parse_pvalue(f.col(\"p_value\"))\n        if \"p_value\" in sumstats_df.columns\n        else neglog_pvalue_to_mantissa_and_exponent(f.col(\"neg_log_10_p_value\"))\n    )\n\n    # The effect allele frequency is an optional column, we have to test if it is there:\n    allele_frequency = (\n        f.col(\"effect_allele_frequency\")\n        if \"effect_allele_frequency\" in sumstats_df.columns\n        else f.lit(None)\n    ).cast(t.FloatType())\n\n    # Do we have sample size? This expression captures 99.7% of sample size columns.\n    sample_size = (f.col(\"n\") if \"n\" in sumstats_df.columns else f.lit(None)).cast(\n        t.IntegerType()\n    )\n\n    # Depending on the input, we might have beta, but the column might not be there at all also old format calls differently:\n    beta_expression = (\n        f.col(\"hm_beta\")\n        if \"hm_beta\" in sumstats_df.columns\n        else f.col(\"beta\")\n        if \"beta\" in sumstats_df.columns\n        # If no column, create one:\n        else f.lit(None)\n    ).cast(t.DoubleType())\n\n    # We might have odds ratio or hazard ratio, wich are basically the same:\n    odds_ratio_expression = (\n        f.col(\"hm_odds_ratio\")\n        if \"hm_odds_ratio\" in sumstats_df.columns\n        else f.col(\"odds_ratio\")\n        if \"odds_ratio\" in sumstats_df.columns\n        else f.col(\"hazard_ratio\")\n        if \"hazard_ratio\" in sumstats_df.columns\n        # If no column, create one:\n        else f.lit(None)\n    ).cast(t.DoubleType())\n\n    # Does the file have standard error column?\n    standard_error = (\n        f.col(\"standard_error\")\n        if \"standard_error\" in sumstats_df.columns\n        else f.lit(None)\n    ).cast(t.DoubleType())\n\n    # Processing columns of interest:\n    processed_sumstats_df = (\n        sumstats_df\n        # Dropping rows which doesn't have proper position:\n        .select(\n            \"studyId\",\n            # Adding variant identifier:\n            f.concat_ws(\n                \"_\",\n                chromosome,\n                position,\n                ref_allele,\n                alt_allele,\n            ).alias(\"variantId\"),\n            chromosome.alias(\"chromosome\"),\n            position.alias(\"position\"),\n            # Parsing p-value mantissa and exponent:\n            *p_value_expression,\n            # Converting/calculating effect and confidence interval:\n            *convert_odds_ratio_to_beta(\n                beta_expression,\n                odds_ratio_expression,\n                standard_error,\n            ),\n            allele_frequency.alias(\"effectAlleleFrequencyFromSource\"),\n            sample_size.alias(\"sampleSize\"),\n        )\n        .filter(\n            # Dropping associations where no harmonized position is available:\n            f.col(\"position\").isNotNull()\n            &amp;\n            # We are not interested in associations with zero effect:\n            (f.col(\"beta\") != 0)\n        )\n        .orderBy(f.col(\"chromosome\"), f.col(\"position\"))\n        # median study size is 200Mb, max is 2.6Gb\n        .repartition(20)\n    )\n\n    # Initializing summary statistics object:\n    return cls(\n        _df=processed_sumstats_df,\n        _schema=cls.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/intervals/_intervals/","title":"Chromatin intervals","text":"<p>TBC</p>"},{"location":"python_api/datasource/intervals/andersson/","title":"Andersson et al.","text":""},{"location":"python_api/datasource/intervals/andersson/#otg.datasource.intervals.andersson.IntervalsAndersson","title":"<code>otg.datasource.intervals.andersson.IntervalsAndersson</code>","text":"<p>Interval dataset from Andersson et al. 2014.</p> Source code in <code>src/otg/datasource/intervals/andersson.py</code> <pre><code>class IntervalsAndersson:\n    \"\"\"Interval dataset from Andersson et al. 2014.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read andersson2014 dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to the dataset\n\n        Returns:\n            DataFrame: Raw Andersson et al. dataframe\n        \"\"\"\n        input_schema = t.StructType.fromJson(\n            json.loads(\n                pkg_resources.read_text(schemas, \"andersson2014.json\", encoding=\"utf-8\")\n            )\n        )\n        return (\n            spark.read.option(\"delimiter\", \"\\t\")\n            .option(\"mode\", \"DROPMALFORMED\")\n            .option(\"header\", \"true\")\n            .schema(input_schema)\n            .csv(path)\n        )\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsAndersson],\n        raw_anderson_df: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse Andersson et al. 2014 dataset.\n\n        Args:\n            raw_anderson_df (DataFrame): Raw Andersson et al. dataset\n            gene_index (GeneIndex): Gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Intervals dataset\n        \"\"\"\n        # Constant values:\n        dataset_name = \"andersson2014\"\n        experiment_type = \"fantom5\"\n        pmid = \"24670763\"\n        bio_feature = \"aggregate\"\n        twosided_threshold = 2.45e6  # &lt;-  this needs to phased out. Filter by percentile instead of absolute value.\n\n        # Read the anderson file:\n        parsed_anderson_df = (\n            raw_anderson_df\n            # Parsing score column and casting as float:\n            .withColumn(\"score\", f.col(\"score\").cast(\"float\") / f.lit(1000))\n            # Parsing the 'name' column:\n            .withColumn(\"parsedName\", f.split(f.col(\"name\"), \";\"))\n            .withColumn(\"gene_symbol\", f.col(\"parsedName\")[2])\n            .withColumn(\"location\", f.col(\"parsedName\")[0])\n            .withColumn(\n                \"chrom\",\n                f.regexp_replace(f.split(f.col(\"location\"), \":|-\")[0], \"chr\", \"\"),\n            )\n            .withColumn(\n                \"start\", f.split(f.col(\"location\"), \":|-\")[1].cast(t.IntegerType())\n            )\n            .withColumn(\n                \"end\", f.split(f.col(\"location\"), \":|-\")[2].cast(t.IntegerType())\n            )\n            # Select relevant columns:\n            .select(\"chrom\", \"start\", \"end\", \"gene_symbol\", \"score\")\n            # Drop rows with non-canonical chromosomes:\n            .filter(\n                f.col(\"chrom\").isin([str(x) for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"])\n            )\n            # For each region/gene, keep only one row with the highest score:\n            .groupBy(\"chrom\", \"start\", \"end\", \"gene_symbol\")\n            .agg(f.max(\"score\").alias(\"resourceScore\"))\n            .orderBy(\"chrom\", \"start\")\n        )\n\n        return Intervals(\n            _df=(\n                # Lift over the intervals:\n                lift.convert_intervals(parsed_anderson_df, \"chrom\", \"start\", \"end\")\n                .drop(\"start\", \"end\")\n                .withColumnRenamed(\"mapped_start\", \"start\")\n                .withColumnRenamed(\"mapped_end\", \"end\")\n                .distinct()\n                # Joining with the gene index\n                .alias(\"intervals\")\n                .join(\n                    gene_index.symbols_lut().alias(\"genes\"),\n                    on=[\n                        f.col(\"intervals.gene_symbol\") == f.col(\"genes.geneSymbol\"),\n                        # Drop rows where the TSS is far from the start of the region\n                        f.abs(\n                            (f.col(\"intervals.start\") + f.col(\"intervals.end\")) / 2\n                            - f.col(\"tss\")\n                        )\n                        &lt;= twosided_threshold,\n                    ],\n                    how=\"left\",\n                )\n                # Select relevant columns:\n                .select(\n                    f.col(\"chrom\").alias(\"chromosome\"),\n                    f.col(\"intervals.start\").alias(\"start\"),\n                    f.col(\"intervals.end\").alias(\"end\"),\n                    \"geneId\",\n                    \"resourceScore\",\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                    f.lit(bio_feature).alias(\"biofeature\"),\n                )\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/intervals/andersson/#otg.datasource.intervals.andersson.IntervalsAndersson.parse","title":"<code>parse(raw_anderson_df: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse Andersson et al. 2014 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>raw_anderson_df</code> <code>DataFrame</code> <p>Raw Andersson et al. dataset</p> required <code>gene_index</code> <code>GeneIndex</code> <p>Gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Intervals dataset</p> Source code in <code>src/otg/datasource/intervals/andersson.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsAndersson],\n    raw_anderson_df: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse Andersson et al. 2014 dataset.\n\n    Args:\n        raw_anderson_df (DataFrame): Raw Andersson et al. dataset\n        gene_index (GeneIndex): Gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Intervals dataset\n    \"\"\"\n    # Constant values:\n    dataset_name = \"andersson2014\"\n    experiment_type = \"fantom5\"\n    pmid = \"24670763\"\n    bio_feature = \"aggregate\"\n    twosided_threshold = 2.45e6  # &lt;-  this needs to phased out. Filter by percentile instead of absolute value.\n\n    # Read the anderson file:\n    parsed_anderson_df = (\n        raw_anderson_df\n        # Parsing score column and casting as float:\n        .withColumn(\"score\", f.col(\"score\").cast(\"float\") / f.lit(1000))\n        # Parsing the 'name' column:\n        .withColumn(\"parsedName\", f.split(f.col(\"name\"), \";\"))\n        .withColumn(\"gene_symbol\", f.col(\"parsedName\")[2])\n        .withColumn(\"location\", f.col(\"parsedName\")[0])\n        .withColumn(\n            \"chrom\",\n            f.regexp_replace(f.split(f.col(\"location\"), \":|-\")[0], \"chr\", \"\"),\n        )\n        .withColumn(\n            \"start\", f.split(f.col(\"location\"), \":|-\")[1].cast(t.IntegerType())\n        )\n        .withColumn(\n            \"end\", f.split(f.col(\"location\"), \":|-\")[2].cast(t.IntegerType())\n        )\n        # Select relevant columns:\n        .select(\"chrom\", \"start\", \"end\", \"gene_symbol\", \"score\")\n        # Drop rows with non-canonical chromosomes:\n        .filter(\n            f.col(\"chrom\").isin([str(x) for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"])\n        )\n        # For each region/gene, keep only one row with the highest score:\n        .groupBy(\"chrom\", \"start\", \"end\", \"gene_symbol\")\n        .agg(f.max(\"score\").alias(\"resourceScore\"))\n        .orderBy(\"chrom\", \"start\")\n    )\n\n    return Intervals(\n        _df=(\n            # Lift over the intervals:\n            lift.convert_intervals(parsed_anderson_df, \"chrom\", \"start\", \"end\")\n            .drop(\"start\", \"end\")\n            .withColumnRenamed(\"mapped_start\", \"start\")\n            .withColumnRenamed(\"mapped_end\", \"end\")\n            .distinct()\n            # Joining with the gene index\n            .alias(\"intervals\")\n            .join(\n                gene_index.symbols_lut().alias(\"genes\"),\n                on=[\n                    f.col(\"intervals.gene_symbol\") == f.col(\"genes.geneSymbol\"),\n                    # Drop rows where the TSS is far from the start of the region\n                    f.abs(\n                        (f.col(\"intervals.start\") + f.col(\"intervals.end\")) / 2\n                        - f.col(\"tss\")\n                    )\n                    &lt;= twosided_threshold,\n                ],\n                how=\"left\",\n            )\n            # Select relevant columns:\n            .select(\n                f.col(\"chrom\").alias(\"chromosome\"),\n                f.col(\"intervals.start\").alias(\"start\"),\n                f.col(\"intervals.end\").alias(\"end\"),\n                \"geneId\",\n                \"resourceScore\",\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n                f.lit(bio_feature).alias(\"biofeature\"),\n            )\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/intervals/andersson/#otg.datasource.intervals.andersson.IntervalsAndersson.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read andersson2014 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to the dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Raw Andersson et al. dataframe</p> Source code in <code>src/otg/datasource/intervals/andersson.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read andersson2014 dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to the dataset\n\n    Returns:\n        DataFrame: Raw Andersson et al. dataframe\n    \"\"\"\n    input_schema = t.StructType.fromJson(\n        json.loads(\n            pkg_resources.read_text(schemas, \"andersson2014.json\", encoding=\"utf-8\")\n        )\n    )\n    return (\n        spark.read.option(\"delimiter\", \"\\t\")\n        .option(\"mode\", \"DROPMALFORMED\")\n        .option(\"header\", \"true\")\n        .schema(input_schema)\n        .csv(path)\n    )\n</code></pre>"},{"location":"python_api/datasource/intervals/javierre/","title":"Javierre et al.","text":""},{"location":"python_api/datasource/intervals/javierre/#otg.datasource.intervals.javierre.IntervalsJavierre","title":"<code>otg.datasource.intervals.javierre.IntervalsJavierre</code>","text":"<p>Interval dataset from Javierre et al. 2016.</p> Source code in <code>src/otg/datasource/intervals/javierre.py</code> <pre><code>class IntervalsJavierre:\n    \"\"\"Interval dataset from Javierre et al. 2016.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read Javierre dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to dataset\n\n        Returns:\n            DataFrame: Raw Javierre dataset\n        \"\"\"\n        return spark.read.parquet(path)\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsJavierre],\n        javierre_raw: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse Javierre et al. 2016 dataset.\n\n        Args:\n            javierre_raw (DataFrame): Raw Javierre data\n            gene_index (GeneIndex): Gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Javierre et al. 2016 interval data\n        \"\"\"\n        # Constant values:\n        dataset_name = \"javierre2016\"\n        experiment_type = \"pchic\"\n        pmid = \"27863249\"\n        twosided_threshold = 2.45e6\n\n        # Read Javierre data:\n        javierre_parsed = (\n            javierre_raw\n            # Splitting name column into chromosome, start, end, and score:\n            .withColumn(\"name_split\", f.split(f.col(\"name\"), r\":|-|,\"))\n            .withColumn(\n                \"name_chr\",\n                f.regexp_replace(f.col(\"name_split\")[0], \"chr\", \"\").cast(\n                    t.StringType()\n                ),\n            )\n            .withColumn(\"name_start\", f.col(\"name_split\")[1].cast(t.IntegerType()))\n            .withColumn(\"name_end\", f.col(\"name_split\")[2].cast(t.IntegerType()))\n            .withColumn(\"name_score\", f.col(\"name_split\")[3].cast(t.FloatType()))\n            # Cleaning up chromosome:\n            .withColumn(\n                \"chrom\",\n                f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").cast(t.StringType()),\n            )\n            .drop(\"name_split\", \"name\", \"annotation\")\n            # Keep canonical chromosomes and consistent chromosomes with scores:\n            .filter(\n                (f.col(\"name_score\").isNotNull())\n                &amp; (f.col(\"chrom\") == f.col(\"name_chr\"))\n                &amp; f.col(\"name_chr\").isin(\n                    [f\"{x}\" for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"]\n                )\n            )\n        )\n\n        # Lifting over intervals:\n        javierre_remapped = (\n            javierre_parsed\n            # Lifting over to GRCh38 interval 1:\n            .transform(lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\"))\n            .drop(\"start\", \"end\")\n            .withColumnRenamed(\"mapped_chrom\", \"chrom\")\n            .withColumnRenamed(\"mapped_start\", \"start\")\n            .withColumnRenamed(\"mapped_end\", \"end\")\n            # Lifting over interval 2 to GRCh38:\n            .transform(\n                lambda df: lift.convert_intervals(\n                    df, \"name_chr\", \"name_start\", \"name_end\"\n                )\n            )\n            .drop(\"name_start\", \"name_end\")\n            .withColumnRenamed(\"mapped_name_chr\", \"name_chr\")\n            .withColumnRenamed(\"mapped_name_start\", \"name_start\")\n            .withColumnRenamed(\"mapped_name_end\", \"name_end\")\n        )\n\n        # Once the intervals are lifted, extracting the unique intervals:\n        unique_intervals_with_genes = (\n            javierre_remapped.select(\n                f.col(\"chrom\"),\n                f.col(\"start\").cast(t.IntegerType()),\n                f.col(\"end\").cast(t.IntegerType()),\n            )\n            .distinct()\n            .alias(\"intervals\")\n            .join(\n                gene_index.locations_lut().alias(\"genes\"),\n                on=[\n                    f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                    (\n                        (f.col(\"intervals.start\") &gt;= f.col(\"genes.start\"))\n                        &amp; (f.col(\"intervals.start\") &lt;= f.col(\"genes.end\"))\n                    )\n                    | (\n                        (f.col(\"intervals.end\") &gt;= f.col(\"genes.start\"))\n                        &amp; (f.col(\"intervals.end\") &lt;= f.col(\"genes.end\"))\n                    ),\n                ],\n                how=\"left\",\n            )\n            .select(\n                f.col(\"intervals.chrom\").alias(\"chrom\"),\n                f.col(\"intervals.start\").alias(\"start\"),\n                f.col(\"intervals.end\").alias(\"end\"),\n                f.col(\"genes.geneId\").alias(\"geneId\"),\n                f.col(\"genes.tss\").alias(\"tss\"),\n            )\n        )\n\n        # Joining back the data:\n        return Intervals(\n            _df=(\n                javierre_remapped.join(\n                    unique_intervals_with_genes,\n                    on=[\"chrom\", \"start\", \"end\"],\n                    how=\"left\",\n                )\n                .filter(\n                    # Drop rows where the TSS is far from the start of the region\n                    f.abs((f.col(\"start\") + f.col(\"end\")) / 2 - f.col(\"tss\"))\n                    &lt;= twosided_threshold\n                )\n                # For each gene, keep only the highest scoring interval:\n                .groupBy(\"name_chr\", \"name_start\", \"name_end\", \"geneId\", \"bio_feature\")\n                .agg(f.max(f.col(\"name_score\")).alias(\"resourceScore\"))\n                # Create the output:\n                .select(\n                    f.col(\"name_chr\").alias(\"chromosome\"),\n                    f.col(\"name_start\").alias(\"start\"),\n                    f.col(\"name_end\").alias(\"end\"),\n                    f.col(\"resourceScore\").cast(t.DoubleType()),\n                    f.col(\"geneId\"),\n                    f.col(\"bio_feature\").alias(\"biofeature\"),\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                )\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/intervals/javierre/#otg.datasource.intervals.javierre.IntervalsJavierre.parse","title":"<code>parse(javierre_raw: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse Javierre et al. 2016 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>javierre_raw</code> <code>DataFrame</code> <p>Raw Javierre data</p> required <code>gene_index</code> <code>GeneIndex</code> <p>Gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Javierre et al. 2016 interval data</p> Source code in <code>src/otg/datasource/intervals/javierre.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsJavierre],\n    javierre_raw: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse Javierre et al. 2016 dataset.\n\n    Args:\n        javierre_raw (DataFrame): Raw Javierre data\n        gene_index (GeneIndex): Gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Javierre et al. 2016 interval data\n    \"\"\"\n    # Constant values:\n    dataset_name = \"javierre2016\"\n    experiment_type = \"pchic\"\n    pmid = \"27863249\"\n    twosided_threshold = 2.45e6\n\n    # Read Javierre data:\n    javierre_parsed = (\n        javierre_raw\n        # Splitting name column into chromosome, start, end, and score:\n        .withColumn(\"name_split\", f.split(f.col(\"name\"), r\":|-|,\"))\n        .withColumn(\n            \"name_chr\",\n            f.regexp_replace(f.col(\"name_split\")[0], \"chr\", \"\").cast(\n                t.StringType()\n            ),\n        )\n        .withColumn(\"name_start\", f.col(\"name_split\")[1].cast(t.IntegerType()))\n        .withColumn(\"name_end\", f.col(\"name_split\")[2].cast(t.IntegerType()))\n        .withColumn(\"name_score\", f.col(\"name_split\")[3].cast(t.FloatType()))\n        # Cleaning up chromosome:\n        .withColumn(\n            \"chrom\",\n            f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").cast(t.StringType()),\n        )\n        .drop(\"name_split\", \"name\", \"annotation\")\n        # Keep canonical chromosomes and consistent chromosomes with scores:\n        .filter(\n            (f.col(\"name_score\").isNotNull())\n            &amp; (f.col(\"chrom\") == f.col(\"name_chr\"))\n            &amp; f.col(\"name_chr\").isin(\n                [f\"{x}\" for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"]\n            )\n        )\n    )\n\n    # Lifting over intervals:\n    javierre_remapped = (\n        javierre_parsed\n        # Lifting over to GRCh38 interval 1:\n        .transform(lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\"))\n        .drop(\"start\", \"end\")\n        .withColumnRenamed(\"mapped_chrom\", \"chrom\")\n        .withColumnRenamed(\"mapped_start\", \"start\")\n        .withColumnRenamed(\"mapped_end\", \"end\")\n        # Lifting over interval 2 to GRCh38:\n        .transform(\n            lambda df: lift.convert_intervals(\n                df, \"name_chr\", \"name_start\", \"name_end\"\n            )\n        )\n        .drop(\"name_start\", \"name_end\")\n        .withColumnRenamed(\"mapped_name_chr\", \"name_chr\")\n        .withColumnRenamed(\"mapped_name_start\", \"name_start\")\n        .withColumnRenamed(\"mapped_name_end\", \"name_end\")\n    )\n\n    # Once the intervals are lifted, extracting the unique intervals:\n    unique_intervals_with_genes = (\n        javierre_remapped.select(\n            f.col(\"chrom\"),\n            f.col(\"start\").cast(t.IntegerType()),\n            f.col(\"end\").cast(t.IntegerType()),\n        )\n        .distinct()\n        .alias(\"intervals\")\n        .join(\n            gene_index.locations_lut().alias(\"genes\"),\n            on=[\n                f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                (\n                    (f.col(\"intervals.start\") &gt;= f.col(\"genes.start\"))\n                    &amp; (f.col(\"intervals.start\") &lt;= f.col(\"genes.end\"))\n                )\n                | (\n                    (f.col(\"intervals.end\") &gt;= f.col(\"genes.start\"))\n                    &amp; (f.col(\"intervals.end\") &lt;= f.col(\"genes.end\"))\n                ),\n            ],\n            how=\"left\",\n        )\n        .select(\n            f.col(\"intervals.chrom\").alias(\"chrom\"),\n            f.col(\"intervals.start\").alias(\"start\"),\n            f.col(\"intervals.end\").alias(\"end\"),\n            f.col(\"genes.geneId\").alias(\"geneId\"),\n            f.col(\"genes.tss\").alias(\"tss\"),\n        )\n    )\n\n    # Joining back the data:\n    return Intervals(\n        _df=(\n            javierre_remapped.join(\n                unique_intervals_with_genes,\n                on=[\"chrom\", \"start\", \"end\"],\n                how=\"left\",\n            )\n            .filter(\n                # Drop rows where the TSS is far from the start of the region\n                f.abs((f.col(\"start\") + f.col(\"end\")) / 2 - f.col(\"tss\"))\n                &lt;= twosided_threshold\n            )\n            # For each gene, keep only the highest scoring interval:\n            .groupBy(\"name_chr\", \"name_start\", \"name_end\", \"geneId\", \"bio_feature\")\n            .agg(f.max(f.col(\"name_score\")).alias(\"resourceScore\"))\n            # Create the output:\n            .select(\n                f.col(\"name_chr\").alias(\"chromosome\"),\n                f.col(\"name_start\").alias(\"start\"),\n                f.col(\"name_end\").alias(\"end\"),\n                f.col(\"resourceScore\").cast(t.DoubleType()),\n                f.col(\"geneId\"),\n                f.col(\"bio_feature\").alias(\"biofeature\"),\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n            )\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/intervals/javierre/#otg.datasource.intervals.javierre.IntervalsJavierre.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read Javierre dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Raw Javierre dataset</p> Source code in <code>src/otg/datasource/intervals/javierre.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read Javierre dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to dataset\n\n    Returns:\n        DataFrame: Raw Javierre dataset\n    \"\"\"\n    return spark.read.parquet(path)\n</code></pre>"},{"location":"python_api/datasource/intervals/jung/","title":"Jung et al.","text":""},{"location":"python_api/datasource/intervals/jung/#otg.datasource.intervals.jung.IntervalsJung","title":"<code>otg.datasource.intervals.jung.IntervalsJung</code>","text":"<p>Interval dataset from Jung et al. 2019.</p> Source code in <code>src/otg/datasource/intervals/jung.py</code> <pre><code>class IntervalsJung:\n    \"\"\"Interval dataset from Jung et al. 2019.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read jung dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to dataset\n\n        Returns:\n            DataFrame: DataFrame with raw jung data\n        \"\"\"\n        return spark.read.csv(path, sep=\",\", header=True)\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsJung],\n        jung_raw: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse the Jung et al. 2019 dataset.\n\n        Args:\n            jung_raw (DataFrame): raw Jung et al. 2019 dataset\n            gene_index (GeneIndex): gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Interval dataset containing Jung et al. 2019 data\n        \"\"\"\n        dataset_name = \"jung2019\"\n        experiment_type = \"pchic\"\n        pmid = \"31501517\"\n\n        # Lifting over the coordinates:\n        return Intervals(\n            _df=(\n                jung_raw.withColumn(\n                    \"interval\", f.split(f.col(\"Interacting_fragment\"), r\"\\.\")\n                )\n                .select(\n                    # Parsing intervals:\n                    f.regexp_replace(f.col(\"interval\")[0], \"chr\", \"\").alias(\"chrom\"),\n                    f.col(\"interval\")[1].cast(t.IntegerType()).alias(\"start\"),\n                    f.col(\"interval\")[2].cast(t.IntegerType()).alias(\"end\"),\n                    # Extract other columns:\n                    f.col(\"Promoter\").alias(\"gene_name\"),\n                    f.col(\"Tissue_type\").alias(\"tissue\"),\n                )\n                # Lifting over to GRCh38 interval 1:\n                .transform(\n                    lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n                )\n                .select(\n                    \"chrom\",\n                    f.col(\"mapped_start\").alias(\"start\"),\n                    f.col(\"mapped_end\").alias(\"end\"),\n                    f.explode(f.split(f.col(\"gene_name\"), \";\")).alias(\"gene_name\"),\n                    \"tissue\",\n                )\n                .alias(\"intervals\")\n                # Joining with genes:\n                .join(\n                    gene_index.symbols_lut().alias(\"genes\"),\n                    on=[f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\")],\n                    how=\"inner\",\n                )\n                # Finalize dataset:\n                .select(\n                    \"chromosome\",\n                    f.col(\"intervals.start\").alias(\"start\"),\n                    f.col(\"intervals.end\").alias(\"end\"),\n                    \"geneId\",\n                    f.col(\"tissue\").alias(\"biofeature\"),\n                    f.lit(1.0).alias(\"score\"),\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                )\n                .drop_duplicates()\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/intervals/jung/#otg.datasource.intervals.jung.IntervalsJung.parse","title":"<code>parse(jung_raw: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse the Jung et al. 2019 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>jung_raw</code> <code>DataFrame</code> <p>raw Jung et al. 2019 dataset</p> required <code>gene_index</code> <code>GeneIndex</code> <p>gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Interval dataset containing Jung et al. 2019 data</p> Source code in <code>src/otg/datasource/intervals/jung.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsJung],\n    jung_raw: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse the Jung et al. 2019 dataset.\n\n    Args:\n        jung_raw (DataFrame): raw Jung et al. 2019 dataset\n        gene_index (GeneIndex): gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Interval dataset containing Jung et al. 2019 data\n    \"\"\"\n    dataset_name = \"jung2019\"\n    experiment_type = \"pchic\"\n    pmid = \"31501517\"\n\n    # Lifting over the coordinates:\n    return Intervals(\n        _df=(\n            jung_raw.withColumn(\n                \"interval\", f.split(f.col(\"Interacting_fragment\"), r\"\\.\")\n            )\n            .select(\n                # Parsing intervals:\n                f.regexp_replace(f.col(\"interval\")[0], \"chr\", \"\").alias(\"chrom\"),\n                f.col(\"interval\")[1].cast(t.IntegerType()).alias(\"start\"),\n                f.col(\"interval\")[2].cast(t.IntegerType()).alias(\"end\"),\n                # Extract other columns:\n                f.col(\"Promoter\").alias(\"gene_name\"),\n                f.col(\"Tissue_type\").alias(\"tissue\"),\n            )\n            # Lifting over to GRCh38 interval 1:\n            .transform(\n                lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n            )\n            .select(\n                \"chrom\",\n                f.col(\"mapped_start\").alias(\"start\"),\n                f.col(\"mapped_end\").alias(\"end\"),\n                f.explode(f.split(f.col(\"gene_name\"), \";\")).alias(\"gene_name\"),\n                \"tissue\",\n            )\n            .alias(\"intervals\")\n            # Joining with genes:\n            .join(\n                gene_index.symbols_lut().alias(\"genes\"),\n                on=[f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\")],\n                how=\"inner\",\n            )\n            # Finalize dataset:\n            .select(\n                \"chromosome\",\n                f.col(\"intervals.start\").alias(\"start\"),\n                f.col(\"intervals.end\").alias(\"end\"),\n                \"geneId\",\n                f.col(\"tissue\").alias(\"biofeature\"),\n                f.lit(1.0).alias(\"score\"),\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n            )\n            .drop_duplicates()\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/intervals/jung/#otg.datasource.intervals.jung.IntervalsJung.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read jung dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>DataFrame with raw jung data</p> Source code in <code>src/otg/datasource/intervals/jung.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read jung dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to dataset\n\n    Returns:\n        DataFrame: DataFrame with raw jung data\n    \"\"\"\n    return spark.read.csv(path, sep=\",\", header=True)\n</code></pre>"},{"location":"python_api/datasource/intervals/thurman/","title":"Thurman et al.","text":""},{"location":"python_api/datasource/intervals/thurman/#otg.datasource.intervals.thurman.IntervalsThurman","title":"<code>otg.datasource.intervals.thurman.IntervalsThurman</code>","text":"<p>Interval dataset from Thurman et al. 2012.</p> Source code in <code>src/otg/datasource/intervals/thurman.py</code> <pre><code>class IntervalsThurman:\n    \"\"\"Interval dataset from Thurman et al. 2012.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read thurman dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to dataset\n\n        Returns:\n            DataFrame: DataFrame with raw thurman data\n        \"\"\"\n        thurman_schema = t.StructType(\n            [\n                t.StructField(\"gene_chr\", t.StringType(), False),\n                t.StructField(\"gene_start\", t.IntegerType(), False),\n                t.StructField(\"gene_end\", t.IntegerType(), False),\n                t.StructField(\"gene_name\", t.StringType(), False),\n                t.StructField(\"chrom\", t.StringType(), False),\n                t.StructField(\"start\", t.IntegerType(), False),\n                t.StructField(\"end\", t.IntegerType(), False),\n                t.StructField(\"score\", t.FloatType(), False),\n            ]\n        )\n        return spark.read.csv(path, sep=\"\\t\", header=True, schema=thurman_schema)\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsThurman],\n        thurman_raw: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse the Thurman et al. 2012 dataset.\n\n        Args:\n            thurman_raw (DataFrame): raw Thurman et al. 2019 dataset\n            gene_index (GeneIndex): gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Interval dataset containing Thurman et al. 2012 data\n        \"\"\"\n        dataset_name = \"thurman2012\"\n        experiment_type = \"dhscor\"\n        pmid = \"22955617\"\n\n        return Intervals(\n            _df=(\n                thurman_raw.select(\n                    f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").alias(\"chrom\"),\n                    \"start\",\n                    \"end\",\n                    \"gene_name\",\n                    \"score\",\n                )\n                # Lift over to the GRCh38 build:\n                .transform(\n                    lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n                )\n                .alias(\"intervals\")\n                # Map gene names to gene IDs:\n                .join(\n                    gene_index.symbols_lut().alias(\"genes\"),\n                    on=[\n                        f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\"),\n                        f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                    ],\n                    how=\"inner\",\n                )\n                # Select relevant columns and add constant columns:\n                .select(\n                    f.col(\"chrom\").alias(\"chromosome\"),\n                    f.col(\"mapped_start\").alias(\"start\"),\n                    f.col(\"mapped_end\").alias(\"end\"),\n                    \"geneId\",\n                    f.col(\"score\").cast(t.DoubleType()).alias(\"resourceScore\"),\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                )\n                .distinct()\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/intervals/thurman/#otg.datasource.intervals.thurman.IntervalsThurman.parse","title":"<code>parse(thurman_raw: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse the Thurman et al. 2012 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>thurman_raw</code> <code>DataFrame</code> <p>raw Thurman et al. 2019 dataset</p> required <code>gene_index</code> <code>GeneIndex</code> <p>gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Interval dataset containing Thurman et al. 2012 data</p> Source code in <code>src/otg/datasource/intervals/thurman.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsThurman],\n    thurman_raw: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse the Thurman et al. 2012 dataset.\n\n    Args:\n        thurman_raw (DataFrame): raw Thurman et al. 2019 dataset\n        gene_index (GeneIndex): gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Interval dataset containing Thurman et al. 2012 data\n    \"\"\"\n    dataset_name = \"thurman2012\"\n    experiment_type = \"dhscor\"\n    pmid = \"22955617\"\n\n    return Intervals(\n        _df=(\n            thurman_raw.select(\n                f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").alias(\"chrom\"),\n                \"start\",\n                \"end\",\n                \"gene_name\",\n                \"score\",\n            )\n            # Lift over to the GRCh38 build:\n            .transform(\n                lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n            )\n            .alias(\"intervals\")\n            # Map gene names to gene IDs:\n            .join(\n                gene_index.symbols_lut().alias(\"genes\"),\n                on=[\n                    f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\"),\n                    f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                ],\n                how=\"inner\",\n            )\n            # Select relevant columns and add constant columns:\n            .select(\n                f.col(\"chrom\").alias(\"chromosome\"),\n                f.col(\"mapped_start\").alias(\"start\"),\n                f.col(\"mapped_end\").alias(\"end\"),\n                \"geneId\",\n                f.col(\"score\").cast(t.DoubleType()).alias(\"resourceScore\"),\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n            )\n            .distinct()\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/intervals/thurman/#otg.datasource.intervals.thurman.IntervalsThurman.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read thurman dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>DataFrame with raw thurman data</p> Source code in <code>src/otg/datasource/intervals/thurman.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read thurman dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to dataset\n\n    Returns:\n        DataFrame: DataFrame with raw thurman data\n    \"\"\"\n    thurman_schema = t.StructType(\n        [\n            t.StructField(\"gene_chr\", t.StringType(), False),\n            t.StructField(\"gene_start\", t.IntegerType(), False),\n            t.StructField(\"gene_end\", t.IntegerType(), False),\n            t.StructField(\"gene_name\", t.StringType(), False),\n            t.StructField(\"chrom\", t.StringType(), False),\n            t.StructField(\"start\", t.IntegerType(), False),\n            t.StructField(\"end\", t.IntegerType(), False),\n            t.StructField(\"score\", t.FloatType(), False),\n        ]\n    )\n    return spark.read.csv(path, sep=\"\\t\", header=True, schema=thurman_schema)\n</code></pre>"},{"location":"python_api/datasource/open_targets/_open_targets/","title":"Open Targets","text":"<p>The Open Targets Platform is a comprehensive resource that aims to aggregate and harmonise various types of data to facilitate the identification, prioritisation, and validation of drug targets. By integrating publicly available datasets including data generated by the Open Targets consortium, the Platform builds and scores target-disease associations to assist in drug target identification and prioritisation. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships.</p> <p>Genomic data from Open Targets integrates human genome-wide association studies (GWAS) and functional genomics data including gene expression, protein abundance, chromatin interaction and conformation data from a wide range of cell types and tissues to make robust connections between GWAS-associated loci, variants and likely causal genes.</p>"},{"location":"python_api/datasource/open_targets/l2g_gold_standard/","title":"L2G Gold Standard","text":""},{"location":"python_api/datasource/open_targets/l2g_gold_standard/#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard","title":"<code>otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard</code>","text":"<p>Parser for OTGenetics locus to gene gold standards curation.</p> The curation is processed to generate a dataset with 2 labels <ul> <li>Gold Standard Positive (GSP): When the lead variant is part of a curated list of GWAS loci with known gene-trait associations.</li> <li>Gold Standard Negative (GSN): When the lead variant is not part of a curated list of GWAS loci with known gene-trait associations but is in the vicinity of a gene's TSS.</li> </ul> Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>class OpenTargetsL2GGoldStandard:\n    \"\"\"Parser for OTGenetics locus to gene gold standards curation.\n\n    The curation is processed to generate a dataset with 2 labels:\n        - Gold Standard Positive (GSP): When the lead variant is part of a curated list of GWAS loci with known gene-trait associations.\n        - Gold Standard Negative (GSN): When the lead variant is not part of a curated list of GWAS loci with known gene-trait associations but is in the vicinity of a gene's TSS.\n    \"\"\"\n\n    LOCUS_TO_GENE_WINDOW = 500_000\n\n    @classmethod\n    def parse_positive_curation(\n        cls: Type[OpenTargetsL2GGoldStandard], gold_standard_curation: DataFrame\n    ) -&gt; DataFrame:\n        \"\"\"Parse positive set from gold standard curation.\n\n        Args:\n            gold_standard_curation (DataFrame): Gold standard curation dataframe\n\n        Returns:\n            DataFrame: Positive set\n        \"\"\"\n        return (\n            gold_standard_curation.filter(\n                f.col(\"gold_standard_info.highest_confidence\").isin([\"High\", \"Medium\"])\n            )\n            .select(\n                f.col(\"association_info.otg_id\").alias(\"studyId\"),\n                f.col(\"gold_standard_info.gene_id\").alias(\"geneId\"),\n                f.concat_ws(\n                    \"_\",\n                    f.col(\"sentinel_variant.locus_GRCh38.chromosome\"),\n                    f.col(\"sentinel_variant.locus_GRCh38.position\"),\n                    f.col(\"sentinel_variant.alleles.reference\"),\n                    f.col(\"sentinel_variant.alleles.alternative\"),\n                ).alias(\"variantId\"),\n                f.col(\"metadata.set_label\").alias(\"source\"),\n            )\n            .withColumn(\n                \"studyLocusId\",\n                StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n            )\n            .groupBy(\"studyLocusId\", \"studyId\", \"variantId\", \"geneId\")\n            .agg(f.collect_set(\"source\").alias(\"sources\"))\n        )\n\n    @classmethod\n    def expand_gold_standard_with_negatives(\n        cls: Type[OpenTargetsL2GGoldStandard], positive_set: DataFrame, v2g: V2G\n    ) -&gt; DataFrame:\n        \"\"\"Create full set of positive and negative evidence of locus to gene associations.\n\n        Negative evidence consists of all genes within a window of 500kb of the lead variant that are not in the positive set.\n\n        Args:\n            positive_set (DataFrame): Positive set from curation\n            v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n        Returns:\n            DataFrame: Full set of positive and negative evidence of locus to gene associations\n        \"\"\"\n        return (\n            positive_set.withColumnRenamed(\"geneId\", \"curated_geneId\")\n            .join(\n                v2g.df.selectExpr(\n                    \"variantId\", \"geneId as non_curated_geneId\", \"distance\"\n                ).filter(f.col(\"distance\") &lt;= cls.LOCUS_TO_GENE_WINDOW),\n                on=\"variantId\",\n                how=\"left\",\n            )\n            .withColumn(\n                \"goldStandardSet\",\n                f.when(\n                    (f.col(\"curated_geneId\") == f.col(\"non_curated_geneId\"))\n                    # to keep the positives that are outside the v2g dataset\n                    | (f.col(\"non_curated_geneId\").isNull()),\n                    f.lit(L2GGoldStandard.GS_POSITIVE_LABEL),\n                ).otherwise(L2GGoldStandard.GS_NEGATIVE_LABEL),\n            )\n            .withColumn(\n                \"geneId\",\n                f.when(\n                    f.col(\"goldStandardSet\") == L2GGoldStandard.GS_POSITIVE_LABEL,\n                    f.col(\"curated_geneId\"),\n                ).otherwise(f.col(\"non_curated_geneId\")),\n            )\n            .drop(\"distance\", \"curated_geneId\", \"non_curated_geneId\")\n        )\n\n    @classmethod\n    def as_l2g_gold_standard(\n        cls: type[OpenTargetsL2GGoldStandard],\n        gold_standard_curation: DataFrame,\n        v2g: V2G,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Initialise L2GGoldStandard from source dataset.\n\n        Args:\n            gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from https://github.com/opentargets/genetics-gold-standards\n            v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n        Returns:\n            L2GGoldStandard: L2G Gold Standard dataset. False negatives have not yet been removed.\n        \"\"\"\n        return L2GGoldStandard(\n            _df=cls.parse_positive_curation(gold_standard_curation).transform(\n                cls.expand_gold_standard_with_negatives, v2g\n            ),\n            _schema=L2GGoldStandard.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/open_targets/l2g_gold_standard/#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard","title":"<code>as_l2g_gold_standard(gold_standard_curation: DataFrame, v2g: V2G) -&gt; L2GGoldStandard</code>  <code>classmethod</code>","text":"<p>Initialise L2GGoldStandard from source dataset.</p> <p>Parameters:</p> Name Type Description Default <code>gold_standard_curation</code> <code>DataFrame</code> <p>Gold standard curation dataframe, extracted from https://github.com/opentargets/genetics-gold-standards</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset to bring distance between a variant and a gene's TSS</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>L2G Gold Standard dataset. False negatives have not yet been removed.</p> Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef as_l2g_gold_standard(\n    cls: type[OpenTargetsL2GGoldStandard],\n    gold_standard_curation: DataFrame,\n    v2g: V2G,\n) -&gt; L2GGoldStandard:\n    \"\"\"Initialise L2GGoldStandard from source dataset.\n\n    Args:\n        gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from https://github.com/opentargets/genetics-gold-standards\n        v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n    Returns:\n        L2GGoldStandard: L2G Gold Standard dataset. False negatives have not yet been removed.\n    \"\"\"\n    return L2GGoldStandard(\n        _df=cls.parse_positive_curation(gold_standard_curation).transform(\n            cls.expand_gold_standard_with_negatives, v2g\n        ),\n        _schema=L2GGoldStandard.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/open_targets/l2g_gold_standard/#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives","title":"<code>expand_gold_standard_with_negatives(positive_set: DataFrame, v2g: V2G) -&gt; DataFrame</code>  <code>classmethod</code>","text":"<p>Create full set of positive and negative evidence of locus to gene associations.</p> <p>Negative evidence consists of all genes within a window of 500kb of the lead variant that are not in the positive set.</p> <p>Parameters:</p> Name Type Description Default <code>positive_set</code> <code>DataFrame</code> <p>Positive set from curation</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset to bring distance between a variant and a gene's TSS</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Full set of positive and negative evidence of locus to gene associations</p> Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef expand_gold_standard_with_negatives(\n    cls: Type[OpenTargetsL2GGoldStandard], positive_set: DataFrame, v2g: V2G\n) -&gt; DataFrame:\n    \"\"\"Create full set of positive and negative evidence of locus to gene associations.\n\n    Negative evidence consists of all genes within a window of 500kb of the lead variant that are not in the positive set.\n\n    Args:\n        positive_set (DataFrame): Positive set from curation\n        v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n    Returns:\n        DataFrame: Full set of positive and negative evidence of locus to gene associations\n    \"\"\"\n    return (\n        positive_set.withColumnRenamed(\"geneId\", \"curated_geneId\")\n        .join(\n            v2g.df.selectExpr(\n                \"variantId\", \"geneId as non_curated_geneId\", \"distance\"\n            ).filter(f.col(\"distance\") &lt;= cls.LOCUS_TO_GENE_WINDOW),\n            on=\"variantId\",\n            how=\"left\",\n        )\n        .withColumn(\n            \"goldStandardSet\",\n            f.when(\n                (f.col(\"curated_geneId\") == f.col(\"non_curated_geneId\"))\n                # to keep the positives that are outside the v2g dataset\n                | (f.col(\"non_curated_geneId\").isNull()),\n                f.lit(L2GGoldStandard.GS_POSITIVE_LABEL),\n            ).otherwise(L2GGoldStandard.GS_NEGATIVE_LABEL),\n        )\n        .withColumn(\n            \"geneId\",\n            f.when(\n                f.col(\"goldStandardSet\") == L2GGoldStandard.GS_POSITIVE_LABEL,\n                f.col(\"curated_geneId\"),\n            ).otherwise(f.col(\"non_curated_geneId\")),\n        )\n        .drop(\"distance\", \"curated_geneId\", \"non_curated_geneId\")\n    )\n</code></pre>"},{"location":"python_api/datasource/open_targets/l2g_gold_standard/#otg.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation","title":"<code>parse_positive_curation(gold_standard_curation: DataFrame) -&gt; DataFrame</code>  <code>classmethod</code>","text":"<p>Parse positive set from gold standard curation.</p> <p>Parameters:</p> Name Type Description Default <code>gold_standard_curation</code> <code>DataFrame</code> <p>Gold standard curation dataframe</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Positive set</p> Source code in <code>src/otg/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef parse_positive_curation(\n    cls: Type[OpenTargetsL2GGoldStandard], gold_standard_curation: DataFrame\n) -&gt; DataFrame:\n    \"\"\"Parse positive set from gold standard curation.\n\n    Args:\n        gold_standard_curation (DataFrame): Gold standard curation dataframe\n\n    Returns:\n        DataFrame: Positive set\n    \"\"\"\n    return (\n        gold_standard_curation.filter(\n            f.col(\"gold_standard_info.highest_confidence\").isin([\"High\", \"Medium\"])\n        )\n        .select(\n            f.col(\"association_info.otg_id\").alias(\"studyId\"),\n            f.col(\"gold_standard_info.gene_id\").alias(\"geneId\"),\n            f.concat_ws(\n                \"_\",\n                f.col(\"sentinel_variant.locus_GRCh38.chromosome\"),\n                f.col(\"sentinel_variant.locus_GRCh38.position\"),\n                f.col(\"sentinel_variant.alleles.reference\"),\n                f.col(\"sentinel_variant.alleles.alternative\"),\n            ).alias(\"variantId\"),\n            f.col(\"metadata.set_label\").alias(\"source\"),\n        )\n        .withColumn(\n            \"studyLocusId\",\n            StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n        )\n        .groupBy(\"studyLocusId\", \"studyId\", \"variantId\", \"geneId\")\n        .agg(f.collect_set(\"source\").alias(\"sources\"))\n    )\n</code></pre>"},{"location":"python_api/datasource/open_targets/target/","title":"Target","text":""},{"location":"python_api/datasource/open_targets/target/#otg.datasource.open_targets.target.OpenTargetsTarget","title":"<code>otg.datasource.open_targets.target.OpenTargetsTarget</code>","text":"<p>Parser for OTPlatform target dataset.</p> <p>Genomic data from Open Targets provides gene identification and genomic coordinates that are integrated into the gene index of our ETL pipeline.</p> <p>The EMBL-EBI Ensembl database is used as a source for human targets in the Platform, with the Ensembl gene ID as the primary identifier. The criteria for target inclusion is: - Genes from all biotypes encoded in canonical chromosomes - Genes in alternative assemblies encoding for a reviewed protein product.</p> Source code in <code>src/otg/datasource/open_targets/target.py</code> <pre><code>class OpenTargetsTarget:\n    \"\"\"Parser for OTPlatform target dataset.\n\n    Genomic data from Open Targets provides gene identification and genomic coordinates that are integrated into the gene index of our ETL pipeline.\n\n    The EMBL-EBI Ensembl database is used as a source for human targets in the Platform, with the Ensembl gene ID as the primary identifier. The criteria for target inclusion is:\n    - Genes from all biotypes encoded in canonical chromosomes\n    - Genes in alternative assemblies encoding for a reviewed protein product.\n    \"\"\"\n\n    @staticmethod\n    def _get_gene_tss(strand_col: Column, start_col: Column, end_col: Column) -&gt; Column:\n        \"\"\"Returns the TSS of a gene based on its orientation.\n\n        Args:\n            strand_col (Column): Column containing 1 if the coding strand of the gene is forward, and -1 if it is reverse.\n            start_col (Column): Column containing the start position of the gene.\n            end_col (Column): Column containing the end position of the gene.\n\n        Returns:\n            Column: Column containing the TSS of the gene.\n\n        Examples:\n            &gt;&gt;&gt; df = spark.createDataFrame([{\"strand\": 1, \"start\": 100, \"end\": 200}, {\"strand\": -1, \"start\": 100, \"end\": 200}])\n            &gt;&gt;&gt; df.withColumn(\"tss\", OpenTargetsTarget._get_gene_tss(f.col(\"strand\"), f.col(\"start\"), f.col(\"end\"))).show()\n            +---+-----+------+---+\n            |end|start|strand|tss|\n            +---+-----+------+---+\n            |200|  100|     1|100|\n            |200|  100|    -1|200|\n            +---+-----+------+---+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return f.when(strand_col == 1, start_col).when(strand_col == -1, end_col)\n\n    @classmethod\n    def as_gene_index(\n        cls: type[OpenTargetsTarget], target_index: DataFrame\n    ) -&gt; GeneIndex:\n        \"\"\"Initialise GeneIndex from source dataset.\n\n        Args:\n            target_index (DataFrame): Target index dataframe\n\n        Returns:\n            GeneIndex: Gene index dataset\n        \"\"\"\n        return GeneIndex(\n            _df=target_index.select(\n                f.coalesce(f.col(\"id\"), f.lit(\"unknown\")).alias(\"geneId\"),\n                \"approvedSymbol\",\n                \"approvedName\",\n                \"biotype\",\n                f.col(\"obsoleteSymbols.label\").alias(\"obsoleteSymbols\"),\n                f.coalesce(f.col(\"genomicLocation.chromosome\"), f.lit(\"unknown\")).alias(\n                    \"chromosome\"\n                ),\n                OpenTargetsTarget._get_gene_tss(\n                    f.col(\"genomicLocation.strand\"),\n                    f.col(\"genomicLocation.start\"),\n                    f.col(\"genomicLocation.end\"),\n                ).alias(\"tss\"),\n                f.col(\"genomicLocation.start\").alias(\"start\"),\n                f.col(\"genomicLocation.end\").alias(\"end\"),\n                f.col(\"genomicLocation.strand\").alias(\"strand\"),\n            ),\n            _schema=GeneIndex.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/open_targets/target/#otg.datasource.open_targets.target.OpenTargetsTarget.as_gene_index","title":"<code>as_gene_index(target_index: DataFrame) -&gt; GeneIndex</code>  <code>classmethod</code>","text":"<p>Initialise GeneIndex from source dataset.</p> <p>Parameters:</p> Name Type Description Default <code>target_index</code> <code>DataFrame</code> <p>Target index dataframe</p> required <p>Returns:</p> Name Type Description <code>GeneIndex</code> <code>GeneIndex</code> <p>Gene index dataset</p> Source code in <code>src/otg/datasource/open_targets/target.py</code> <pre><code>@classmethod\ndef as_gene_index(\n    cls: type[OpenTargetsTarget], target_index: DataFrame\n) -&gt; GeneIndex:\n    \"\"\"Initialise GeneIndex from source dataset.\n\n    Args:\n        target_index (DataFrame): Target index dataframe\n\n    Returns:\n        GeneIndex: Gene index dataset\n    \"\"\"\n    return GeneIndex(\n        _df=target_index.select(\n            f.coalesce(f.col(\"id\"), f.lit(\"unknown\")).alias(\"geneId\"),\n            \"approvedSymbol\",\n            \"approvedName\",\n            \"biotype\",\n            f.col(\"obsoleteSymbols.label\").alias(\"obsoleteSymbols\"),\n            f.coalesce(f.col(\"genomicLocation.chromosome\"), f.lit(\"unknown\")).alias(\n                \"chromosome\"\n            ),\n            OpenTargetsTarget._get_gene_tss(\n                f.col(\"genomicLocation.strand\"),\n                f.col(\"genomicLocation.start\"),\n                f.col(\"genomicLocation.end\"),\n            ).alias(\"tss\"),\n            f.col(\"genomicLocation.start\").alias(\"start\"),\n            f.col(\"genomicLocation.end\").alias(\"end\"),\n            f.col(\"genomicLocation.strand\").alias(\"strand\"),\n        ),\n        _schema=GeneIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasource/ukbiobank/_ukbiobank/","title":"UK Biobank","text":"<p>The UK Biobank is a large-scale biomedical database and research resource that contains a diverse range of in-depth information from 500,000 volunteers in the United Kingdom. Its genomic data comprises whole-genome sequencing for a subset of participants, along with genotyping arrays for the entire cohort. The data has been a cornerstone for numerous genome-wide association studies (GWAS) and other genetic analyses, advancing our understanding of human health and disease.</p> <p>Recent efforts to rapidly and systematically apply established GWAS methods to all available data fields in UK Biobank have made available large repositories of summary statistics. To leverage these data disease locus discovery, we used full summary statistics from: The Neale lab Round 2 (N=2139).</p> <ul> <li>These analyses applied GWAS (implemented in Hail) to all data fields using imputed genotypes from HRC as released by UK Biobank in May 2017, consisting of 337,199 individuals post-QC. Full details of the Neale lab GWAS implementation are available here. We have remove all ICD-10 related traits from the Neale data to reduce overlap with the SAIGE results.</li> <li>http://www.nealelab.is/uk-biobank/   The University of Michigan SAIGE analysis (N=1281).</li> <li>The SAIGE analysis uses PheCode derived phenotypes and applies a new method that \"provides accurate P values even when case-control ratios are extremely unbalanced\". See Zhou et al. (2018) for further details.</li> <li>https://pubmed.ncbi.nlm.nih.gov/30104761/</li> </ul>"},{"location":"python_api/datasource/ukbiobank/study_index/","title":"Study Index","text":""},{"location":"python_api/datasource/ukbiobank/study_index/#otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex","title":"<code>otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex</code>","text":"<p>Study index dataset from UKBiobank.</p> <p>The following information is extracted:</p> <ul> <li>studyId</li> <li>pubmedId</li> <li>publicationDate</li> <li>publicationJournal</li> <li>publicationTitle</li> <li>publicationFirstAuthor</li> <li>traitFromSource</li> <li>ancestry_discoverySamples</li> <li>ancestry_replicationSamples</li> <li>initialSampleSize</li> <li>nCases</li> <li>replicationSamples</li> </ul> <p>Some fields are populated as constants, such as projectID, studyType, and initial sample size.</p> Source code in <code>src/otg/datasource/ukbiobank/study_index.py</code> <pre><code>class UKBiobankStudyIndex:\n    \"\"\"Study index dataset from UKBiobank.\n\n    The following information is extracted:\n\n    - studyId\n    - pubmedId\n    - publicationDate\n    - publicationJournal\n    - publicationTitle\n    - publicationFirstAuthor\n    - traitFromSource\n    - ancestry_discoverySamples\n    - ancestry_replicationSamples\n    - initialSampleSize\n    - nCases\n    - replicationSamples\n\n    Some fields are populated as constants, such as projectID, studyType, and initial sample size.\n    \"\"\"\n\n    @classmethod\n    def from_source(\n        cls: type[UKBiobankStudyIndex],\n        ukbiobank_studies: DataFrame,\n    ) -&gt; StudyIndex:\n        \"\"\"This function ingests study level metadata from UKBiobank.\n\n        The University of Michigan SAIGE analysis (N=1281) utilized PheCode derived phenotypes and a novel method that ensures accurate P values, even with highly unbalanced case-control ratios (Zhou et al., 2018).\n\n        The Neale lab Round 2 study (N=2139) used GWAS with imputed genotypes from HRC to analyze all data fields in UK Biobank, excluding ICD-10 related traits to reduce overlap with the SAIGE results.\n\n        Args:\n            ukbiobank_studies (DataFrame): UKBiobank study manifest file loaded in spark session.\n\n        Returns:\n            StudyIndex: Annotated UKBiobank study table.\n        \"\"\"\n        return StudyIndex(\n            _df=(\n                ukbiobank_studies.select(\n                    f.col(\"code\").alias(\"studyId\"),\n                    f.lit(\"UKBiobank\").alias(\"projectId\"),\n                    f.lit(\"gwas\").alias(\"studyType\"),\n                    f.col(\"trait\").alias(\"traitFromSource\"),\n                    # Make publication and ancestry schema columns.\n                    f.when(f.col(\"code\").startswith(\"SAIGE_\"), \"30104761\").alias(\n                        \"pubmedId\"\n                    ),\n                    f.when(\n                        f.col(\"code\").startswith(\"SAIGE_\"),\n                        \"Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies\",\n                    )\n                    .otherwise(None)\n                    .alias(\"publicationTitle\"),\n                    f.when(f.col(\"code\").startswith(\"SAIGE_\"), \"Wei Zhou\").alias(\n                        \"publicationFirstAuthor\"\n                    ),\n                    f.when(f.col(\"code\").startswith(\"NEALE2_\"), \"2018-08-01\")\n                    .otherwise(\"2018-10-24\")\n                    .alias(\"publicationDate\"),\n                    f.when(f.col(\"code\").startswith(\"SAIGE_\"), \"Nature Genetics\").alias(\n                        \"publicationJournal\"\n                    ),\n                    f.col(\"n_total\").cast(\"string\").alias(\"initialSampleSize\"),\n                    f.col(\"n_cases\").cast(\"long\").alias(\"nCases\"),\n                    f.array(\n                        f.struct(\n                            f.col(\"n_total\").cast(\"long\").alias(\"sampleSize\"),\n                            f.concat(f.lit(\"European=\"), f.col(\"n_total\")).alias(\n                                \"ancestry\"\n                            ),\n                        )\n                    ).alias(\"discoverySamples\"),\n                    f.col(\"in_path\").alias(\"summarystatsLocation\"),\n                    f.lit(True).alias(\"hasSumstats\"),\n                )\n                .withColumn(\n                    \"traitFromSource\",\n                    f.when(\n                        f.col(\"traitFromSource\").contains(\":\"),\n                        f.concat(\n                            f.initcap(\n                                f.split(f.col(\"traitFromSource\"), \": \").getItem(1)\n                            ),\n                            f.lit(\" | \"),\n                            f.lower(f.split(f.col(\"traitFromSource\"), \": \").getItem(0)),\n                        ),\n                    ).otherwise(f.col(\"traitFromSource\")),\n                )\n                .withColumn(\n                    \"ldPopulationStructure\",\n                    StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n                )\n            ),\n            _schema=StudyIndex.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasource/ukbiobank/study_index/#otg.datasource.ukbiobank.study_index.UKBiobankStudyIndex.from_source","title":"<code>from_source(ukbiobank_studies: DataFrame) -&gt; StudyIndex</code>  <code>classmethod</code>","text":"<p>This function ingests study level metadata from UKBiobank.</p> <p>The University of Michigan SAIGE analysis (N=1281) utilized PheCode derived phenotypes and a novel method that ensures accurate P values, even with highly unbalanced case-control ratios (Zhou et al., 2018).</p> <p>The Neale lab Round 2 study (N=2139) used GWAS with imputed genotypes from HRC to analyze all data fields in UK Biobank, excluding ICD-10 related traits to reduce overlap with the SAIGE results.</p> <p>Parameters:</p> Name Type Description Default <code>ukbiobank_studies</code> <code>DataFrame</code> <p>UKBiobank study manifest file loaded in spark session.</p> required <p>Returns:</p> Name Type Description <code>StudyIndex</code> <code>StudyIndex</code> <p>Annotated UKBiobank study table.</p> Source code in <code>src/otg/datasource/ukbiobank/study_index.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[UKBiobankStudyIndex],\n    ukbiobank_studies: DataFrame,\n) -&gt; StudyIndex:\n    \"\"\"This function ingests study level metadata from UKBiobank.\n\n    The University of Michigan SAIGE analysis (N=1281) utilized PheCode derived phenotypes and a novel method that ensures accurate P values, even with highly unbalanced case-control ratios (Zhou et al., 2018).\n\n    The Neale lab Round 2 study (N=2139) used GWAS with imputed genotypes from HRC to analyze all data fields in UK Biobank, excluding ICD-10 related traits to reduce overlap with the SAIGE results.\n\n    Args:\n        ukbiobank_studies (DataFrame): UKBiobank study manifest file loaded in spark session.\n\n    Returns:\n        StudyIndex: Annotated UKBiobank study table.\n    \"\"\"\n    return StudyIndex(\n        _df=(\n            ukbiobank_studies.select(\n                f.col(\"code\").alias(\"studyId\"),\n                f.lit(\"UKBiobank\").alias(\"projectId\"),\n                f.lit(\"gwas\").alias(\"studyType\"),\n                f.col(\"trait\").alias(\"traitFromSource\"),\n                # Make publication and ancestry schema columns.\n                f.when(f.col(\"code\").startswith(\"SAIGE_\"), \"30104761\").alias(\n                    \"pubmedId\"\n                ),\n                f.when(\n                    f.col(\"code\").startswith(\"SAIGE_\"),\n                    \"Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies\",\n                )\n                .otherwise(None)\n                .alias(\"publicationTitle\"),\n                f.when(f.col(\"code\").startswith(\"SAIGE_\"), \"Wei Zhou\").alias(\n                    \"publicationFirstAuthor\"\n                ),\n                f.when(f.col(\"code\").startswith(\"NEALE2_\"), \"2018-08-01\")\n                .otherwise(\"2018-10-24\")\n                .alias(\"publicationDate\"),\n                f.when(f.col(\"code\").startswith(\"SAIGE_\"), \"Nature Genetics\").alias(\n                    \"publicationJournal\"\n                ),\n                f.col(\"n_total\").cast(\"string\").alias(\"initialSampleSize\"),\n                f.col(\"n_cases\").cast(\"long\").alias(\"nCases\"),\n                f.array(\n                    f.struct(\n                        f.col(\"n_total\").cast(\"long\").alias(\"sampleSize\"),\n                        f.concat(f.lit(\"European=\"), f.col(\"n_total\")).alias(\n                            \"ancestry\"\n                        ),\n                    )\n                ).alias(\"discoverySamples\"),\n                f.col(\"in_path\").alias(\"summarystatsLocation\"),\n                f.lit(True).alias(\"hasSumstats\"),\n            )\n            .withColumn(\n                \"traitFromSource\",\n                f.when(\n                    f.col(\"traitFromSource\").contains(\":\"),\n                    f.concat(\n                        f.initcap(\n                            f.split(f.col(\"traitFromSource\"), \": \").getItem(1)\n                        ),\n                        f.lit(\" | \"),\n                        f.lower(f.split(f.col(\"traitFromSource\"), \": \").getItem(0)),\n                    ),\n                ).otherwise(f.col(\"traitFromSource\")),\n            )\n            .withColumn(\n                \"ldPopulationStructure\",\n                StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n            )\n        ),\n        _schema=StudyIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/method/_method/","title":"Method","text":"<p>TBC</p>"},{"location":"python_api/method/clumping/","title":"Clumping","text":"<p>Clumping is a commonly used post-processing method that allows for identification of independent association signals from GWAS summary statistics and curated associations. This process is critical because of the complex linkage disequilibrium (LD) structure in human populations, which can result in multiple statistically significant associations within the same genomic region. Clumping methods help reduce redundancy in GWAS results and ensure that each reported association represents an independent signal.</p> <p>We have implemented 2 clumping methods:</p>"},{"location":"python_api/method/clumping/#otg.method.clump.LDclumping","title":"<code>otg.method.clump.LDclumping</code>","text":"<p>LD clumping reports the most significant genetic associations in a region in terms of a smaller number of \u201cclumps\u201d of genetically linked SNPs.</p> Source code in <code>src/otg/method/clump.py</code> <pre><code>class LDclumping:\n    \"\"\"LD clumping reports the most significant genetic associations in a region in terms of a smaller number of \u201cclumps\u201d of genetically linked SNPs.\"\"\"\n\n    @staticmethod\n    def _is_lead_linked(\n        study_id: Column,\n        variant_id: Column,\n        p_value_exponent: Column,\n        p_value_mantissa: Column,\n        ld_set: Column,\n    ) -&gt; Column:\n        \"\"\"Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.\n\n        Args:\n            study_id (Column): studyId\n            variant_id (Column): Lead variant id\n            p_value_exponent (Column): p-value exponent\n            p_value_mantissa (Column): p-value mantissa\n            ld_set (Column): Array of variants in LD with the lead variant\n\n        Returns:\n            Column: Boolean in which True indicates that the lead is linked to another tag in the same dataset.\n        \"\"\"\n        leads_in_study = f.collect_set(variant_id).over(Window.partitionBy(study_id))\n        tags_in_studylocus = f.array_union(\n            # Get all tag variants from the credible set per studyLocusId\n            f.transform(ld_set, lambda x: x.tagVariantId),\n            # And append the lead variant so that the intersection is the same for all studyLocusIds in a study\n            f.array(variant_id),\n        )\n        intersect_lead_tags = f.array_sort(\n            f.array_intersect(leads_in_study, tags_in_studylocus)\n        )\n        return (\n            # If the lead is in the credible set, we rank the peaks by p-value\n            f.when(\n                f.size(intersect_lead_tags) &gt; 0,\n                f.row_number().over(\n                    Window.partitionBy(study_id, intersect_lead_tags).orderBy(\n                        p_value_exponent, p_value_mantissa\n                    )\n                )\n                &gt; 1,\n            )\n            # If the intersection is empty (lead is not in the credible set or cred set is empty), the association is not linked\n            .otherwise(f.lit(False))\n        )\n\n    @classmethod\n    def clump(cls: type[LDclumping], associations: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Perform clumping on studyLocus dataset.\n\n        Args:\n            associations (StudyLocus): StudyLocus dataset\n\n        Returns:\n            StudyLocus: including flag and removing locus information for LD clumped loci.\n        \"\"\"\n        return associations.clump()\n</code></pre>"},{"location":"python_api/method/clumping/#otg.method.clump.LDclumping.clump","title":"<code>clump(associations: StudyLocus) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Perform clumping on studyLocus dataset.</p> <p>Parameters:</p> Name Type Description Default <code>associations</code> <code>StudyLocus</code> <p>StudyLocus dataset</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>including flag and removing locus information for LD clumped loci.</p> Source code in <code>src/otg/method/clump.py</code> <pre><code>@classmethod\ndef clump(cls: type[LDclumping], associations: StudyLocus) -&gt; StudyLocus:\n    \"\"\"Perform clumping on studyLocus dataset.\n\n    Args:\n        associations (StudyLocus): StudyLocus dataset\n\n    Returns:\n        StudyLocus: including flag and removing locus information for LD clumped loci.\n    \"\"\"\n    return associations.clump()\n</code></pre>"},{"location":"python_api/method/coloc/","title":"Coloc","text":""},{"location":"python_api/method/coloc/#otg.method.colocalisation.Coloc","title":"<code>otg.method.colocalisation.Coloc</code>","text":"<p>Calculate bayesian colocalisation based on overlapping signals from credible sets.</p> <p>Based on the R COLOC package, which uses the Bayes factors from the credible set to estimate the posterior probability of colocalisation. This method makes the simplifying assumption that only one single causal variant exists for any given trait in any genomic region.</p> Hypothesis Description H<sub>0</sub> no association with either trait in the region H<sub>1</sub> association with trait 1 only H<sub>2</sub> association with trait 2 only H<sub>3</sub> both traits are associated, but have different single causal variants H<sub>4</sub> both traits are associated and share the same single causal variant <p>Approximate Bayes factors required</p> <p>Coloc requires the availability of approximate Bayes factors (ABF) for each variant in the credible set (<code>logABF</code> column).</p> Source code in <code>src/otg/method/colocalisation.py</code> <pre><code>class Coloc:\n    \"\"\"Calculate bayesian colocalisation based on overlapping signals from credible sets.\n\n    Based on the [R COLOC package](https://github.com/chr1swallace/coloc/blob/main/R/claudia.R), which uses the Bayes factors from the credible set to estimate the posterior probability of colocalisation. This method makes the simplifying assumption that **only one single causal variant** exists for any given trait in any genomic region.\n\n    | Hypothesis    | Description                                                           |\n    | ------------- | --------------------------------------------------------------------- |\n    | H&lt;sub&gt;0&lt;/sub&gt; | no association with either trait in the region                        |\n    | H&lt;sub&gt;1&lt;/sub&gt; | association with trait 1 only                                         |\n    | H&lt;sub&gt;2&lt;/sub&gt; | association with trait 2 only                                         |\n    | H&lt;sub&gt;3&lt;/sub&gt; | both traits are associated, but have different single causal variants |\n    | H&lt;sub&gt;4&lt;/sub&gt; | both traits are associated and share the same single causal variant   |\n\n    !!! warning \"Approximate Bayes factors required\"\n        Coloc requires the availability of approximate Bayes factors (ABF) for each variant in the credible set (`logABF` column).\n\n    \"\"\"\n\n    @staticmethod\n    def _get_logsum(log_abf: NDArray[np.float64]) -&gt; float:\n        \"\"\"Calculates logsum of vector.\n\n        This function calculates the log of the sum of the exponentiated\n        logs taking out the max, i.e. insuring that the sum is not Inf\n\n        Args:\n            log_abf (NDArray[np.float64]): log approximate bayes factor\n\n        Returns:\n            float: logsum\n\n        Example:\n            &gt;&gt;&gt; l = [0.2, 0.1, 0.05, 0]\n            &gt;&gt;&gt; round(Coloc._get_logsum(l), 6)\n            1.476557\n        \"\"\"\n        themax = np.max(log_abf)\n        result = themax + np.log(np.sum(np.exp(log_abf - themax)))\n        return float(result)\n\n    @staticmethod\n    def _get_posteriors(all_abfs: NDArray[np.float64]) -&gt; DenseVector:\n        \"\"\"Calculate posterior probabilities for each hypothesis.\n\n        Args:\n            all_abfs (NDArray[np.float64]): h0-h4 bayes factors\n\n        Returns:\n            DenseVector: Posterior\n\n        Example:\n            &gt;&gt;&gt; l = np.array([0.2, 0.1, 0.05, 0])\n            &gt;&gt;&gt; Coloc._get_posteriors(l)\n            DenseVector([0.279, 0.2524, 0.2401, 0.2284])\n        \"\"\"\n        diff = all_abfs - Coloc._get_logsum(all_abfs)\n        abfs_posteriors = np.exp(diff)\n        return Vectors.dense(abfs_posteriors)\n\n    @classmethod\n    def colocalise(\n        cls: type[Coloc],\n        overlapping_signals: StudyLocusOverlap,\n        priorc1: float = 1e-4,\n        priorc2: float = 1e-4,\n        priorc12: float = 1e-5,\n    ) -&gt; Colocalisation:\n        \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n        Args:\n            overlapping_signals (StudyLocusOverlap): overlapping peaks\n            priorc1 (float): Prior on variant being causal for trait 1. Defaults to 1e-4.\n            priorc2 (float): Prior on variant being causal for trait 2. Defaults to 1e-4.\n            priorc12 (float): Prior on variant being causal for traits 1 and 2. Defaults to 1e-5.\n\n        Returns:\n            Colocalisation: Colocalisation results\n        \"\"\"\n        # register udfs\n        logsum = f.udf(Coloc._get_logsum, DoubleType())\n        posteriors = f.udf(Coloc._get_posteriors, VectorUDT())\n        return Colocalisation(\n            _df=(\n                overlapping_signals.df\n                # Before summing log_abf columns nulls need to be filled with 0:\n                .fillna(0, subset=[\"statistics.left_logABF\", \"statistics.right_logABF\"])\n                # Sum of log_abfs for each pair of signals\n                .withColumn(\n                    \"sum_log_abf\",\n                    f.col(\"statistics.left_logABF\") + f.col(\"statistics.right_logABF\"),\n                )\n                # Group by overlapping peak and generating dense vectors of log_abf:\n                .groupBy(\"chromosome\", \"leftStudyLocusId\", \"rightStudyLocusId\")\n                .agg(\n                    f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                    fml.array_to_vector(\n                        f.collect_list(f.col(\"statistics.left_logABF\"))\n                    ).alias(\"left_logABF\"),\n                    fml.array_to_vector(\n                        f.collect_list(f.col(\"statistics.right_logABF\"))\n                    ).alias(\"right_logABF\"),\n                    fml.array_to_vector(f.collect_list(f.col(\"sum_log_abf\"))).alias(\n                        \"sum_log_abf\"\n                    ),\n                )\n                .withColumn(\"logsum1\", logsum(f.col(\"left_logABF\")))\n                .withColumn(\"logsum2\", logsum(f.col(\"right_logABF\")))\n                .withColumn(\"logsum12\", logsum(f.col(\"sum_log_abf\")))\n                .drop(\"left_logABF\", \"right_logABF\", \"sum_log_abf\")\n                # Add priors\n                # priorc1 Prior on variant being causal for trait 1\n                .withColumn(\"priorc1\", f.lit(priorc1))\n                # priorc2 Prior on variant being causal for trait 2\n                .withColumn(\"priorc2\", f.lit(priorc2))\n                # priorc12 Prior on variant being causal for traits 1 and 2\n                .withColumn(\"priorc12\", f.lit(priorc12))\n                # h0-h2\n                .withColumn(\"lH0abf\", f.lit(0))\n                .withColumn(\"lH1abf\", f.log(f.col(\"priorc1\")) + f.col(\"logsum1\"))\n                .withColumn(\"lH2abf\", f.log(f.col(\"priorc2\")) + f.col(\"logsum2\"))\n                # h3\n                .withColumn(\"sumlogsum\", f.col(\"logsum1\") + f.col(\"logsum2\"))\n                # exclude null H3/H4s: due to sumlogsum == logsum12\n                .filter(f.col(\"sumlogsum\") != f.col(\"logsum12\"))\n                .withColumn(\"max\", f.greatest(\"sumlogsum\", \"logsum12\"))\n                .withColumn(\n                    \"logdiff\",\n                    (\n                        f.col(\"max\")\n                        + f.log(\n                            f.exp(f.col(\"sumlogsum\") - f.col(\"max\"))\n                            - f.exp(f.col(\"logsum12\") - f.col(\"max\"))\n                        )\n                    ),\n                )\n                .withColumn(\n                    \"lH3abf\",\n                    f.log(f.col(\"priorc1\"))\n                    + f.log(f.col(\"priorc2\"))\n                    + f.col(\"logdiff\"),\n                )\n                .drop(\"right_logsum\", \"left_logsum\", \"sumlogsum\", \"max\", \"logdiff\")\n                # h4\n                .withColumn(\"lH4abf\", f.log(f.col(\"priorc12\")) + f.col(\"logsum12\"))\n                # cleaning\n                .drop(\n                    \"priorc1\", \"priorc2\", \"priorc12\", \"logsum1\", \"logsum2\", \"logsum12\"\n                )\n                # posteriors\n                .withColumn(\n                    \"allABF\",\n                    fml.array_to_vector(\n                        f.array(\n                            f.col(\"lH0abf\"),\n                            f.col(\"lH1abf\"),\n                            f.col(\"lH2abf\"),\n                            f.col(\"lH3abf\"),\n                            f.col(\"lH4abf\"),\n                        )\n                    ),\n                )\n                .withColumn(\n                    \"posteriors\", fml.vector_to_array(posteriors(f.col(\"allABF\")))\n                )\n                .withColumn(\"h0\", f.col(\"posteriors\").getItem(0))\n                .withColumn(\"h1\", f.col(\"posteriors\").getItem(1))\n                .withColumn(\"h2\", f.col(\"posteriors\").getItem(2))\n                .withColumn(\"h3\", f.col(\"posteriors\").getItem(3))\n                .withColumn(\"h4\", f.col(\"posteriors\").getItem(4))\n                .withColumn(\"h4h3\", f.col(\"h4\") / f.col(\"h3\"))\n                .withColumn(\"log2h4h3\", f.log2(f.col(\"h4h3\")))\n                # clean up\n                .drop(\n                    \"posteriors\",\n                    \"allABF\",\n                    \"h4h3\",\n                    \"lH0abf\",\n                    \"lH1abf\",\n                    \"lH2abf\",\n                    \"lH3abf\",\n                    \"lH4abf\",\n                )\n                .withColumn(\"colocalisationMethod\", f.lit(\"COLOC\"))\n            ),\n            _schema=Colocalisation.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/method/coloc/#otg.method.colocalisation.Coloc.colocalise","title":"<code>colocalise(overlapping_signals: StudyLocusOverlap, priorc1: float = 0.0001, priorc2: float = 0.0001, priorc12: float = 1e-05) -&gt; Colocalisation</code>  <code>classmethod</code>","text":"<p>Calculate bayesian colocalisation based on overlapping signals.</p> <p>Parameters:</p> Name Type Description Default <code>overlapping_signals</code> <code>StudyLocusOverlap</code> <p>overlapping peaks</p> required <code>priorc1</code> <code>float</code> <p>Prior on variant being causal for trait 1. Defaults to 1e-4.</p> <code>0.0001</code> <code>priorc2</code> <code>float</code> <p>Prior on variant being causal for trait 2. Defaults to 1e-4.</p> <code>0.0001</code> <code>priorc12</code> <code>float</code> <p>Prior on variant being causal for traits 1 and 2. Defaults to 1e-5.</p> <code>1e-05</code> <p>Returns:</p> Name Type Description <code>Colocalisation</code> <code>Colocalisation</code> <p>Colocalisation results</p> Source code in <code>src/otg/method/colocalisation.py</code> <pre><code>@classmethod\ndef colocalise(\n    cls: type[Coloc],\n    overlapping_signals: StudyLocusOverlap,\n    priorc1: float = 1e-4,\n    priorc2: float = 1e-4,\n    priorc12: float = 1e-5,\n) -&gt; Colocalisation:\n    \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n    Args:\n        overlapping_signals (StudyLocusOverlap): overlapping peaks\n        priorc1 (float): Prior on variant being causal for trait 1. Defaults to 1e-4.\n        priorc2 (float): Prior on variant being causal for trait 2. Defaults to 1e-4.\n        priorc12 (float): Prior on variant being causal for traits 1 and 2. Defaults to 1e-5.\n\n    Returns:\n        Colocalisation: Colocalisation results\n    \"\"\"\n    # register udfs\n    logsum = f.udf(Coloc._get_logsum, DoubleType())\n    posteriors = f.udf(Coloc._get_posteriors, VectorUDT())\n    return Colocalisation(\n        _df=(\n            overlapping_signals.df\n            # Before summing log_abf columns nulls need to be filled with 0:\n            .fillna(0, subset=[\"statistics.left_logABF\", \"statistics.right_logABF\"])\n            # Sum of log_abfs for each pair of signals\n            .withColumn(\n                \"sum_log_abf\",\n                f.col(\"statistics.left_logABF\") + f.col(\"statistics.right_logABF\"),\n            )\n            # Group by overlapping peak and generating dense vectors of log_abf:\n            .groupBy(\"chromosome\", \"leftStudyLocusId\", \"rightStudyLocusId\")\n            .agg(\n                f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                fml.array_to_vector(\n                    f.collect_list(f.col(\"statistics.left_logABF\"))\n                ).alias(\"left_logABF\"),\n                fml.array_to_vector(\n                    f.collect_list(f.col(\"statistics.right_logABF\"))\n                ).alias(\"right_logABF\"),\n                fml.array_to_vector(f.collect_list(f.col(\"sum_log_abf\"))).alias(\n                    \"sum_log_abf\"\n                ),\n            )\n            .withColumn(\"logsum1\", logsum(f.col(\"left_logABF\")))\n            .withColumn(\"logsum2\", logsum(f.col(\"right_logABF\")))\n            .withColumn(\"logsum12\", logsum(f.col(\"sum_log_abf\")))\n            .drop(\"left_logABF\", \"right_logABF\", \"sum_log_abf\")\n            # Add priors\n            # priorc1 Prior on variant being causal for trait 1\n            .withColumn(\"priorc1\", f.lit(priorc1))\n            # priorc2 Prior on variant being causal for trait 2\n            .withColumn(\"priorc2\", f.lit(priorc2))\n            # priorc12 Prior on variant being causal for traits 1 and 2\n            .withColumn(\"priorc12\", f.lit(priorc12))\n            # h0-h2\n            .withColumn(\"lH0abf\", f.lit(0))\n            .withColumn(\"lH1abf\", f.log(f.col(\"priorc1\")) + f.col(\"logsum1\"))\n            .withColumn(\"lH2abf\", f.log(f.col(\"priorc2\")) + f.col(\"logsum2\"))\n            # h3\n            .withColumn(\"sumlogsum\", f.col(\"logsum1\") + f.col(\"logsum2\"))\n            # exclude null H3/H4s: due to sumlogsum == logsum12\n            .filter(f.col(\"sumlogsum\") != f.col(\"logsum12\"))\n            .withColumn(\"max\", f.greatest(\"sumlogsum\", \"logsum12\"))\n            .withColumn(\n                \"logdiff\",\n                (\n                    f.col(\"max\")\n                    + f.log(\n                        f.exp(f.col(\"sumlogsum\") - f.col(\"max\"))\n                        - f.exp(f.col(\"logsum12\") - f.col(\"max\"))\n                    )\n                ),\n            )\n            .withColumn(\n                \"lH3abf\",\n                f.log(f.col(\"priorc1\"))\n                + f.log(f.col(\"priorc2\"))\n                + f.col(\"logdiff\"),\n            )\n            .drop(\"right_logsum\", \"left_logsum\", \"sumlogsum\", \"max\", \"logdiff\")\n            # h4\n            .withColumn(\"lH4abf\", f.log(f.col(\"priorc12\")) + f.col(\"logsum12\"))\n            # cleaning\n            .drop(\n                \"priorc1\", \"priorc2\", \"priorc12\", \"logsum1\", \"logsum2\", \"logsum12\"\n            )\n            # posteriors\n            .withColumn(\n                \"allABF\",\n                fml.array_to_vector(\n                    f.array(\n                        f.col(\"lH0abf\"),\n                        f.col(\"lH1abf\"),\n                        f.col(\"lH2abf\"),\n                        f.col(\"lH3abf\"),\n                        f.col(\"lH4abf\"),\n                    )\n                ),\n            )\n            .withColumn(\n                \"posteriors\", fml.vector_to_array(posteriors(f.col(\"allABF\")))\n            )\n            .withColumn(\"h0\", f.col(\"posteriors\").getItem(0))\n            .withColumn(\"h1\", f.col(\"posteriors\").getItem(1))\n            .withColumn(\"h2\", f.col(\"posteriors\").getItem(2))\n            .withColumn(\"h3\", f.col(\"posteriors\").getItem(3))\n            .withColumn(\"h4\", f.col(\"posteriors\").getItem(4))\n            .withColumn(\"h4h3\", f.col(\"h4\") / f.col(\"h3\"))\n            .withColumn(\"log2h4h3\", f.log2(f.col(\"h4h3\")))\n            # clean up\n            .drop(\n                \"posteriors\",\n                \"allABF\",\n                \"h4h3\",\n                \"lH0abf\",\n                \"lH1abf\",\n                \"lH2abf\",\n                \"lH3abf\",\n                \"lH4abf\",\n            )\n            .withColumn(\"colocalisationMethod\", f.lit(\"COLOC\"))\n        ),\n        _schema=Colocalisation.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/method/ecaviar/","title":"eCAVIAR","text":""},{"location":"python_api/method/ecaviar/#otg.method.colocalisation.ECaviar","title":"<code>otg.method.colocalisation.ECaviar</code>","text":"<p>ECaviar-based colocalisation analysis.</p> <p>It extends CAVIAR\u00a0framework to explicitly estimate the posterior probability that the same variant is causal in 2 studies while accounting for the uncertainty of LD. eCAVIAR computes the colocalization posterior probability (CLPP) by utilizing the marginal posterior probabilities. This framework allows for multiple variants to be causal in a single locus.</p> Source code in <code>src/otg/method/colocalisation.py</code> <pre><code>class ECaviar:\n    \"\"\"ECaviar-based colocalisation analysis.\n\n    It extends [CAVIAR](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142122/#bib18)\u00a0framework to explicitly estimate the posterior probability that the same variant is causal in 2 studies while accounting for the uncertainty of LD. eCAVIAR computes the colocalization posterior probability (**CLPP**) by utilizing the marginal posterior probabilities. This framework allows for **multiple variants to be causal** in a single locus.\n    \"\"\"\n\n    @staticmethod\n    def _get_clpp(left_pp: Column, right_pp: Column) -&gt; Column:\n        \"\"\"Calculate the colocalisation posterior probability (CLPP).\n\n        If the fact that the same variant is found causal for two studies are independent events,\n        CLPP is defined as the product of posterior porbabilities that a variant is causal in both studies.\n\n        Args:\n            left_pp (Column): left posterior probability\n            right_pp (Column): right posterior probability\n\n        Returns:\n            Column: CLPP\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"left_pp\": 0.5, \"right_pp\": 0.5}, {\"left_pp\": 0.25, \"right_pp\": 0.75}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"clpp\", ECaviar._get_clpp(f.col(\"left_pp\"), f.col(\"right_pp\"))).show()\n            +-------+--------+------+\n            |left_pp|right_pp|  clpp|\n            +-------+--------+------+\n            |    0.5|     0.5|  0.25|\n            |   0.25|    0.75|0.1875|\n            +-------+--------+------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return left_pp * right_pp\n\n    @classmethod\n    def colocalise(\n        cls: type[ECaviar], overlapping_signals: StudyLocusOverlap\n    ) -&gt; Colocalisation:\n        \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n        Args:\n            overlapping_signals (StudyLocusOverlap): overlapping signals.\n\n        Returns:\n            Colocalisation: colocalisation results based on eCAVIAR.\n        \"\"\"\n        return Colocalisation(\n            _df=(\n                overlapping_signals.df.withColumn(\n                    \"clpp\",\n                    ECaviar._get_clpp(\n                        f.col(\"statistics.left_posteriorProbability\"),\n                        f.col(\"statistics.right_posteriorProbability\"),\n                    ),\n                )\n                .groupBy(\"leftStudyLocusId\", \"rightStudyLocusId\", \"chromosome\")\n                .agg(\n                    f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                    f.sum(f.col(\"clpp\")).alias(\"clpp\"),\n                )\n                .withColumn(\"colocalisationMethod\", f.lit(\"eCAVIAR\"))\n            ),\n            _schema=Colocalisation.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/method/ecaviar/#otg.method.colocalisation.ECaviar.colocalise","title":"<code>colocalise(overlapping_signals: StudyLocusOverlap) -&gt; Colocalisation</code>  <code>classmethod</code>","text":"<p>Calculate bayesian colocalisation based on overlapping signals.</p> <p>Parameters:</p> Name Type Description Default <code>overlapping_signals</code> <code>StudyLocusOverlap</code> <p>overlapping signals.</p> required <p>Returns:</p> Name Type Description <code>Colocalisation</code> <code>Colocalisation</code> <p>colocalisation results based on eCAVIAR.</p> Source code in <code>src/otg/method/colocalisation.py</code> <pre><code>@classmethod\ndef colocalise(\n    cls: type[ECaviar], overlapping_signals: StudyLocusOverlap\n) -&gt; Colocalisation:\n    \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n    Args:\n        overlapping_signals (StudyLocusOverlap): overlapping signals.\n\n    Returns:\n        Colocalisation: colocalisation results based on eCAVIAR.\n    \"\"\"\n    return Colocalisation(\n        _df=(\n            overlapping_signals.df.withColumn(\n                \"clpp\",\n                ECaviar._get_clpp(\n                    f.col(\"statistics.left_posteriorProbability\"),\n                    f.col(\"statistics.right_posteriorProbability\"),\n                ),\n            )\n            .groupBy(\"leftStudyLocusId\", \"rightStudyLocusId\", \"chromosome\")\n            .agg(\n                f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                f.sum(f.col(\"clpp\")).alias(\"clpp\"),\n            )\n            .withColumn(\"colocalisationMethod\", f.lit(\"eCAVIAR\"))\n        ),\n        _schema=Colocalisation.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/method/ld_annotator/","title":"LDAnnotator","text":""},{"location":"python_api/method/ld_annotator/#otg.method.ld.LDAnnotator","title":"<code>otg.method.ld.LDAnnotator</code>","text":"<p>Class to annotate linkage disequilibrium (LD) operations from GnomAD.</p> Source code in <code>src/otg/method/ld.py</code> <pre><code>class LDAnnotator:\n    \"\"\"Class to annotate linkage disequilibrium (LD) operations from GnomAD.\"\"\"\n\n    @staticmethod\n    def _calculate_weighted_r_overall(ld_set: Column) -&gt; Column:\n        \"\"\"Aggregation of weighted R information using ancestry proportions.\n\n        Args:\n            ld_set (Column): LD set\n\n        Returns:\n            Column: LD set with added 'r2Overall' field\n        \"\"\"\n        return f.transform(\n            ld_set,\n            lambda x: f.struct(\n                x[\"tagVariantId\"].alias(\"tagVariantId\"),\n                # r2Overall is the accumulated sum of each r2 relative to the population size\n                f.aggregate(\n                    x[\"rValues\"],\n                    f.lit(0.0),\n                    lambda acc, y: acc\n                    + f.coalesce(\n                        f.pow(y[\"r\"], 2) * y[\"relativeSampleSize\"], f.lit(0.0)\n                    ),  # we use coalesce to avoid problems when r/relativeSampleSize is null\n                ).alias(\"r2Overall\"),\n            ),\n        )\n\n    @staticmethod\n    def _add_population_size(ld_set: Column, study_populations: Column) -&gt; Column:\n        \"\"\"Add population size to each rValues entry in the ldSet.\n\n        Args:\n            ld_set (Column): LD set\n            study_populations (Column): Study populations\n\n        Returns:\n            Column: LD set with added 'relativeSampleSize' field\n        \"\"\"\n        # Create a population to relativeSampleSize map from the struct\n        populations_map = f.map_from_arrays(\n            study_populations[\"ldPopulation\"],\n            study_populations[\"relativeSampleSize\"],\n        )\n        return f.transform(\n            ld_set,\n            lambda x: f.struct(\n                x[\"tagVariantId\"].alias(\"tagVariantId\"),\n                f.transform(\n                    x[\"rValues\"],\n                    lambda y: f.struct(\n                        y[\"population\"].alias(\"population\"),\n                        y[\"r\"].alias(\"r\"),\n                        populations_map[y[\"population\"]].alias(\"relativeSampleSize\"),\n                    ),\n                ).alias(\"rValues\"),\n            ),\n        )\n\n    @classmethod\n    def ld_annotate(\n        cls: type[LDAnnotator],\n        associations: StudyLocus,\n        studies: StudyIndex,\n        ld_index: LDIndex,\n    ) -&gt; StudyLocus:\n        \"\"\"Annotate linkage disequilibrium (LD) information to a set of studyLocus.\n\n        This function:\n            1. Annotates study locus with population structure information from the study index\n            2. Joins the LD index to the StudyLocus\n            3. Adds the population size of the study to each rValues entry in the ldSet\n            4. Calculates the overall R weighted by the ancestry proportions in every given study.\n\n        Args:\n            associations (StudyLocus): Dataset to be LD annotated\n            studies (StudyIndex): Dataset with study information\n            ld_index (LDIndex): Dataset with LD information for every variant present in LD matrix\n\n        Returns:\n            StudyLocus: including additional column with LD information.\n        \"\"\"\n        return (\n            StudyLocus(\n                _df=(\n                    associations.df\n                    # Drop ldSet column if already available\n                    .select(*[col for col in associations.df.columns if col != \"ldSet\"])\n                    # Annotate study locus with population structure from study index\n                    .join(\n                        studies.df.select(\"studyId\", \"ldPopulationStructure\"),\n                        on=\"studyId\",\n                        how=\"left\",\n                    )\n                    # Bring LD information from LD Index\n                    .join(\n                        ld_index.df,\n                        on=[\"variantId\", \"chromosome\"],\n                        how=\"left\",\n                    )\n                    # Add population size to each rValues entry in the ldSet if population structure available:\n                    .withColumn(\n                        \"ldSet\",\n                        f.when(\n                            f.col(\"ldPopulationStructure\").isNotNull(),\n                            cls._add_population_size(\n                                f.col(\"ldSet\"), f.col(\"ldPopulationStructure\")\n                            ),\n                        ),\n                    )\n                    # Aggregate weighted R information using ancestry proportions\n                    .withColumn(\n                        \"ldSet\",\n                        f.when(\n                            f.col(\"ldPopulationStructure\").isNotNull(),\n                            cls._calculate_weighted_r_overall(f.col(\"ldSet\")),\n                        ),\n                    ).drop(\"ldPopulationStructure\")\n                ),\n                _schema=StudyLocus.get_schema(),\n            )\n            ._qc_no_population()\n            ._qc_unresolved_ld()\n        )\n</code></pre>"},{"location":"python_api/method/ld_annotator/#otg.method.ld.LDAnnotator.ld_annotate","title":"<code>ld_annotate(associations: StudyLocus, studies: StudyIndex, ld_index: LDIndex) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Annotate linkage disequilibrium (LD) information to a set of studyLocus.</p> This function <ol> <li>Annotates study locus with population structure information from the study index</li> <li>Joins the LD index to the StudyLocus</li> <li>Adds the population size of the study to each rValues entry in the ldSet</li> <li>Calculates the overall R weighted by the ancestry proportions in every given study.</li> </ol> <p>Parameters:</p> Name Type Description Default <code>associations</code> <code>StudyLocus</code> <p>Dataset to be LD annotated</p> required <code>studies</code> <code>StudyIndex</code> <p>Dataset with study information</p> required <code>ld_index</code> <code>LDIndex</code> <p>Dataset with LD information for every variant present in LD matrix</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>including additional column with LD information.</p> Source code in <code>src/otg/method/ld.py</code> <pre><code>@classmethod\ndef ld_annotate(\n    cls: type[LDAnnotator],\n    associations: StudyLocus,\n    studies: StudyIndex,\n    ld_index: LDIndex,\n) -&gt; StudyLocus:\n    \"\"\"Annotate linkage disequilibrium (LD) information to a set of studyLocus.\n\n    This function:\n        1. Annotates study locus with population structure information from the study index\n        2. Joins the LD index to the StudyLocus\n        3. Adds the population size of the study to each rValues entry in the ldSet\n        4. Calculates the overall R weighted by the ancestry proportions in every given study.\n\n    Args:\n        associations (StudyLocus): Dataset to be LD annotated\n        studies (StudyIndex): Dataset with study information\n        ld_index (LDIndex): Dataset with LD information for every variant present in LD matrix\n\n    Returns:\n        StudyLocus: including additional column with LD information.\n    \"\"\"\n    return (\n        StudyLocus(\n            _df=(\n                associations.df\n                # Drop ldSet column if already available\n                .select(*[col for col in associations.df.columns if col != \"ldSet\"])\n                # Annotate study locus with population structure from study index\n                .join(\n                    studies.df.select(\"studyId\", \"ldPopulationStructure\"),\n                    on=\"studyId\",\n                    how=\"left\",\n                )\n                # Bring LD information from LD Index\n                .join(\n                    ld_index.df,\n                    on=[\"variantId\", \"chromosome\"],\n                    how=\"left\",\n                )\n                # Add population size to each rValues entry in the ldSet if population structure available:\n                .withColumn(\n                    \"ldSet\",\n                    f.when(\n                        f.col(\"ldPopulationStructure\").isNotNull(),\n                        cls._add_population_size(\n                            f.col(\"ldSet\"), f.col(\"ldPopulationStructure\")\n                        ),\n                    ),\n                )\n                # Aggregate weighted R information using ancestry proportions\n                .withColumn(\n                    \"ldSet\",\n                    f.when(\n                        f.col(\"ldPopulationStructure\").isNotNull(),\n                        cls._calculate_weighted_r_overall(f.col(\"ldSet\")),\n                    ),\n                ).drop(\"ldPopulationStructure\")\n            ),\n            _schema=StudyLocus.get_schema(),\n        )\n        ._qc_no_population()\n        ._qc_unresolved_ld()\n    )\n</code></pre>"},{"location":"python_api/method/pics/","title":"PICS","text":""},{"location":"python_api/method/pics/#otg.method.pics.PICS","title":"<code>otg.method.pics.PICS</code>","text":"<p>Probabilistic Identification of Causal SNPs (PICS), an algorithm estimating the probability that an individual variant is causal considering the haplotype structure and observed pattern of association at the genetic locus.</p> Source code in <code>src/otg/method/pics.py</code> <pre><code>class PICS:\n    \"\"\"Probabilistic Identification of Causal SNPs (PICS), an algorithm estimating the probability that an individual variant is causal considering the haplotype structure and observed pattern of association at the genetic locus.\"\"\"\n\n    @staticmethod\n    def _pics_relative_posterior_probability(\n        neglog_p: float, pics_snp_mu: float, pics_snp_std: float\n    ) -&gt; float:\n        \"\"\"Compute the PICS posterior probability for a given SNP.\n\n        !!! info \"This probability needs to be scaled to take into account the probabilities of the other variants in the locus.\"\n\n        Args:\n            neglog_p (float): Negative log p-value of the lead variant\n            pics_snp_mu (float): Mean P value of the association between a SNP and a trait\n            pics_snp_std (float): Standard deviation for the P value of the association between a SNP and a trait\n\n        Returns:\n            float: Posterior probability of the association between a SNP and a trait\n\n        Examples:\n            &gt;&gt;&gt; rel_prob = PICS._pics_relative_posterior_probability(neglog_p=10.0, pics_snp_mu=1.0, pics_snp_std=10.0)\n            &gt;&gt;&gt; round(rel_prob, 3)\n            0.368\n        \"\"\"\n        return float(norm(pics_snp_mu, pics_snp_std).sf(neglog_p) * 2)\n\n    @staticmethod\n    def _pics_standard_deviation(neglog_p: float, r2: float, k: float) -&gt; float | None:\n        \"\"\"Compute the PICS standard deviation.\n\n        This distribution is obtained after a series of permutation tests described in the PICS method, and it is only\n        valid when the SNP is highly linked with the lead (r2 &gt; 0.5).\n\n        Args:\n            neglog_p (float): Negative log p-value of the lead variant\n            r2 (float): LD score between a given SNP and the lead variant\n            k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n        Returns:\n            float | None: Standard deviation for the P value of the association between a SNP and a trait\n\n        Examples:\n            &gt;&gt;&gt; PICS._pics_standard_deviation(neglog_p=1.0, r2=1.0, k=6.4)\n            0.0\n            &gt;&gt;&gt; round(PICS._pics_standard_deviation(neglog_p=10.0, r2=0.5, k=6.4), 3)\n            1.493\n            &gt;&gt;&gt; print(PICS._pics_standard_deviation(neglog_p=1.0, r2=0.0, k=6.4))\n            None\n        \"\"\"\n        return (\n            abs(((1 - (r2**0.5) ** k) ** 0.5) * (neglog_p**0.5) / 2)\n            if r2 &gt;= 0.5\n            else None\n        )\n\n    @staticmethod\n    def _pics_mu(neglog_p: float, r2: float) -&gt; float | None:\n        \"\"\"Compute the PICS mu that estimates the probability of association between a given SNP and the trait.\n\n        This distribution is obtained after a series of permutation tests described in the PICS method, and it is only\n        valid when the SNP is highly linked with the lead (r2 &gt; 0.5).\n\n        Args:\n            neglog_p (float): Negative log p-value of the lead variant\n            r2 (float): LD score between a given SNP and the lead variant\n\n        Returns:\n            float | None: Mean P value of the association between a SNP and a trait\n\n        Examples:\n            &gt;&gt;&gt; PICS._pics_mu(neglog_p=1.0, r2=1.0)\n            1.0\n            &gt;&gt;&gt; PICS._pics_mu(neglog_p=10.0, r2=0.5)\n            5.0\n            &gt;&gt;&gt; print(PICS._pics_mu(neglog_p=10.0, r2=0.3))\n            None\n        \"\"\"\n        return neglog_p * r2 if r2 &gt;= 0.5 else None\n\n    @staticmethod\n    def _finemap(\n        ld_set: list[Row], lead_neglog_p: float, k: float\n    ) -&gt; list[dict[str, Any]] | None:\n        \"\"\"Calculates the probability of a variant being causal in a study-locus context by applying the PICS method.\n\n        It is intended to be applied as an UDF in `PICS.finemap`, where each row is a StudyLocus association.\n        The function iterates over every SNP in the `ldSet` array, and it returns an updated locus with\n        its association signal and causality probability as of PICS.\n\n        Args:\n            ld_set (list[Row]): list of tagging variants after expanding the locus\n            lead_neglog_p (float): P value of the association signal between the lead variant and the study in the form of -log10.\n            k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n        Returns:\n            list[dict[str, Any]] | None: List of tagging variants with an estimation of the association signal and their posterior probability as of PICS.\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.sql import Row\n            &gt;&gt;&gt; ld_set = [\n            ...     Row(variantId=\"var1\", r2Overall=0.8),\n            ...     Row(variantId=\"var2\", r2Overall=1),\n            ... ]\n            &gt;&gt;&gt; PICS._finemap(ld_set, lead_neglog_p=10.0, k=6.4)\n            [{'variantId': 'var1', 'r2Overall': 0.8, 'standardError': 0.07420896512708416, 'posteriorProbability': 0.07116959886882368}, {'variantId': 'var2', 'r2Overall': 1, 'standardError': 0.9977000638225533, 'posteriorProbability': 0.9288304011311763}]\n            &gt;&gt;&gt; empty_ld_set = []\n            &gt;&gt;&gt; PICS._finemap(empty_ld_set, lead_neglog_p=10.0, k=6.4)\n            []\n            &gt;&gt;&gt; ld_set_with_no_r2 = [\n            ...     Row(variantId=\"var1\", r2Overall=None),\n            ...     Row(variantId=\"var2\", r2Overall=None),\n            ... ]\n            &gt;&gt;&gt; PICS._finemap(ld_set_with_no_r2, lead_neglog_p=10.0, k=6.4)\n            [{'variantId': 'var1', 'r2Overall': None}, {'variantId': 'var2', 'r2Overall': None}]\n        \"\"\"\n        if ld_set is None:\n            return None\n        elif not ld_set:\n            return []\n        tmp_credible_set = []\n        new_credible_set = []\n        # First iteration: calculation of mu, standard deviation, and the relative posterior probability\n        for tag_struct in ld_set:\n            tag_dict = (\n                tag_struct.asDict()\n            )  # tag_struct is of type pyspark.Row, we'll represent it as a dict\n            if (\n                not tag_dict[\"r2Overall\"]\n                or tag_dict[\"r2Overall\"] &lt; 0.5\n                or not lead_neglog_p\n            ):\n                # If PICS cannot be calculated, we'll return the original credible set\n                new_credible_set.append(tag_dict)\n                continue\n\n            pics_snp_mu = PICS._pics_mu(lead_neglog_p, tag_dict[\"r2Overall\"])\n            pics_snp_std = PICS._pics_standard_deviation(\n                lead_neglog_p, tag_dict[\"r2Overall\"], k\n            )\n            pics_snp_std = 0.001 if pics_snp_std == 0 else pics_snp_std\n            if pics_snp_mu is not None and pics_snp_std is not None:\n                posterior_probability = PICS._pics_relative_posterior_probability(\n                    lead_neglog_p, pics_snp_mu, pics_snp_std\n                )\n                tag_dict[\"standardError\"] = 10**-pics_snp_std\n                tag_dict[\"relativePosteriorProbability\"] = posterior_probability\n\n                tmp_credible_set.append(tag_dict)\n\n        # Second iteration: calculation of the sum of all the posteriors in each study-locus, so that we scale them between 0-1\n        total_posteriors = sum(\n            tag_dict.get(\"relativePosteriorProbability\", 0)\n            for tag_dict in tmp_credible_set\n        )\n\n        # Third iteration: calculation of the final posteriorProbability\n        for tag_dict in tmp_credible_set:\n            if total_posteriors != 0:\n                tag_dict[\"posteriorProbability\"] = float(\n                    tag_dict.get(\"relativePosteriorProbability\", 0) / total_posteriors\n                )\n            tag_dict.pop(\"relativePosteriorProbability\")\n            new_credible_set.append(tag_dict)\n        return new_credible_set\n\n    @classmethod\n    def finemap(\n        cls: type[PICS], associations: StudyLocus, k: float = 6.4\n    ) -&gt; StudyLocus:\n        \"\"\"Run PICS on a study locus.\n\n        !!! info \"Study locus needs to be LD annotated\"\n            The study locus needs to be LD annotated before PICS can be calculated.\n\n        Args:\n            associations (StudyLocus): Study locus to finemap using PICS\n            k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n        Returns:\n            StudyLocus: Study locus with PICS results\n        \"\"\"\n        # Register UDF by defining the structure of the output locus array of structs\n        # it also renames tagVariantId to variantId\n\n        picsed_ldset_schema = t.ArrayType(\n            t.StructType(\n                [\n                    t.StructField(\"tagVariantId\", t.StringType(), True),\n                    t.StructField(\"r2Overall\", t.DoubleType(), True),\n                    t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                    t.StructField(\"standardError\", t.DoubleType(), True),\n                ]\n            )\n        )\n        picsed_study_locus_schema = t.ArrayType(\n            t.StructType(\n                [\n                    t.StructField(\"variantId\", t.StringType(), True),\n                    t.StructField(\"r2Overall\", t.DoubleType(), True),\n                    t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                    t.StructField(\"standardError\", t.DoubleType(), True),\n                ]\n            )\n        )\n        _finemap_udf = f.udf(\n            lambda locus, neglog_p: PICS._finemap(locus, neglog_p, k),\n            picsed_ldset_schema,\n        )\n        return StudyLocus(\n            _df=(\n                associations.df\n                # Old locus column will be dropped if available\n                .select(*[col for col in associations.df.columns if col != \"locus\"])\n                # Estimate neglog_pvalue for the lead variant\n                .withColumn(\"neglog_pvalue\", associations.neglog_pvalue())\n                # New locus containing the PICS results\n                .withColumn(\n                    \"locus\",\n                    f.when(\n                        f.col(\"ldSet\").isNotNull(),\n                        _finemap_udf(f.col(\"ldSet\"), f.col(\"neglog_pvalue\")).cast(\n                            picsed_study_locus_schema\n                        ),\n                    ),\n                )\n                # Rename tagVariantId to variantId\n                .drop(\"neglog_pvalue\")\n            ),\n            _schema=StudyLocus.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/method/pics/#otg.method.pics.PICS.finemap","title":"<code>finemap(associations: StudyLocus, k: float = 6.4) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Run PICS on a study locus.</p> <p>Study locus needs to be LD annotated</p> <p>The study locus needs to be LD annotated before PICS can be calculated.</p> <p>Parameters:</p> Name Type Description Default <code>associations</code> <code>StudyLocus</code> <p>Study locus to finemap using PICS</p> required <code>k</code> <code>float</code> <p>Empiric constant that can be adjusted to fit the curve, 6.4 recommended.</p> <code>6.4</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Study locus with PICS results</p> Source code in <code>src/otg/method/pics.py</code> <pre><code>@classmethod\ndef finemap(\n    cls: type[PICS], associations: StudyLocus, k: float = 6.4\n) -&gt; StudyLocus:\n    \"\"\"Run PICS on a study locus.\n\n    !!! info \"Study locus needs to be LD annotated\"\n        The study locus needs to be LD annotated before PICS can be calculated.\n\n    Args:\n        associations (StudyLocus): Study locus to finemap using PICS\n        k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n    Returns:\n        StudyLocus: Study locus with PICS results\n    \"\"\"\n    # Register UDF by defining the structure of the output locus array of structs\n    # it also renames tagVariantId to variantId\n\n    picsed_ldset_schema = t.ArrayType(\n        t.StructType(\n            [\n                t.StructField(\"tagVariantId\", t.StringType(), True),\n                t.StructField(\"r2Overall\", t.DoubleType(), True),\n                t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                t.StructField(\"standardError\", t.DoubleType(), True),\n            ]\n        )\n    )\n    picsed_study_locus_schema = t.ArrayType(\n        t.StructType(\n            [\n                t.StructField(\"variantId\", t.StringType(), True),\n                t.StructField(\"r2Overall\", t.DoubleType(), True),\n                t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                t.StructField(\"standardError\", t.DoubleType(), True),\n            ]\n        )\n    )\n    _finemap_udf = f.udf(\n        lambda locus, neglog_p: PICS._finemap(locus, neglog_p, k),\n        picsed_ldset_schema,\n    )\n    return StudyLocus(\n        _df=(\n            associations.df\n            # Old locus column will be dropped if available\n            .select(*[col for col in associations.df.columns if col != \"locus\"])\n            # Estimate neglog_pvalue for the lead variant\n            .withColumn(\"neglog_pvalue\", associations.neglog_pvalue())\n            # New locus containing the PICS results\n            .withColumn(\n                \"locus\",\n                f.when(\n                    f.col(\"ldSet\").isNotNull(),\n                    _finemap_udf(f.col(\"ldSet\"), f.col(\"neglog_pvalue\")).cast(\n                        picsed_study_locus_schema\n                    ),\n                ),\n            )\n            # Rename tagVariantId to variantId\n            .drop(\"neglog_pvalue\")\n        ),\n        _schema=StudyLocus.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/method/window_based_clumping/","title":"Window-based clumping","text":""},{"location":"python_api/method/window_based_clumping/#otg.method.window_based_clumping.WindowBasedClumping","title":"<code>otg.method.window_based_clumping.WindowBasedClumping</code>","text":"<p>Get semi-lead snps from summary statistics using a window based function.</p> Source code in <code>src/otg/method/window_based_clumping.py</code> <pre><code>class WindowBasedClumping:\n    \"\"\"Get semi-lead snps from summary statistics using a window based function.\"\"\"\n\n    @staticmethod\n    def _cluster_peaks(\n        study: Column, chromosome: Column, position: Column, window_length: int\n    ) -&gt; Column:\n        \"\"\"Cluster GWAS significant variants, were clusters are separated by a defined distance.\n\n        !! Important to note that the length of the clusters can be arbitrarily big.\n\n        Args:\n            study (Column): study identifier\n            chromosome (Column): chromosome identifier\n            position (Column): position of the variant\n            window_length (int): window length in basepair\n\n        Returns:\n            Column: containing cluster identifier\n\n        Examples:\n            &gt;&gt;&gt; data = [\n            ...     # Cluster 1:\n            ...     ('s1', 'chr1', 2),\n            ...     ('s1', 'chr1', 4),\n            ...     ('s1', 'chr1', 12),\n            ...     # Cluster 2 - Same chromosome:\n            ...     ('s1', 'chr1', 31),\n            ...     ('s1', 'chr1', 38),\n            ...     ('s1', 'chr1', 42),\n            ...     # Cluster 3 - New chromosome:\n            ...     ('s1', 'chr2', 41),\n            ...     ('s1', 'chr2', 44),\n            ...     ('s1', 'chr2', 50),\n            ...     # Cluster 4 - other study:\n            ...     ('s2', 'chr2', 55),\n            ...     ('s2', 'chr2', 62),\n            ...     ('s2', 'chr2', 70),\n            ... ]\n            &gt;&gt;&gt; window_length = 10\n            &gt;&gt;&gt; (\n            ...     spark.createDataFrame(data, ['studyId', 'chromosome', 'position'])\n            ...     .withColumn(\"cluster_id\",\n            ...         WindowBasedClumping._cluster_peaks(\n            ...             f.col('studyId'),\n            ...             f.col('chromosome'),\n            ...             f.col('position'),\n            ...             window_length\n            ...         )\n            ...     ).show()\n            ... )\n            +-------+----------+--------+----------+\n            |studyId|chromosome|position|cluster_id|\n            +-------+----------+--------+----------+\n            |     s1|      chr1|       2| s1_chr1_2|\n            |     s1|      chr1|       4| s1_chr1_2|\n            |     s1|      chr1|      12| s1_chr1_2|\n            |     s1|      chr1|      31|s1_chr1_31|\n            |     s1|      chr1|      38|s1_chr1_31|\n            |     s1|      chr1|      42|s1_chr1_31|\n            |     s1|      chr2|      41|s1_chr2_41|\n            |     s1|      chr2|      44|s1_chr2_41|\n            |     s1|      chr2|      50|s1_chr2_41|\n            |     s2|      chr2|      55|s2_chr2_55|\n            |     s2|      chr2|      62|s2_chr2_55|\n            |     s2|      chr2|      70|s2_chr2_55|\n            +-------+----------+--------+----------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # By adding previous position, the cluster boundary can be identified:\n        previous_position = f.lag(position).over(\n            Window.partitionBy(study, chromosome).orderBy(position)\n        )\n        # We consider a cluster boudary if subsequent snps are further than the defined window:\n        cluster_id = f.when(\n            (previous_position.isNull())\n            | (position - previous_position &gt; window_length),\n            f.concat_ws(\"_\", study, chromosome, position),\n        )\n        # The cluster identifier is propagated across every variant of the cluster:\n        return f.when(\n            cluster_id.isNull(),\n            f.last(cluster_id, ignorenulls=True).over(\n                Window.partitionBy(study, chromosome)\n                .orderBy(position)\n                .rowsBetween(Window.unboundedPreceding, Window.currentRow)\n            ),\n        ).otherwise(cluster_id)\n\n    @staticmethod\n    def _prune_peak(position: NDArray[np.float64], window_size: int) -&gt; DenseVector:\n        \"\"\"Establish lead snps based on their positions listed by p-value.\n\n        The function `find_peak` assigns lead SNPs based on their positions listed by p-value within a specified window size.\n\n        Args:\n            position (NDArray[np.float64]): positions of the SNPs sorted by p-value.\n            window_size (int): the distance in bp within which associations are clumped together around the lead snp.\n\n        Returns:\n            DenseVector: binary vector where 1 indicates a lead SNP and 0 indicates a non-lead SNP.\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.ml import functions as fml\n            &gt;&gt;&gt; from pyspark.ml.linalg import DenseVector\n            &gt;&gt;&gt; WindowBasedClumping._prune_peak(np.array((3, 9, 8, 4, 6)), 2)\n            DenseVector([1.0, 1.0, 0.0, 0.0, 1.0])\n\n        \"\"\"\n        # Initializing the lead list with zeroes:\n        is_lead = np.zeros(len(position))\n\n        # List containing indices of leads:\n        lead_indices: list[int] = []\n\n        # Looping through all positions:\n        for index in range(len(position)):\n            # Looping through leads to find out if they are within a window:\n            for lead_index in lead_indices:\n                # If any of the leads within the window:\n                if abs(position[lead_index] - position[index]) &lt; window_size:\n                    # Skipping further checks:\n                    break\n            else:\n                # None of the leads were within the window:\n                lead_indices.append(index)\n                is_lead[index] = 1\n\n        return DenseVector(is_lead)\n\n    @classmethod\n    def clump(\n        cls: type[WindowBasedClumping],\n        summary_stats: SummaryStatistics,\n        window_length: int,\n        p_value_significance: float = 5e-8,\n    ) -&gt; StudyLocus:\n        \"\"\"Clump summary statistics by distance.\n\n        Args:\n            summary_stats (SummaryStatistics): summary statistics to clump\n            window_length (int): window length in basepair\n            p_value_significance (float): only more significant variants are considered\n\n        Returns:\n            StudyLocus: clumped summary statistics\n        \"\"\"\n        # Create window for locus clusters\n        # - variants where the distance between subsequent variants is below the defined threshold.\n        # - Variants are sorted by descending significance\n        cluster_window = Window.partitionBy(\n            \"studyId\", \"chromosome\", \"cluster_id\"\n        ).orderBy(f.col(\"pValueExponent\").asc(), f.col(\"pValueMantissa\").asc())\n\n        return StudyLocus(\n            _df=(\n                summary_stats\n                # Dropping snps below significance - all subsequent steps are done on significant variants:\n                .pvalue_filter(p_value_significance)\n                .df\n                # Clustering summary variants for efficient windowing (complexity reduction):\n                .withColumn(\n                    \"cluster_id\",\n                    WindowBasedClumping._cluster_peaks(\n                        f.col(\"studyId\"),\n                        f.col(\"chromosome\"),\n                        f.col(\"position\"),\n                        window_length,\n                    ),\n                )\n                # Within each cluster variants are ranked by significance:\n                .withColumn(\"pvRank\", f.row_number().over(cluster_window))\n                # Collect positions in cluster for the most significant variant (complexity reduction):\n                .withColumn(\n                    \"collectedPositions\",\n                    f.when(\n                        f.col(\"pvRank\") == 1,\n                        f.collect_list(f.col(\"position\")).over(\n                            cluster_window.rowsBetween(\n                                Window.currentRow, Window.unboundedFollowing\n                            )\n                        ),\n                    ).otherwise(f.array()),\n                )\n                # Get semi indices only ONCE per cluster:\n                .withColumn(\n                    \"semiIndices\",\n                    f.when(\n                        f.size(f.col(\"collectedPositions\")) &gt; 0,\n                        fml.vector_to_array(\n                            f.udf(WindowBasedClumping._prune_peak, VectorUDT())(\n                                fml.array_to_vector(f.col(\"collectedPositions\")),\n                                f.lit(window_length),\n                            )\n                        ),\n                    ),\n                )\n                # Propagating the result of the above calculation for all rows:\n                .withColumn(\n                    \"semiIndices\",\n                    f.when(\n                        f.col(\"semiIndices\").isNull(),\n                        f.first(f.col(\"semiIndices\"), ignorenulls=True).over(\n                            cluster_window\n                        ),\n                    ).otherwise(f.col(\"semiIndices\")),\n                )\n                # Keeping semi indices only:\n                .filter(f.col(\"semiIndices\")[f.col(\"pvRank\") - 1] &gt; 0)\n                .drop(\"pvRank\", \"collectedPositions\", \"semiIndices\", \"cluster_id\")\n                # Adding study-locus id:\n                .withColumn(\n                    \"studyLocusId\",\n                    StudyLocus.assign_study_locus_id(\n                        f.col(\"studyId\"), f.col(\"variantId\")\n                    ),\n                )\n                # Initialize QC column as array of strings:\n                .withColumn(\n                    \"qualityControls\", f.array().cast(t.ArrayType(t.StringType()))\n                )\n            ),\n            _schema=StudyLocus.get_schema(),\n        )\n\n    @classmethod\n    def clump_with_locus(\n        cls: type[WindowBasedClumping],\n        summary_stats: SummaryStatistics,\n        window_length: int,\n        p_value_significance: float = 5e-8,\n        p_value_baseline: float = 0.05,\n        locus_window_length: int | None = None,\n    ) -&gt; StudyLocus:\n        \"\"\"Clump significant associations while collecting locus around them.\n\n        Args:\n            summary_stats (SummaryStatistics): Input summary statistics dataset\n            window_length (int): Window size in  bp, used for distance based clumping.\n            p_value_significance (float): GWAS significance threshold used to filter peaks. Defaults to 5e-8.\n            p_value_baseline (float): Least significant threshold. Below this, all snps are dropped. Defaults to 0.05.\n            locus_window_length (int | None): The distance for collecting locus around the semi indices. Defaults to None.\n\n        Returns:\n            StudyLocus: StudyLocus after clumping with information about the `locus`\n        \"\"\"\n        # If no locus window provided, using the same value:\n        if locus_window_length is None:\n            locus_window_length = window_length\n\n        # Run distance based clumping on the summary stats:\n        clumped_dataframe = WindowBasedClumping.clump(\n            summary_stats,\n            window_length=window_length,\n            p_value_significance=p_value_significance,\n        ).df.alias(\"clumped\")\n\n        # Get list of columns from clumped dataset for further propagation:\n        clumped_columns = clumped_dataframe.columns\n\n        # Dropping variants not meeting the baseline criteria:\n        sumstats_baseline = summary_stats.pvalue_filter(p_value_baseline).df\n\n        # Renaming columns:\n        sumstats_baseline_renamed = sumstats_baseline.selectExpr(\n            *[f\"{col} as tag_{col}\" for col in sumstats_baseline.columns]\n        ).alias(\"sumstat\")\n\n        study_locus_df = (\n            sumstats_baseline_renamed\n            # Joining the two datasets together:\n            .join(\n                f.broadcast(clumped_dataframe),\n                on=[\n                    (f.col(\"sumstat.tag_studyId\") == f.col(\"clumped.studyId\"))\n                    &amp; (f.col(\"sumstat.tag_chromosome\") == f.col(\"clumped.chromosome\"))\n                    &amp; (\n                        f.col(\"sumstat.tag_position\")\n                        &gt;= (f.col(\"clumped.position\") - locus_window_length)\n                    )\n                    &amp; (\n                        f.col(\"sumstat.tag_position\")\n                        &lt;= (f.col(\"clumped.position\") + locus_window_length)\n                    )\n                ],\n                how=\"right\",\n            )\n            .withColumn(\n                \"locus\",\n                f.struct(\n                    f.col(\"tag_variantId\").alias(\"variantId\"),\n                    f.col(\"tag_beta\").alias(\"beta\"),\n                    f.col(\"tag_pValueMantissa\").alias(\"pValueMantissa\"),\n                    f.col(\"tag_pValueExponent\").alias(\"pValueExponent\"),\n                    f.col(\"tag_standardError\").alias(\"standardError\"),\n                ),\n            )\n            .groupby(\"studyLocusId\")\n            .agg(\n                *[\n                    f.first(col).alias(col)\n                    for col in clumped_columns\n                    if col != \"studyLocusId\"\n                ],\n                f.collect_list(f.col(\"locus\")).alias(\"locus\"),\n            )\n        )\n\n        return StudyLocus(\n            _df=study_locus_df,\n            _schema=StudyLocus.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/method/window_based_clumping/#otg.method.window_based_clumping.WindowBasedClumping.clump","title":"<code>clump(summary_stats: SummaryStatistics, window_length: int, p_value_significance: float = 5e-08) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Clump summary statistics by distance.</p> <p>Parameters:</p> Name Type Description Default <code>summary_stats</code> <code>SummaryStatistics</code> <p>summary statistics to clump</p> required <code>window_length</code> <code>int</code> <p>window length in basepair</p> required <code>p_value_significance</code> <code>float</code> <p>only more significant variants are considered</p> <code>5e-08</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>clumped summary statistics</p> Source code in <code>src/otg/method/window_based_clumping.py</code> <pre><code>@classmethod\ndef clump(\n    cls: type[WindowBasedClumping],\n    summary_stats: SummaryStatistics,\n    window_length: int,\n    p_value_significance: float = 5e-8,\n) -&gt; StudyLocus:\n    \"\"\"Clump summary statistics by distance.\n\n    Args:\n        summary_stats (SummaryStatistics): summary statistics to clump\n        window_length (int): window length in basepair\n        p_value_significance (float): only more significant variants are considered\n\n    Returns:\n        StudyLocus: clumped summary statistics\n    \"\"\"\n    # Create window for locus clusters\n    # - variants where the distance between subsequent variants is below the defined threshold.\n    # - Variants are sorted by descending significance\n    cluster_window = Window.partitionBy(\n        \"studyId\", \"chromosome\", \"cluster_id\"\n    ).orderBy(f.col(\"pValueExponent\").asc(), f.col(\"pValueMantissa\").asc())\n\n    return StudyLocus(\n        _df=(\n            summary_stats\n            # Dropping snps below significance - all subsequent steps are done on significant variants:\n            .pvalue_filter(p_value_significance)\n            .df\n            # Clustering summary variants for efficient windowing (complexity reduction):\n            .withColumn(\n                \"cluster_id\",\n                WindowBasedClumping._cluster_peaks(\n                    f.col(\"studyId\"),\n                    f.col(\"chromosome\"),\n                    f.col(\"position\"),\n                    window_length,\n                ),\n            )\n            # Within each cluster variants are ranked by significance:\n            .withColumn(\"pvRank\", f.row_number().over(cluster_window))\n            # Collect positions in cluster for the most significant variant (complexity reduction):\n            .withColumn(\n                \"collectedPositions\",\n                f.when(\n                    f.col(\"pvRank\") == 1,\n                    f.collect_list(f.col(\"position\")).over(\n                        cluster_window.rowsBetween(\n                            Window.currentRow, Window.unboundedFollowing\n                        )\n                    ),\n                ).otherwise(f.array()),\n            )\n            # Get semi indices only ONCE per cluster:\n            .withColumn(\n                \"semiIndices\",\n                f.when(\n                    f.size(f.col(\"collectedPositions\")) &gt; 0,\n                    fml.vector_to_array(\n                        f.udf(WindowBasedClumping._prune_peak, VectorUDT())(\n                            fml.array_to_vector(f.col(\"collectedPositions\")),\n                            f.lit(window_length),\n                        )\n                    ),\n                ),\n            )\n            # Propagating the result of the above calculation for all rows:\n            .withColumn(\n                \"semiIndices\",\n                f.when(\n                    f.col(\"semiIndices\").isNull(),\n                    f.first(f.col(\"semiIndices\"), ignorenulls=True).over(\n                        cluster_window\n                    ),\n                ).otherwise(f.col(\"semiIndices\")),\n            )\n            # Keeping semi indices only:\n            .filter(f.col(\"semiIndices\")[f.col(\"pvRank\") - 1] &gt; 0)\n            .drop(\"pvRank\", \"collectedPositions\", \"semiIndices\", \"cluster_id\")\n            # Adding study-locus id:\n            .withColumn(\n                \"studyLocusId\",\n                StudyLocus.assign_study_locus_id(\n                    f.col(\"studyId\"), f.col(\"variantId\")\n                ),\n            )\n            # Initialize QC column as array of strings:\n            .withColumn(\n                \"qualityControls\", f.array().cast(t.ArrayType(t.StringType()))\n            )\n        ),\n        _schema=StudyLocus.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/method/window_based_clumping/#otg.method.window_based_clumping.WindowBasedClumping.clump_with_locus","title":"<code>clump_with_locus(summary_stats: SummaryStatistics, window_length: int, p_value_significance: float = 5e-08, p_value_baseline: float = 0.05, locus_window_length: int | None = None) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Clump significant associations while collecting locus around them.</p> <p>Parameters:</p> Name Type Description Default <code>summary_stats</code> <code>SummaryStatistics</code> <p>Input summary statistics dataset</p> required <code>window_length</code> <code>int</code> <p>Window size in  bp, used for distance based clumping.</p> required <code>p_value_significance</code> <code>float</code> <p>GWAS significance threshold used to filter peaks. Defaults to 5e-8.</p> <code>5e-08</code> <code>p_value_baseline</code> <code>float</code> <p>Least significant threshold. Below this, all snps are dropped. Defaults to 0.05.</p> <code>0.05</code> <code>locus_window_length</code> <code>int | None</code> <p>The distance for collecting locus around the semi indices. Defaults to None.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>StudyLocus after clumping with information about the <code>locus</code></p> Source code in <code>src/otg/method/window_based_clumping.py</code> <pre><code>@classmethod\ndef clump_with_locus(\n    cls: type[WindowBasedClumping],\n    summary_stats: SummaryStatistics,\n    window_length: int,\n    p_value_significance: float = 5e-8,\n    p_value_baseline: float = 0.05,\n    locus_window_length: int | None = None,\n) -&gt; StudyLocus:\n    \"\"\"Clump significant associations while collecting locus around them.\n\n    Args:\n        summary_stats (SummaryStatistics): Input summary statistics dataset\n        window_length (int): Window size in  bp, used for distance based clumping.\n        p_value_significance (float): GWAS significance threshold used to filter peaks. Defaults to 5e-8.\n        p_value_baseline (float): Least significant threshold. Below this, all snps are dropped. Defaults to 0.05.\n        locus_window_length (int | None): The distance for collecting locus around the semi indices. Defaults to None.\n\n    Returns:\n        StudyLocus: StudyLocus after clumping with information about the `locus`\n    \"\"\"\n    # If no locus window provided, using the same value:\n    if locus_window_length is None:\n        locus_window_length = window_length\n\n    # Run distance based clumping on the summary stats:\n    clumped_dataframe = WindowBasedClumping.clump(\n        summary_stats,\n        window_length=window_length,\n        p_value_significance=p_value_significance,\n    ).df.alias(\"clumped\")\n\n    # Get list of columns from clumped dataset for further propagation:\n    clumped_columns = clumped_dataframe.columns\n\n    # Dropping variants not meeting the baseline criteria:\n    sumstats_baseline = summary_stats.pvalue_filter(p_value_baseline).df\n\n    # Renaming columns:\n    sumstats_baseline_renamed = sumstats_baseline.selectExpr(\n        *[f\"{col} as tag_{col}\" for col in sumstats_baseline.columns]\n    ).alias(\"sumstat\")\n\n    study_locus_df = (\n        sumstats_baseline_renamed\n        # Joining the two datasets together:\n        .join(\n            f.broadcast(clumped_dataframe),\n            on=[\n                (f.col(\"sumstat.tag_studyId\") == f.col(\"clumped.studyId\"))\n                &amp; (f.col(\"sumstat.tag_chromosome\") == f.col(\"clumped.chromosome\"))\n                &amp; (\n                    f.col(\"sumstat.tag_position\")\n                    &gt;= (f.col(\"clumped.position\") - locus_window_length)\n                )\n                &amp; (\n                    f.col(\"sumstat.tag_position\")\n                    &lt;= (f.col(\"clumped.position\") + locus_window_length)\n                )\n            ],\n            how=\"right\",\n        )\n        .withColumn(\n            \"locus\",\n            f.struct(\n                f.col(\"tag_variantId\").alias(\"variantId\"),\n                f.col(\"tag_beta\").alias(\"beta\"),\n                f.col(\"tag_pValueMantissa\").alias(\"pValueMantissa\"),\n                f.col(\"tag_pValueExponent\").alias(\"pValueExponent\"),\n                f.col(\"tag_standardError\").alias(\"standardError\"),\n            ),\n        )\n        .groupby(\"studyLocusId\")\n        .agg(\n            *[\n                f.first(col).alias(col)\n                for col in clumped_columns\n                if col != \"studyLocusId\"\n            ],\n            f.collect_list(f.col(\"locus\")).alias(\"locus\"),\n        )\n    )\n\n    return StudyLocus(\n        _df=study_locus_df,\n        _schema=StudyLocus.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/method/l2g/_l2g/","title":"Locus to Gene (L2G) classifier","text":"<p>TBC</p>"},{"location":"python_api/method/l2g/evaluator/","title":"W&B evaluator","text":""},{"location":"python_api/method/l2g/evaluator/#otg.method.l2g.evaluator.WandbEvaluator","title":"<code>otg.method.l2g.evaluator.WandbEvaluator</code>","text":"<p>             Bases: <code>Evaluator</code></p> <p>Wrapper for pyspark Evaluators. It is expected that the user will provide an Evaluators, and this wrapper will log metrics from said evaluator to W&amp;B.</p> Source code in <code>src/otg/method/l2g/evaluator.py</code> <pre><code>class WandbEvaluator(Evaluator):\n    \"\"\"Wrapper for pyspark Evaluators. It is expected that the user will provide an Evaluators, and this wrapper will log metrics from said evaluator to W&amp;B.\"\"\"\n\n    spark_ml_evaluator: Param[Evaluator] = Param(\n        Params._dummy(), \"spark_ml_evaluator\", \"evaluator from pyspark.ml.evaluation\"\n    )\n\n    wandb_run: Param[Run] = Param(\n        Params._dummy(),\n        \"wandb_run\",\n        \"wandb run.  Expects an already initialized run.  You should set this, or wandb_run_kwargs, NOT BOTH\",\n    )\n\n    wandb_run_kwargs: Param[Any] = Param(\n        Params._dummy(),\n        \"wandb_run_kwargs\",\n        \"kwargs to be passed to wandb.init.  You should set this, or wandb_runId, NOT BOTH.  Setting this is useful when using with WandbCrossValdidator\",\n    )\n\n    wandb_runId: Param[str] = Param(  # noqa: N815\n        Params._dummy(),\n        \"wandb_runId\",\n        \"wandb run id.  if not providing an intialized run to wandb_run, a run with id wandb_runId will be resumed\",\n    )\n\n    wandb_project_name: Param[str] = Param(\n        Params._dummy(),\n        \"wandb_project_name\",\n        \"name of W&amp;B project\",\n        typeConverter=TypeConverters.toString,\n    )\n\n    label_values: Param[list[str]] = Param(\n        Params._dummy(),\n        \"label_values\",\n        \"for classification and multiclass classification, this is a list of values the label can assume\\nIf provided Multiclass or Multilabel evaluator without label_values, we'll figure it out from dataset passed through to evaluate.\",\n    )\n\n    _input_kwargs: Dict[str, Any]\n\n    @keyword_only\n    def __init__(\n        self: WandbEvaluator,\n        label_values: list[str] | None = None,\n        **kwargs: BinaryClassificationEvaluator\n        | MulticlassClassificationEvaluator\n        | Run,\n    ) -&gt; None:\n        \"\"\"Initialize a WandbEvaluator.\n\n        Args:\n            label_values (list[str] | None): List of label values.\n            **kwargs (BinaryClassificationEvaluator | MulticlassClassificationEvaluator | Run): Keyword arguments.\n        \"\"\"\n        if label_values is None:\n            label_values = []\n        super(Evaluator, self).__init__()\n\n        self.metrics = {\n            MulticlassClassificationEvaluator: [\n                \"f1\",\n                \"accuracy\",\n                \"weightedPrecision\",\n                \"weightedRecall\",\n                \"weightedTruePositiveRate\",\n                \"weightedFalsePositiveRate\",\n                \"weightedFMeasure\",\n                \"truePositiveRateByLabel\",\n                \"falsePositiveRateByLabel\",\n                \"precisionByLabel\",\n                \"recallByLabel\",\n                \"fMeasureByLabel\",\n                \"logLoss\",\n                \"hammingLoss\",\n            ],\n            BinaryClassificationEvaluator: [\"areaUnderROC\", \"areaUnderPR\"],\n        }\n\n        self._setDefault(label_values=[])\n        kwargs = self._input_kwargs\n        self._set(**kwargs)\n\n    def setspark_ml_evaluator(self: WandbEvaluator, value: Evaluator) -&gt; None:\n        \"\"\"Set the spark_ml_evaluator parameter.\n\n        Args:\n            value (Evaluator): Spark ML evaluator.\n        \"\"\"\n        self._set(spark_ml_evaluator=value)\n\n    def setlabel_values(self: WandbEvaluator, value: list[str]) -&gt; None:\n        \"\"\"Set the label_values parameter.\n\n        Args:\n            value (list[str]): List of label values.\n        \"\"\"\n        self._set(label_values=value)\n\n    def getspark_ml_evaluator(self: WandbEvaluator) -&gt; Evaluator:\n        \"\"\"Get the spark_ml_evaluator parameter.\n\n        Returns:\n            Evaluator: Spark ML evaluator.\n        \"\"\"\n        return self.getOrDefault(self.spark_ml_evaluator)\n\n    def getwandb_run(self: WandbEvaluator) -&gt; wandb.sdk.wandb_run.Run:\n        \"\"\"Get the wandb_run parameter.\n\n        Returns:\n            wandb.sdk.wandb_run.Run: Wandb run object.\n        \"\"\"\n        return self.getOrDefault(self.wandb_run)\n\n    def getwandb_project_name(self: WandbEvaluator) -&gt; Any:\n        \"\"\"Get the wandb_project_name parameter.\n\n        Returns:\n            Any: Name of the W&amp;B project.\n        \"\"\"\n        return self.getOrDefault(self.wandb_project_name)\n\n    def getlabel_values(self: WandbEvaluator) -&gt; list[str]:\n        \"\"\"Get the label_values parameter.\n\n        Returns:\n            list[str]: List of label values.\n        \"\"\"\n        return self.getOrDefault(self.label_values)\n\n    def _evaluate(self: WandbEvaluator, dataset: DataFrame) -&gt; float:\n        \"\"\"Evaluate the model on the given dataset.\n\n        Args:\n            dataset (DataFrame): Dataset to evaluate the model on.\n\n        Returns:\n            float: Metric value.\n        \"\"\"\n        dataset.persist()\n        metric_values: list[tuple[str, Any]] = []\n        label_values = self.getlabel_values()\n        spark_ml_evaluator: BinaryClassificationEvaluator | MulticlassClassificationEvaluator = (\n            self.getspark_ml_evaluator()  # type: ignore[assignment, unused-ignore]\n        )\n        run = self.getwandb_run()\n        evaluator_type = type(spark_ml_evaluator)\n        for metric in self.metrics[evaluator_type]:\n            if \"ByLabel\" in metric and label_values == []:\n                print(  # noqa: T201\n                    \"no label_values for the target have been provided and will be determined by the dataset.  This could take some time\"\n                )\n                label_values = [\n                    r[spark_ml_evaluator.getLabelCol()]\n                    for r in dataset.select(spark_ml_evaluator.getLabelCol())\n                    .distinct()\n                    .collect()\n                ]\n                if isinstance(label_values[0], list):\n                    merged = list(itertools.chain(*label_values))\n                    label_values = list(dict.fromkeys(merged).keys())\n                    self.setlabel_values(label_values)\n            for label in label_values:\n                out = spark_ml_evaluator.evaluate(\n                    dataset,\n                    {\n                        spark_ml_evaluator.metricLabel: label,  # type: ignore[assignment, unused-ignore]\n                        spark_ml_evaluator.metricName: metric,\n                    },\n                )\n                metric_values.append((f\"{metric}:{label}\", out))\n            out = spark_ml_evaluator.evaluate(\n                dataset, {spark_ml_evaluator.metricName: metric}\n            )\n            metric_values.append((f\"{metric}\", out))\n        run.log(dict(metric_values))\n        config = [\n            (f\"{k.parent.split('_')[0]}.{k.name}\", v)\n            for k, v in spark_ml_evaluator.extractParamMap().items()\n            if \"metric\" not in k.name\n        ]\n        run.config.update(dict(config))\n        return_metric = spark_ml_evaluator.evaluate(dataset)\n        dataset.unpersist()\n        return return_metric\n</code></pre>"},{"location":"python_api/method/l2g/evaluator/#otg.method.l2g.evaluator.WandbEvaluator.getlabel_values","title":"<code>getlabel_values() -&gt; list[str]</code>","text":"<p>Get the label_values parameter.</p> <p>Returns:</p> Type Description <code>list[str]</code> <p>list[str]: List of label values.</p> Source code in <code>src/otg/method/l2g/evaluator.py</code> <pre><code>def getlabel_values(self: WandbEvaluator) -&gt; list[str]:\n    \"\"\"Get the label_values parameter.\n\n    Returns:\n        list[str]: List of label values.\n    \"\"\"\n    return self.getOrDefault(self.label_values)\n</code></pre>"},{"location":"python_api/method/l2g/evaluator/#otg.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator","title":"<code>getspark_ml_evaluator() -&gt; Evaluator</code>","text":"<p>Get the spark_ml_evaluator parameter.</p> <p>Returns:</p> Name Type Description <code>Evaluator</code> <code>Evaluator</code> <p>Spark ML evaluator.</p> Source code in <code>src/otg/method/l2g/evaluator.py</code> <pre><code>def getspark_ml_evaluator(self: WandbEvaluator) -&gt; Evaluator:\n    \"\"\"Get the spark_ml_evaluator parameter.\n\n    Returns:\n        Evaluator: Spark ML evaluator.\n    \"\"\"\n    return self.getOrDefault(self.spark_ml_evaluator)\n</code></pre>"},{"location":"python_api/method/l2g/evaluator/#otg.method.l2g.evaluator.WandbEvaluator.getwandb_project_name","title":"<code>getwandb_project_name() -&gt; Any</code>","text":"<p>Get the wandb_project_name parameter.</p> <p>Returns:</p> Name Type Description <code>Any</code> <code>Any</code> <p>Name of the W&amp;B project.</p> Source code in <code>src/otg/method/l2g/evaluator.py</code> <pre><code>def getwandb_project_name(self: WandbEvaluator) -&gt; Any:\n    \"\"\"Get the wandb_project_name parameter.\n\n    Returns:\n        Any: Name of the W&amp;B project.\n    \"\"\"\n    return self.getOrDefault(self.wandb_project_name)\n</code></pre>"},{"location":"python_api/method/l2g/evaluator/#otg.method.l2g.evaluator.WandbEvaluator.getwandb_run","title":"<code>getwandb_run() -&gt; wandb.sdk.wandb_run.Run</code>","text":"<p>Get the wandb_run parameter.</p> <p>Returns:</p> Type Description <code>Run</code> <p>wandb.sdk.wandb_run.Run: Wandb run object.</p> Source code in <code>src/otg/method/l2g/evaluator.py</code> <pre><code>def getwandb_run(self: WandbEvaluator) -&gt; wandb.sdk.wandb_run.Run:\n    \"\"\"Get the wandb_run parameter.\n\n    Returns:\n        wandb.sdk.wandb_run.Run: Wandb run object.\n    \"\"\"\n    return self.getOrDefault(self.wandb_run)\n</code></pre>"},{"location":"python_api/method/l2g/evaluator/#otg.method.l2g.evaluator.WandbEvaluator.setlabel_values","title":"<code>setlabel_values(value: list[str]) -&gt; None</code>","text":"<p>Set the label_values parameter.</p> <p>Parameters:</p> Name Type Description Default <code>value</code> <code>list[str]</code> <p>List of label values.</p> required Source code in <code>src/otg/method/l2g/evaluator.py</code> <pre><code>def setlabel_values(self: WandbEvaluator, value: list[str]) -&gt; None:\n    \"\"\"Set the label_values parameter.\n\n    Args:\n        value (list[str]): List of label values.\n    \"\"\"\n    self._set(label_values=value)\n</code></pre>"},{"location":"python_api/method/l2g/evaluator/#otg.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator","title":"<code>setspark_ml_evaluator(value: Evaluator) -&gt; None</code>","text":"<p>Set the spark_ml_evaluator parameter.</p> <p>Parameters:</p> Name Type Description Default <code>value</code> <code>Evaluator</code> <p>Spark ML evaluator.</p> required Source code in <code>src/otg/method/l2g/evaluator.py</code> <pre><code>def setspark_ml_evaluator(self: WandbEvaluator, value: Evaluator) -&gt; None:\n    \"\"\"Set the spark_ml_evaluator parameter.\n\n    Args:\n        value (Evaluator): Spark ML evaluator.\n    \"\"\"\n    self._set(spark_ml_evaluator=value)\n</code></pre>"},{"location":"python_api/method/l2g/feature_factory/","title":"L2G Feature Factory","text":""},{"location":"python_api/method/l2g/feature_factory/#otg.method.l2g.feature_factory.ColocalisationFactory","title":"<code>otg.method.l2g.feature_factory.ColocalisationFactory</code>","text":"<p>Feature extraction in colocalisation.</p> Source code in <code>src/otg/method/l2g/feature_factory.py</code> <pre><code>class ColocalisationFactory:\n    \"\"\"Feature extraction in colocalisation.\"\"\"\n\n    @staticmethod\n    def _get_max_coloc_per_study_locus(\n        study_locus: StudyLocus,\n        studies: StudyIndex,\n        colocalisation: Colocalisation,\n        colocalisation_method: str,\n    ) -&gt; L2GFeature:\n        \"\"\"Get the maximum colocalisation posterior probability for each pair of overlapping study-locus per type of colocalisation method and QTL type.\n\n        Args:\n            study_locus (StudyLocus): Study locus dataset\n            studies (StudyIndex): Study index dataset\n            colocalisation (Colocalisation): Colocalisation dataset\n            colocalisation_method (str): Colocalisation method to extract the max from\n\n        Returns:\n            L2GFeature: Stores the features with the max coloc probabilities for each pair of study-locus\n\n        Raises:\n            ValueError: If the colocalisation method is not supported\n        \"\"\"\n        if colocalisation_method not in [\"COLOC\", \"eCAVIAR\"]:\n            raise ValueError(\n                f\"Colocalisation method {colocalisation_method} not supported\"\n            )\n        if colocalisation_method == \"COLOC\":\n            coloc_score_col_name = \"log2h4h3\"\n            coloc_feature_col_template = \"max_coloc_llr\"\n\n        elif colocalisation_method == \"eCAVIAR\":\n            coloc_score_col_name = \"clpp\"\n            coloc_feature_col_template = \"max_coloc_clpp\"\n\n        colocalising_study_locus = (\n            study_locus.df.select(\"studyLocusId\", \"studyId\")\n            # annotate studyLoci with overlapping IDs on the left - to just keep GWAS associations\n            .join(\n                colocalisation._df.selectExpr(\n                    \"leftStudyLocusId as studyLocusId\",\n                    \"rightStudyLocusId\",\n                    \"colocalisationMethod\",\n                    f\"{coloc_score_col_name} as coloc_score\",\n                ),\n                on=\"studyLocusId\",\n                how=\"inner\",\n            )\n            # bring study metadata to just keep QTL studies on the right\n            .join(\n                study_locus.df.selectExpr(\n                    \"studyLocusId as rightStudyLocusId\", \"studyId as right_studyId\"\n                ),\n                on=\"rightStudyLocusId\",\n                how=\"inner\",\n            )\n            .join(\n                f.broadcast(\n                    studies._df.selectExpr(\n                        \"studyId as right_studyId\",\n                        \"studyType as right_studyType\",\n                        \"geneId\",\n                    )\n                ),\n                on=\"right_studyId\",\n                how=\"inner\",\n            )\n            .filter(\n                (f.col(\"colocalisationMethod\") == colocalisation_method)\n                &amp; (f.col(\"right_studyType\") != \"gwas\")\n            )\n            .select(\"studyLocusId\", \"right_studyType\", \"geneId\", \"coloc_score\")\n        )\n\n        # Max LLR calculation per studyLocus AND type of QTL\n        local_max = get_record_with_maximum_value(\n            colocalising_study_locus,\n            [\"studyLocusId\", \"right_studyType\", \"geneId\"],\n            \"coloc_score\",\n        )\n        neighbourhood_max = (\n            get_record_with_maximum_value(\n                colocalising_study_locus,\n                [\"studyLocusId\", \"right_studyType\"],\n                \"coloc_score\",\n            )\n            .join(\n                local_max.selectExpr(\"studyLocusId\", \"coloc_score as coloc_local_max\"),\n                on=\"studyLocusId\",\n                how=\"inner\",\n            )\n            .withColumn(\n                f\"{coloc_feature_col_template}_nbh\",\n                f.col(\"coloc_local_max\") - f.col(\"coloc_score\"),\n            )\n        )\n\n        # Split feature per molQTL\n        local_dfs = []\n        nbh_dfs = []\n        for qtl_type in [\"eqtl\", \"sqtl\", \"pqtl\"]:\n            local_max = local_max.filter(\n                f.col(\"right_studyType\") == qtl_type\n            ).withColumnRenamed(\n                \"coloc_score\", f\"{qtl_type}_{coloc_feature_col_template}_local\"\n            )\n            local_dfs.append(local_max)\n\n            neighbourhood_max = neighbourhood_max.filter(\n                f.col(\"right_studyType\") == qtl_type\n            ).withColumnRenamed(\n                f\"{coloc_feature_col_template}_nbh\",\n                f\"{qtl_type}_{coloc_feature_col_template}_nbh\",\n            )\n            nbh_dfs.append(neighbourhood_max)\n\n        wide_dfs = reduce(\n            lambda x, y: x.unionByName(y, allowMissingColumns=True),\n            local_dfs + nbh_dfs,\n            colocalising_study_locus.limit(0),\n        )\n\n        return L2GFeature(\n            _df=convert_from_wide_to_long(\n                wide_dfs,\n                id_vars=(\"studyLocusId\", \"geneId\"),\n                var_name=\"featureName\",\n                value_name=\"featureValue\",\n            ),\n            _schema=L2GFeature.get_schema(),\n        )\n\n    @staticmethod\n    def _get_coloc_features(\n        study_locus: StudyLocus, studies: StudyIndex, colocalisation: Colocalisation\n    ) -&gt; L2GFeature:\n        \"\"\"Calls _get_max_coloc_per_study_locus for both methods and concatenates the results.\n\n        Args:\n            study_locus (StudyLocus): Study locus dataset\n            studies (StudyIndex): Study index dataset\n            colocalisation (Colocalisation): Colocalisation dataset\n\n        Returns:\n            L2GFeature: Stores the features with the max coloc probabilities for each pair of study-locus\n        \"\"\"\n        coloc_llr = ColocalisationFactory._get_max_coloc_per_study_locus(\n            study_locus,\n            studies,\n            colocalisation,\n            \"COLOC\",\n        )\n        coloc_clpp = ColocalisationFactory._get_max_coloc_per_study_locus(\n            study_locus,\n            studies,\n            colocalisation,\n            \"eCAVIAR\",\n        )\n\n        return L2GFeature(\n            _df=coloc_llr.df.unionByName(coloc_clpp.df, allowMissingColumns=True),\n            _schema=L2GFeature.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/method/l2g/feature_factory/#otg.method.l2g.feature_factory.StudyLocusFactory","title":"<code>otg.method.l2g.feature_factory.StudyLocusFactory</code>","text":"<p>             Bases: <code>StudyLocus</code></p> <p>Feature extraction in study locus.</p> Source code in <code>src/otg/method/l2g/feature_factory.py</code> <pre><code>class StudyLocusFactory(StudyLocus):\n    \"\"\"Feature extraction in study locus.\"\"\"\n\n    @staticmethod\n    def _get_tss_distance_features(\n        study_locus: StudyLocus, distances: V2G\n    ) -&gt; L2GFeature:\n        \"\"\"Joins StudyLocus with the V2G to extract the minimum distance to a gene TSS of all variants in a StudyLocus credible set.\n\n        Args:\n            study_locus (StudyLocus): Study locus dataset\n            distances (V2G): Dataframe containing the distances of all variants to all genes TSS within a region\n\n        Returns:\n            L2GFeature: Stores the features with the minimum distance among all variants in the credible set and a gene TSS.\n\n        \"\"\"\n        wide_df = (\n            study_locus.filter_credible_set(CredibleInterval.IS95)\n            .df.select(\n                \"studyLocusId\",\n                \"variantId\",\n                f.explode(\"locus.variantId\").alias(\"tagVariantId\"),\n            )\n            .join(\n                distances.df.selectExpr(\n                    \"variantId as tagVariantId\", \"geneId\", \"distance\"\n                ),\n                on=\"tagVariantId\",\n                how=\"inner\",\n            )\n            .groupBy(\"studyLocusId\", \"geneId\")\n            .agg(\n                f.min(\"distance\").alias(\"distanceTssMinimum\"),\n                f.mean(\"distance\").alias(\"distanceTssMean\"),\n            )\n        )\n\n        return L2GFeature(\n            _df=convert_from_wide_to_long(\n                wide_df,\n                id_vars=(\"studyLocusId\", \"geneId\"),\n                var_name=\"featureName\",\n                value_name=\"featureValue\",\n            ),\n            _schema=L2GFeature.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/method/l2g/model/","title":"L2G Model","text":""},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel","title":"<code>otg.method.l2g.model.LocusToGeneModel</code>  <code>dataclass</code>","text":"<p>Wrapper for the Locus to Gene classifier.</p> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>@dataclass\nclass LocusToGeneModel:\n    \"\"\"Wrapper for the Locus to Gene classifier.\"\"\"\n\n    features_list: list[str]\n    estimator: Any = None\n    pipeline: Pipeline = Pipeline(stages=[])\n    model: PipelineModel | None = None\n    wandb_l2g_project_name: str = \"otg_l2g\"\n\n    def __post_init__(self: LocusToGeneModel) -&gt; None:\n        \"\"\"Post init that adds the model to the ML pipeline.\"\"\"\n        label_indexer = StringIndexer(\n            inputCol=\"goldStandardSet\", outputCol=\"label\", handleInvalid=\"keep\"\n        )\n        vector_assembler = LocusToGeneModel.features_vector_assembler(\n            self.features_list\n        )\n\n        self.pipeline = Pipeline(\n            stages=[\n                label_indexer,\n                vector_assembler,\n            ]\n        )\n\n    def save(self: LocusToGeneModel, path: str) -&gt; None:\n        \"\"\"Saves fitted pipeline model to disk.\n\n        Args:\n            path (str): Path to save the model to\n\n        Raises:\n            ValueError: If the model has not been fitted yet\n        \"\"\"\n        if self.model is None:\n            raise ValueError(\"Model has not been fitted yet.\")\n        self.model.write().overwrite().save(path)\n\n    @property\n    def classifier(self: LocusToGeneModel) -&gt; Any:\n        \"\"\"Return the model.\n\n        Returns:\n            Any: An estimator object from Spark ML\n        \"\"\"\n        return self.estimator\n\n    @staticmethod\n    def features_vector_assembler(features_cols: list[str]) -&gt; VectorAssembler:\n        \"\"\"Spark transformer to assemble the feature columns into a vector.\n\n        Args:\n            features_cols (list[str]): List of feature columns to assemble\n\n        Returns:\n            VectorAssembler: Spark transformer to assemble the feature columns into a vector\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.ml.feature import VectorAssembler\n            &gt;&gt;&gt; df = spark.createDataFrame([(5.2, 3.5)], schema=\"feature_1 FLOAT, feature_2 FLOAT\")\n            &gt;&gt;&gt; assembler = LocusToGeneModel.features_vector_assembler([\"feature_1\", \"feature_2\"])\n            &gt;&gt;&gt; assembler.transform(df).show()\n            +---------+---------+--------------------+\n            |feature_1|feature_2|            features|\n            +---------+---------+--------------------+\n            |      5.2|      3.5|[5.19999980926513...|\n            +---------+---------+--------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        return (\n            VectorAssembler(handleInvalid=\"error\")\n            .setInputCols(features_cols)\n            .setOutputCol(\"features\")\n        )\n\n    def log_to_wandb(\n        self: LocusToGeneModel,\n        results: DataFrame,\n        training_data: L2GFeatureMatrix,\n        evaluators: list[\n            BinaryClassificationEvaluator | MulticlassClassificationEvaluator\n        ],\n        wandb_run: Run,\n    ) -&gt; None:\n        \"\"\"Log evaluation results and feature importance to W&amp;B.\n\n        Args:\n            results (DataFrame): Dataframe containing the predictions\n            training_data (L2GFeatureMatrix): Training data used for the model. If provided, the table and the number of positive and negative labels will be logged to W&amp;B\n            evaluators (list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator]): List of Spark ML evaluators to use for evaluation\n            wandb_run (Run): W&amp;B run to log the results to\n        \"\"\"\n        ## Track evaluation metrics\n        for evaluator in evaluators:\n            wandb_evaluator = WandbEvaluator(\n                spark_ml_evaluator=evaluator, wandb_run=wandb_run\n            )\n            wandb_evaluator.evaluate(results)\n        ## Track feature importance\n        wandb_run.log({\"importances\": self.get_feature_importance()})\n        ## Track training set\n        training_table = wandb.Table(dataframe=training_data.df.toPandas())\n        wandb_run.log({\"trainingSet\": training_table})\n        # Count number of positive and negative labels\n        gs_counts_dict = {\n            \"goldStandard\" + row[\"goldStandardSet\"].capitalize(): row[\"count\"]\n            for row in training_data.df.groupBy(\"goldStandardSet\").count().collect()\n        }\n        wandb_run.log(gs_counts_dict)\n        # Missingness rates\n        wandb_run.log(\n            {\"missingnessRates\": training_data.calculate_feature_missingness_rate()}\n        )\n\n    @classmethod\n    def load_from_disk(\n        cls: Type[LocusToGeneModel], path: str, features_list: list[str]\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Load a fitted pipeline model from disk.\n\n        Args:\n            path (str): Path to the model\n            features_list (list[str]): List of features used for the model\n\n        Returns:\n            LocusToGeneModel: L2G model loaded from disk\n        \"\"\"\n        return cls(model=PipelineModel.load(path), features_list=features_list)\n\n    @classifier.setter  # type: ignore\n    def classifier(self: LocusToGeneModel, new_estimator: Any) -&gt; None:\n        \"\"\"Set the model.\n\n        Args:\n            new_estimator (Any): An estimator object from Spark ML\n        \"\"\"\n        self.estimator = new_estimator\n\n    def get_param_grid(self: LocusToGeneModel) -&gt; list[Any]:\n        \"\"\"Return the parameter grid for the model.\n\n        Returns:\n            list[Any]: List of parameter maps to use for cross validation\n        \"\"\"\n        return (\n            ParamGridBuilder()\n            .addGrid(self.estimator.max_depth, [3, 5, 7])\n            .addGrid(self.estimator.learning_rate, [0.01, 0.1, 1.0])\n            .build()\n        )\n\n    def add_pipeline_stage(\n        self: LocusToGeneModel, transformer: Transformer\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Adds a stage to the L2G pipeline.\n\n        Args:\n            transformer (Transformer): Spark transformer to add to the pipeline\n\n        Returns:\n            LocusToGeneModel: L2G model with the new transformer\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.ml.regression import LinearRegression\n            &gt;&gt;&gt; estimator = LinearRegression()\n            &gt;&gt;&gt; test_model = LocusToGeneModel(features_list=[\"a\", \"b\"])\n            &gt;&gt;&gt; print(len(test_model.pipeline.getStages()))\n            2\n            &gt;&gt;&gt; print(len(test_model.add_pipeline_stage(estimator).pipeline.getStages()))\n            3\n        \"\"\"\n        pipeline_stages = self.pipeline.getStages()\n        new_stages = pipeline_stages + [transformer]\n        self.pipeline = Pipeline(stages=new_stages)\n        return self\n\n    def evaluate(\n        self: LocusToGeneModel,\n        results: DataFrame,\n        hyperparameters: dict[str, Any],\n        wandb_run_name: str | None,\n        training_data: L2GFeatureMatrix | None = None,\n    ) -&gt; None:\n        \"\"\"Perform evaluation of the model predictions for the test set and track the results with W&amp;B.\n\n        Args:\n            results (DataFrame): Dataframe containing the predictions\n            hyperparameters (dict[str, Any]): Hyperparameters used for the model\n            wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n            training_data (L2GFeatureMatrix | None): Training data used for the model. If provided, the ratio of positive to negative labels will be logged to W&amp;B\n        \"\"\"\n        binary_evaluator = BinaryClassificationEvaluator(\n            rawPredictionCol=\"rawPrediction\", labelCol=\"label\"\n        )\n        multi_evaluator = MulticlassClassificationEvaluator(\n            labelCol=\"label\", predictionCol=\"prediction\"\n        )\n\n        if wandb_run_name and training_data:\n            run = wandb.init(\n                project=self.wandb_l2g_project_name,\n                config=hyperparameters,\n                name=wandb_run_name,\n            )\n            if isinstance(run, Run):\n                self.log_to_wandb(\n                    results, training_data, [binary_evaluator, multi_evaluator], run\n                )\n                run.finish()\n\n    @property\n    def feature_name_map(self: LocusToGeneModel) -&gt; dict[str, str]:\n        \"\"\"Return a dictionary mapping encoded feature names to the original names.\n\n        Returns:\n            dict[str, str]: Feature name map of the model\n\n        Raises:\n            ValueError: If the model has not been fitted yet\n        \"\"\"\n        if not self.model:\n            raise ValueError(\"Model not fitted yet. `fit()` has to be called first.\")\n        elif isinstance(self.model.stages[1], VectorAssembler):\n            feature_names = self.model.stages[1].getInputCols()\n        return {f\"f{i}\": feature_name for i, feature_name in enumerate(feature_names)}\n\n    def get_feature_importance(self: LocusToGeneModel) -&gt; dict[str, float]:\n        \"\"\"Return dictionary with relative importances of every feature in the model. Feature names are encoded and have to be mapped back to their original names.\n\n        Returns:\n            dict[str, float]: Dictionary mapping feature names to their importance\n\n        Raises:\n            ValueError: If the model has not been fitted yet or is not an XGBoost model\n        \"\"\"\n        if not self.model or not isinstance(\n            self.model.stages[-1], SparkXGBClassifierModel\n        ):\n            raise ValueError(\n                f\"Model type {type(self.model)} not supported for feature importance.\"\n            )\n        importance_map = self.model.stages[-1].get_feature_importances()\n        return {self.feature_name_map[k]: v for k, v in importance_map.items()}\n\n    def fit(\n        self: LocusToGeneModel,\n        feature_matrix: L2GFeatureMatrix,\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Fit the pipeline to the feature matrix dataframe.\n\n        Args:\n            feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to fit the model to\n\n        Returns:\n            LocusToGeneModel: Fitted model\n        \"\"\"\n        self.model = self.pipeline.fit(feature_matrix.df)\n        return self\n\n    def predict(\n        self: LocusToGeneModel,\n        feature_matrix: L2GFeatureMatrix,\n    ) -&gt; DataFrame:\n        \"\"\"Apply the model to a given feature matrix dataframe. The feature matrix needs to be preprocessed first.\n\n        Args:\n            feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to apply the model to\n\n        Returns:\n            DataFrame: Dataframe with predictions\n\n        Raises:\n            ValueError: If the model has not been fitted yet\n        \"\"\"\n        if not self.model:\n            raise ValueError(\"Model not fitted yet. `fit()` has to be called first.\")\n        return self.model.transform(feature_matrix.df)\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.classifier","title":"<code>classifier: Any</code>  <code>property</code> <code>writable</code>","text":"<p>Return the model.</p> <p>Returns:</p> Name Type Description <code>Any</code> <code>Any</code> <p>An estimator object from Spark ML</p>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.feature_name_map","title":"<code>feature_name_map: dict[str, str]</code>  <code>property</code>","text":"<p>Return a dictionary mapping encoded feature names to the original names.</p> <p>Returns:</p> Type Description <code>dict[str, str]</code> <p>dict[str, str]: Feature name map of the model</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet</p>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.add_pipeline_stage","title":"<code>add_pipeline_stage(transformer: Transformer) -&gt; LocusToGeneModel</code>","text":"<p>Adds a stage to the L2G pipeline.</p> <p>Parameters:</p> Name Type Description Default <code>transformer</code> <code>Transformer</code> <p>Spark transformer to add to the pipeline</p> required <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>L2G model with the new transformer</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; from pyspark.ml.regression import LinearRegression\n&gt;&gt;&gt; estimator = LinearRegression()\n&gt;&gt;&gt; test_model = LocusToGeneModel(features_list=[\"a\", \"b\"])\n&gt;&gt;&gt; print(len(test_model.pipeline.getStages()))\n2\n&gt;&gt;&gt; print(len(test_model.add_pipeline_stage(estimator).pipeline.getStages()))\n3\n</code></pre> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def add_pipeline_stage(\n    self: LocusToGeneModel, transformer: Transformer\n) -&gt; LocusToGeneModel:\n    \"\"\"Adds a stage to the L2G pipeline.\n\n    Args:\n        transformer (Transformer): Spark transformer to add to the pipeline\n\n    Returns:\n        LocusToGeneModel: L2G model with the new transformer\n\n    Examples:\n        &gt;&gt;&gt; from pyspark.ml.regression import LinearRegression\n        &gt;&gt;&gt; estimator = LinearRegression()\n        &gt;&gt;&gt; test_model = LocusToGeneModel(features_list=[\"a\", \"b\"])\n        &gt;&gt;&gt; print(len(test_model.pipeline.getStages()))\n        2\n        &gt;&gt;&gt; print(len(test_model.add_pipeline_stage(estimator).pipeline.getStages()))\n        3\n    \"\"\"\n    pipeline_stages = self.pipeline.getStages()\n    new_stages = pipeline_stages + [transformer]\n    self.pipeline = Pipeline(stages=new_stages)\n    return self\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.evaluate","title":"<code>evaluate(results: DataFrame, hyperparameters: dict[str, Any], wandb_run_name: str | None, training_data: L2GFeatureMatrix | None = None) -&gt; None</code>","text":"<p>Perform evaluation of the model predictions for the test set and track the results with W&amp;B.</p> <p>Parameters:</p> Name Type Description Default <code>results</code> <code>DataFrame</code> <p>Dataframe containing the predictions</p> required <code>hyperparameters</code> <code>dict[str, Any]</code> <p>Hyperparameters used for the model</p> required <code>wandb_run_name</code> <code>str | None</code> <p>Descriptive name for the run to be tracked with W&amp;B</p> required <code>training_data</code> <code>L2GFeatureMatrix | None</code> <p>Training data used for the model. If provided, the ratio of positive to negative labels will be logged to W&amp;B</p> <code>None</code> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def evaluate(\n    self: LocusToGeneModel,\n    results: DataFrame,\n    hyperparameters: dict[str, Any],\n    wandb_run_name: str | None,\n    training_data: L2GFeatureMatrix | None = None,\n) -&gt; None:\n    \"\"\"Perform evaluation of the model predictions for the test set and track the results with W&amp;B.\n\n    Args:\n        results (DataFrame): Dataframe containing the predictions\n        hyperparameters (dict[str, Any]): Hyperparameters used for the model\n        wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n        training_data (L2GFeatureMatrix | None): Training data used for the model. If provided, the ratio of positive to negative labels will be logged to W&amp;B\n    \"\"\"\n    binary_evaluator = BinaryClassificationEvaluator(\n        rawPredictionCol=\"rawPrediction\", labelCol=\"label\"\n    )\n    multi_evaluator = MulticlassClassificationEvaluator(\n        labelCol=\"label\", predictionCol=\"prediction\"\n    )\n\n    if wandb_run_name and training_data:\n        run = wandb.init(\n            project=self.wandb_l2g_project_name,\n            config=hyperparameters,\n            name=wandb_run_name,\n        )\n        if isinstance(run, Run):\n            self.log_to_wandb(\n                results, training_data, [binary_evaluator, multi_evaluator], run\n            )\n            run.finish()\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.features_vector_assembler","title":"<code>features_vector_assembler(features_cols: list[str]) -&gt; VectorAssembler</code>  <code>staticmethod</code>","text":"<p>Spark transformer to assemble the feature columns into a vector.</p> <p>Parameters:</p> Name Type Description Default <code>features_cols</code> <code>list[str]</code> <p>List of feature columns to assemble</p> required <p>Returns:</p> Name Type Description <code>VectorAssembler</code> <code>VectorAssembler</code> <p>Spark transformer to assemble the feature columns into a vector</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; from pyspark.ml.feature import VectorAssembler\n&gt;&gt;&gt; df = spark.createDataFrame([(5.2, 3.5)], schema=\"feature_1 FLOAT, feature_2 FLOAT\")\n&gt;&gt;&gt; assembler = LocusToGeneModel.features_vector_assembler([\"feature_1\", \"feature_2\"])\n&gt;&gt;&gt; assembler.transform(df).show()\n+---------+---------+--------------------+\n|feature_1|feature_2|            features|\n+---------+---------+--------------------+\n|      5.2|      3.5|[5.19999980926513...|\n+---------+---------+--------------------+\n</code></pre> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>@staticmethod\ndef features_vector_assembler(features_cols: list[str]) -&gt; VectorAssembler:\n    \"\"\"Spark transformer to assemble the feature columns into a vector.\n\n    Args:\n        features_cols (list[str]): List of feature columns to assemble\n\n    Returns:\n        VectorAssembler: Spark transformer to assemble the feature columns into a vector\n\n    Examples:\n        &gt;&gt;&gt; from pyspark.ml.feature import VectorAssembler\n        &gt;&gt;&gt; df = spark.createDataFrame([(5.2, 3.5)], schema=\"feature_1 FLOAT, feature_2 FLOAT\")\n        &gt;&gt;&gt; assembler = LocusToGeneModel.features_vector_assembler([\"feature_1\", \"feature_2\"])\n        &gt;&gt;&gt; assembler.transform(df).show()\n        +---------+---------+--------------------+\n        |feature_1|feature_2|            features|\n        +---------+---------+--------------------+\n        |      5.2|      3.5|[5.19999980926513...|\n        +---------+---------+--------------------+\n        &lt;BLANKLINE&gt;\n    \"\"\"\n    return (\n        VectorAssembler(handleInvalid=\"error\")\n        .setInputCols(features_cols)\n        .setOutputCol(\"features\")\n    )\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.fit","title":"<code>fit(feature_matrix: L2GFeatureMatrix) -&gt; LocusToGeneModel</code>","text":"<p>Fit the pipeline to the feature matrix dataframe.</p> <p>Parameters:</p> Name Type Description Default <code>feature_matrix</code> <code>L2GFeatureMatrix</code> <p>Feature matrix dataframe to fit the model to</p> required <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>Fitted model</p> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def fit(\n    self: LocusToGeneModel,\n    feature_matrix: L2GFeatureMatrix,\n) -&gt; LocusToGeneModel:\n    \"\"\"Fit the pipeline to the feature matrix dataframe.\n\n    Args:\n        feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to fit the model to\n\n    Returns:\n        LocusToGeneModel: Fitted model\n    \"\"\"\n    self.model = self.pipeline.fit(feature_matrix.df)\n    return self\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.get_feature_importance","title":"<code>get_feature_importance() -&gt; dict[str, float]</code>","text":"<p>Return dictionary with relative importances of every feature in the model. Feature names are encoded and have to be mapped back to their original names.</p> <p>Returns:</p> Type Description <code>dict[str, float]</code> <p>dict[str, float]: Dictionary mapping feature names to their importance</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet or is not an XGBoost model</p> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def get_feature_importance(self: LocusToGeneModel) -&gt; dict[str, float]:\n    \"\"\"Return dictionary with relative importances of every feature in the model. Feature names are encoded and have to be mapped back to their original names.\n\n    Returns:\n        dict[str, float]: Dictionary mapping feature names to their importance\n\n    Raises:\n        ValueError: If the model has not been fitted yet or is not an XGBoost model\n    \"\"\"\n    if not self.model or not isinstance(\n        self.model.stages[-1], SparkXGBClassifierModel\n    ):\n        raise ValueError(\n            f\"Model type {type(self.model)} not supported for feature importance.\"\n        )\n    importance_map = self.model.stages[-1].get_feature_importances()\n    return {self.feature_name_map[k]: v for k, v in importance_map.items()}\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.get_param_grid","title":"<code>get_param_grid() -&gt; list[Any]</code>","text":"<p>Return the parameter grid for the model.</p> <p>Returns:</p> Type Description <code>list[Any]</code> <p>list[Any]: List of parameter maps to use for cross validation</p> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def get_param_grid(self: LocusToGeneModel) -&gt; list[Any]:\n    \"\"\"Return the parameter grid for the model.\n\n    Returns:\n        list[Any]: List of parameter maps to use for cross validation\n    \"\"\"\n    return (\n        ParamGridBuilder()\n        .addGrid(self.estimator.max_depth, [3, 5, 7])\n        .addGrid(self.estimator.learning_rate, [0.01, 0.1, 1.0])\n        .build()\n    )\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.load_from_disk","title":"<code>load_from_disk(path: str, features_list: list[str]) -&gt; LocusToGeneModel</code>  <code>classmethod</code>","text":"<p>Load a fitted pipeline model from disk.</p> <p>Parameters:</p> Name Type Description Default <code>path</code> <code>str</code> <p>Path to the model</p> required <code>features_list</code> <code>list[str]</code> <p>List of features used for the model</p> required <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>L2G model loaded from disk</p> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>@classmethod\ndef load_from_disk(\n    cls: Type[LocusToGeneModel], path: str, features_list: list[str]\n) -&gt; LocusToGeneModel:\n    \"\"\"Load a fitted pipeline model from disk.\n\n    Args:\n        path (str): Path to the model\n        features_list (list[str]): List of features used for the model\n\n    Returns:\n        LocusToGeneModel: L2G model loaded from disk\n    \"\"\"\n    return cls(model=PipelineModel.load(path), features_list=features_list)\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.log_to_wandb","title":"<code>log_to_wandb(results: DataFrame, training_data: L2GFeatureMatrix, evaluators: list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator], wandb_run: Run) -&gt; None</code>","text":"<p>Log evaluation results and feature importance to W&amp;B.</p> <p>Parameters:</p> Name Type Description Default <code>results</code> <code>DataFrame</code> <p>Dataframe containing the predictions</p> required <code>training_data</code> <code>L2GFeatureMatrix</code> <p>Training data used for the model. If provided, the table and the number of positive and negative labels will be logged to W&amp;B</p> required <code>evaluators</code> <code>list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator]</code> <p>List of Spark ML evaluators to use for evaluation</p> required <code>wandb_run</code> <code>Run</code> <p>W&amp;B run to log the results to</p> required Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def log_to_wandb(\n    self: LocusToGeneModel,\n    results: DataFrame,\n    training_data: L2GFeatureMatrix,\n    evaluators: list[\n        BinaryClassificationEvaluator | MulticlassClassificationEvaluator\n    ],\n    wandb_run: Run,\n) -&gt; None:\n    \"\"\"Log evaluation results and feature importance to W&amp;B.\n\n    Args:\n        results (DataFrame): Dataframe containing the predictions\n        training_data (L2GFeatureMatrix): Training data used for the model. If provided, the table and the number of positive and negative labels will be logged to W&amp;B\n        evaluators (list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator]): List of Spark ML evaluators to use for evaluation\n        wandb_run (Run): W&amp;B run to log the results to\n    \"\"\"\n    ## Track evaluation metrics\n    for evaluator in evaluators:\n        wandb_evaluator = WandbEvaluator(\n            spark_ml_evaluator=evaluator, wandb_run=wandb_run\n        )\n        wandb_evaluator.evaluate(results)\n    ## Track feature importance\n    wandb_run.log({\"importances\": self.get_feature_importance()})\n    ## Track training set\n    training_table = wandb.Table(dataframe=training_data.df.toPandas())\n    wandb_run.log({\"trainingSet\": training_table})\n    # Count number of positive and negative labels\n    gs_counts_dict = {\n        \"goldStandard\" + row[\"goldStandardSet\"].capitalize(): row[\"count\"]\n        for row in training_data.df.groupBy(\"goldStandardSet\").count().collect()\n    }\n    wandb_run.log(gs_counts_dict)\n    # Missingness rates\n    wandb_run.log(\n        {\"missingnessRates\": training_data.calculate_feature_missingness_rate()}\n    )\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.predict","title":"<code>predict(feature_matrix: L2GFeatureMatrix) -&gt; DataFrame</code>","text":"<p>Apply the model to a given feature matrix dataframe. The feature matrix needs to be preprocessed first.</p> <p>Parameters:</p> Name Type Description Default <code>feature_matrix</code> <code>L2GFeatureMatrix</code> <p>Feature matrix dataframe to apply the model to</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Dataframe with predictions</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet</p> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def predict(\n    self: LocusToGeneModel,\n    feature_matrix: L2GFeatureMatrix,\n) -&gt; DataFrame:\n    \"\"\"Apply the model to a given feature matrix dataframe. The feature matrix needs to be preprocessed first.\n\n    Args:\n        feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to apply the model to\n\n    Returns:\n        DataFrame: Dataframe with predictions\n\n    Raises:\n        ValueError: If the model has not been fitted yet\n    \"\"\"\n    if not self.model:\n        raise ValueError(\"Model not fitted yet. `fit()` has to be called first.\")\n    return self.model.transform(feature_matrix.df)\n</code></pre>"},{"location":"python_api/method/l2g/model/#otg.method.l2g.model.LocusToGeneModel.save","title":"<code>save(path: str) -&gt; None</code>","text":"<p>Saves fitted pipeline model to disk.</p> <p>Parameters:</p> Name Type Description Default <code>path</code> <code>str</code> <p>Path to save the model to</p> required <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet</p> Source code in <code>src/otg/method/l2g/model.py</code> <pre><code>def save(self: LocusToGeneModel, path: str) -&gt; None:\n    \"\"\"Saves fitted pipeline model to disk.\n\n    Args:\n        path (str): Path to save the model to\n\n    Raises:\n        ValueError: If the model has not been fitted yet\n    \"\"\"\n    if self.model is None:\n        raise ValueError(\"Model has not been fitted yet.\")\n    self.model.write().overwrite().save(path)\n</code></pre>"},{"location":"python_api/method/l2g/trainer/","title":"L2G Trainer","text":""},{"location":"python_api/method/l2g/trainer/#otg.method.l2g.trainer.LocusToGeneTrainer","title":"<code>otg.method.l2g.trainer.LocusToGeneTrainer</code>  <code>dataclass</code>","text":"<p>Modelling of what is the most likely causal gene associated with a given locus.</p> Source code in <code>src/otg/method/l2g/trainer.py</code> <pre><code>@dataclass\nclass LocusToGeneTrainer:\n    \"\"\"Modelling of what is the most likely causal gene associated with a given locus.\"\"\"\n\n    _model: LocusToGeneModel\n    train_set: L2GFeatureMatrix\n\n    @classmethod\n    def train(\n        cls: type[LocusToGeneTrainer],\n        data: L2GFeatureMatrix,\n        l2g_model: LocusToGeneModel,\n        features_list: list[str],\n        evaluate: bool,\n        wandb_run_name: str | None = None,\n        model_path: str | None = None,\n        **hyperparams: dict[str, Any],\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Train the Locus to Gene model.\n\n        Args:\n            data (L2GFeatureMatrix): Feature matrix containing the data\n            l2g_model (LocusToGeneModel): Model to fit to the data on\n            features_list (list[str]): List of features to use for the model\n            evaluate (bool): Whether to evaluate the model on a test set\n            wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n            model_path (str | None): Path to save the model to\n            **hyperparams (dict[str, Any]): Hyperparameters to use for the model\n\n        Returns:\n            LocusToGeneModel: Trained model\n        \"\"\"\n        train, test = data.select_features(features_list).train_test_split(fraction=0.8)\n\n        model = l2g_model.add_pipeline_stage(l2g_model.estimator).fit(train)\n\n        if evaluate:\n            l2g_model.evaluate(\n                results=model.predict(test),\n                hyperparameters=hyperparams,\n                wandb_run_name=wandb_run_name,\n                training_data=train,\n            )\n        if model_path:\n            l2g_model.save(model_path)\n        return l2g_model\n\n    @classmethod\n    def cross_validate(\n        cls: type[LocusToGeneTrainer],\n        l2g_model: LocusToGeneModel,\n        data: L2GFeatureMatrix,\n        num_folds: int,\n        param_grid: Optional[list] = None,  # type: ignore\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Perform k-fold cross validation on the model.\n\n        By providing a model with a parameter grid, this method will perform k-fold cross validation on the model for each\n        combination of parameters and return the best model.\n\n        Args:\n            l2g_model (LocusToGeneModel): Model to fit to the data on\n            data (L2GFeatureMatrix): Data to perform cross validation on\n            num_folds (int): Number of folds to use for cross validation\n            param_grid (Optional[list]): List of parameter maps to use for cross validation\n\n        Returns:\n            LocusToGeneModel: Trained model fitted with the best hyperparameters\n\n        Raises:\n            ValueError: Parameter grid is empty. Cannot perform cross-validation.\n            ValueError: Unable to retrieve the best model.\n        \"\"\"\n        evaluator = MulticlassClassificationEvaluator()\n        params_grid = param_grid or l2g_model.get_param_grid()\n        if not param_grid:\n            raise ValueError(\n                \"Parameter grid is empty. Cannot perform cross-validation.\"\n            )\n        cv = CrossValidator(\n            numFolds=num_folds,\n            estimator=l2g_model.estimator,\n            estimatorParamMaps=params_grid,\n            evaluator=evaluator,\n            parallelism=2,\n            collectSubModels=False,\n            seed=42,\n        )\n\n        l2g_model.add_pipeline_stage(cv)  # type: ignore[assignment, unused-ignore]\n\n        # Integrate the best model from the last stage of the pipeline\n        if (full_pipeline_model := l2g_model.fit(data).model) is None or not hasattr(\n            full_pipeline_model, \"stages\"\n        ):\n            raise ValueError(\"Unable to retrieve the best model.\")\n        l2g_model.model = full_pipeline_model.stages[-1].bestModel  # type: ignore[assignment, unused-ignore]\n        return l2g_model\n</code></pre>"},{"location":"python_api/method/l2g/trainer/#otg.method.l2g.trainer.LocusToGeneTrainer.cross_validate","title":"<code>cross_validate(l2g_model: LocusToGeneModel, data: L2GFeatureMatrix, num_folds: int, param_grid: Optional[list] = None) -&gt; LocusToGeneModel</code>  <code>classmethod</code>","text":"<p>Perform k-fold cross validation on the model.</p> <p>By providing a model with a parameter grid, this method will perform k-fold cross validation on the model for each combination of parameters and return the best model.</p> <p>Parameters:</p> Name Type Description Default <code>l2g_model</code> <code>LocusToGeneModel</code> <p>Model to fit to the data on</p> required <code>data</code> <code>L2GFeatureMatrix</code> <p>Data to perform cross validation on</p> required <code>num_folds</code> <code>int</code> <p>Number of folds to use for cross validation</p> required <code>param_grid</code> <code>Optional[list]</code> <p>List of parameter maps to use for cross validation</p> <code>None</code> <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>Trained model fitted with the best hyperparameters</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>Parameter grid is empty. Cannot perform cross-validation.</p> <code>ValueError</code> <p>Unable to retrieve the best model.</p> Source code in <code>src/otg/method/l2g/trainer.py</code> <pre><code>@classmethod\ndef cross_validate(\n    cls: type[LocusToGeneTrainer],\n    l2g_model: LocusToGeneModel,\n    data: L2GFeatureMatrix,\n    num_folds: int,\n    param_grid: Optional[list] = None,  # type: ignore\n) -&gt; LocusToGeneModel:\n    \"\"\"Perform k-fold cross validation on the model.\n\n    By providing a model with a parameter grid, this method will perform k-fold cross validation on the model for each\n    combination of parameters and return the best model.\n\n    Args:\n        l2g_model (LocusToGeneModel): Model to fit to the data on\n        data (L2GFeatureMatrix): Data to perform cross validation on\n        num_folds (int): Number of folds to use for cross validation\n        param_grid (Optional[list]): List of parameter maps to use for cross validation\n\n    Returns:\n        LocusToGeneModel: Trained model fitted with the best hyperparameters\n\n    Raises:\n        ValueError: Parameter grid is empty. Cannot perform cross-validation.\n        ValueError: Unable to retrieve the best model.\n    \"\"\"\n    evaluator = MulticlassClassificationEvaluator()\n    params_grid = param_grid or l2g_model.get_param_grid()\n    if not param_grid:\n        raise ValueError(\n            \"Parameter grid is empty. Cannot perform cross-validation.\"\n        )\n    cv = CrossValidator(\n        numFolds=num_folds,\n        estimator=l2g_model.estimator,\n        estimatorParamMaps=params_grid,\n        evaluator=evaluator,\n        parallelism=2,\n        collectSubModels=False,\n        seed=42,\n    )\n\n    l2g_model.add_pipeline_stage(cv)  # type: ignore[assignment, unused-ignore]\n\n    # Integrate the best model from the last stage of the pipeline\n    if (full_pipeline_model := l2g_model.fit(data).model) is None or not hasattr(\n        full_pipeline_model, \"stages\"\n    ):\n        raise ValueError(\"Unable to retrieve the best model.\")\n    l2g_model.model = full_pipeline_model.stages[-1].bestModel  # type: ignore[assignment, unused-ignore]\n    return l2g_model\n</code></pre>"},{"location":"python_api/method/l2g/trainer/#otg.method.l2g.trainer.LocusToGeneTrainer.train","title":"<code>train(data: L2GFeatureMatrix, l2g_model: LocusToGeneModel, features_list: list[str], evaluate: bool, wandb_run_name: str | None = None, model_path: str | None = None, **hyperparams: dict[str, Any]) -&gt; LocusToGeneModel</code>  <code>classmethod</code>","text":"<p>Train the Locus to Gene model.</p> <p>Parameters:</p> Name Type Description Default <code>data</code> <code>L2GFeatureMatrix</code> <p>Feature matrix containing the data</p> required <code>l2g_model</code> <code>LocusToGeneModel</code> <p>Model to fit to the data on</p> required <code>features_list</code> <code>list[str]</code> <p>List of features to use for the model</p> required <code>evaluate</code> <code>bool</code> <p>Whether to evaluate the model on a test set</p> required <code>wandb_run_name</code> <code>str | None</code> <p>Descriptive name for the run to be tracked with W&amp;B</p> <code>None</code> <code>model_path</code> <code>str | None</code> <p>Path to save the model to</p> <code>None</code> <code>**hyperparams</code> <code>dict[str, Any]</code> <p>Hyperparameters to use for the model</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>Trained model</p> Source code in <code>src/otg/method/l2g/trainer.py</code> <pre><code>@classmethod\ndef train(\n    cls: type[LocusToGeneTrainer],\n    data: L2GFeatureMatrix,\n    l2g_model: LocusToGeneModel,\n    features_list: list[str],\n    evaluate: bool,\n    wandb_run_name: str | None = None,\n    model_path: str | None = None,\n    **hyperparams: dict[str, Any],\n) -&gt; LocusToGeneModel:\n    \"\"\"Train the Locus to Gene model.\n\n    Args:\n        data (L2GFeatureMatrix): Feature matrix containing the data\n        l2g_model (LocusToGeneModel): Model to fit to the data on\n        features_list (list[str]): List of features to use for the model\n        evaluate (bool): Whether to evaluate the model on a test set\n        wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n        model_path (str | None): Path to save the model to\n        **hyperparams (dict[str, Any]): Hyperparameters to use for the model\n\n    Returns:\n        LocusToGeneModel: Trained model\n    \"\"\"\n    train, test = data.select_features(features_list).train_test_split(fraction=0.8)\n\n    model = l2g_model.add_pipeline_stage(l2g_model.estimator).fit(train)\n\n    if evaluate:\n        l2g_model.evaluate(\n            results=model.predict(test),\n            hyperparameters=hyperparams,\n            wandb_run_name=wandb_run_name,\n            training_data=train,\n        )\n    if model_path:\n        l2g_model.save(model_path)\n    return l2g_model\n</code></pre>"},{"location":"python_api/step/_step/","title":"Step","text":"<p>TBC</p>"},{"location":"python_api/step/clump/","title":"Clump","text":""},{"location":"python_api/step/clump/#otg.clump.ClumpStep","title":"<code>otg.clump.ClumpStep</code>  <code>dataclass</code>","text":"<p>Perform clumping of an association dataset to identify independent signals.</p> <p>Two types of clumping are supported and are applied based on the input dataset: - Clumping of summary statistics based on a window-based approach. - Clumping of study locus based on LD.</p> <p>Both approaches yield a StudyLocus dataset.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>input_path</code> <code>str</code> <p>Input path for the study locus or summary statistics files.</p> <code>study_index_path</code> <code>str</code> <p>Path to study index.</p> <code>ld_index_path</code> <code>str</code> <p>Path to LD index.</p> <code>locus_collect_distance</code> <code>int | None</code> <p>The distance to collect locus around semi-indices.</p> <code>clumped_study_locus_path</code> <code>str</code> <p>Output path for the clumped study locus dataset.</p> Source code in <code>src/otg/clump.py</code> <pre><code>@dataclass\nclass ClumpStep:\n    \"\"\"Perform clumping of an association dataset to identify independent signals.\n\n    Two types of clumping are supported and are applied based on the input dataset:\n    - Clumping of summary statistics based on a window-based approach.\n    - Clumping of study locus based on LD.\n\n    Both approaches yield a StudyLocus dataset.\n\n    Attributes:\n        session (Session): Session object.\n        input_path (str): Input path for the study locus or summary statistics files.\n        study_index_path (str): Path to study index.\n        ld_index_path (str): Path to LD index.\n        locus_collect_distance (int | None): The distance to collect locus around semi-indices.\n        clumped_study_locus_path (str): Output path for the clumped study locus dataset.\n    \"\"\"\n\n    session: Session = MISSING\n    input_path: str = MISSING\n    clumped_study_locus_path: str = MISSING\n    study_index_path: str | None = field(default=None)\n    ld_index_path: str | None = field(default=None)\n\n    locus_collect_distance: int | None = field(default=None)\n\n    def __post_init__(self: ClumpStep) -&gt; None:\n        \"\"\"Run the clumping step.\n\n        Raises:\n            ValueError: If study index and LD index paths are not provided for study locus.\n        \"\"\"\n        input_cols = self.session.spark.read.parquet(\n            self.input_path, recursiveFileLookup=True\n        ).columns\n        if \"studyLocusId\" in input_cols:\n            if self.study_index_path is None or self.ld_index_path is None:\n                raise ValueError(\n                    \"Study index and LD index paths are required for clumping study locus.\"\n                )\n            study_locus = StudyLocus.from_parquet(self.session, self.input_path)\n            ld_index = LDIndex.from_parquet(self.session, self.ld_index_path)\n            study_index = StudyIndex.from_parquet(self.session, self.study_index_path)\n\n            clumped_study_locus = study_locus.annotate_ld(\n                study_index=study_index, ld_index=ld_index\n            ).clump()\n        else:\n            sumstats = SummaryStatistics.from_parquet(\n                self.session, self.input_path, recursiveFileLookup=True\n            ).coalesce(4000)\n            clumped_study_locus = sumstats.window_based_clumping(\n                locus_collect_distance=self.locus_collect_distance\n            )\n\n        clumped_study_locus.df.write.mode(self.session.write_mode).parquet(\n            self.clumped_study_locus_path\n        )\n</code></pre>"},{"location":"python_api/step/colocalisation/","title":"Colocalisation","text":""},{"location":"python_api/step/colocalisation/#otg.colocalisation.ColocalisationStep","title":"<code>otg.colocalisation.ColocalisationStep</code>  <code>dataclass</code>","text":"<p>Colocalisation step.</p> <p>This workflow runs colocalization analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>study_locus_path</code> <code>DictConfig</code> <p>Input Study-locus path.</p> <code>coloc_path</code> <code>DictConfig</code> <p>Output Colocalisation path.</p> <code>priorc1</code> <code>float</code> <p>Prior on variant being causal for trait 1.</p> <code>priorc2</code> <code>float</code> <p>Prior on variant being causal for trait 2.</p> <code>priorc12</code> <code>float</code> <p>Prior on variant being causal for traits 1 and 2.</p> Source code in <code>src/otg/colocalisation.py</code> <pre><code>@dataclass\nclass ColocalisationStep:\n    \"\"\"Colocalisation step.\n\n    This workflow runs colocalization analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).\n\n    Attributes:\n        session (Session): Session object.\n        study_locus_path (DictConfig): Input Study-locus path.\n        coloc_path (DictConfig): Output Colocalisation path.\n        priorc1 (float): Prior on variant being causal for trait 1.\n        priorc2 (float): Prior on variant being causal for trait 2.\n        priorc12 (float): Prior on variant being causal for traits 1 and 2.\n    \"\"\"\n\n    session: Session = MISSING\n    study_locus_path: str = MISSING\n    study_index_path: str = MISSING\n    coloc_path: str = MISSING\n    priorc1: float = 1e-4\n    priorc2: float = 1e-4\n    priorc12: float = 1e-5\n\n    def __post_init__(self: ColocalisationStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Study-locus information\n        sl = StudyLocus.from_parquet(self.session, self.study_locus_path)\n        si = StudyIndex.from_parquet(self.session, self.study_index_path)\n\n        # Study-locus overlaps for 95% credible sets\n        sl_overlaps = sl.filter_credible_set(CredibleInterval.IS95).find_overlaps(si)\n\n        coloc_results = Coloc.colocalise(\n            sl_overlaps, self.priorc1, self.priorc2, self.priorc12\n        )\n        ecaviar_results = ECaviar.colocalise(sl_overlaps)\n\n        coloc_results.df.unionByName(ecaviar_results.df, allowMissingColumns=True)\n\n        coloc_results.df.write.mode(self.session.write_mode).parquet(self.coloc_path)\n</code></pre>"},{"location":"python_api/step/eqtl_catalogue/","title":"eQTL Catalogue","text":""},{"location":"python_api/step/eqtl_catalogue/#otg.eqtl_catalogue.EqtlCatalogueStep","title":"<code>otg.eqtl_catalogue.EqtlCatalogueStep</code>  <code>dataclass</code>","text":"<p>eQTL Catalogue ingestion step.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>eqtl_catalogue_paths_imported</code> <code>str</code> <p>eQTL Catalogue input files for the harmonised and imported data.</p> <code>eqtl_catalogue_study_index_out</code> <code>str</code> <p>Output path for the eQTL Catalogue study index dataset.</p> <code>eqtl_catalogue_summary_stats_out</code> <code>str</code> <p>Output path for the eQTL Catalogue summary stats.</p> Source code in <code>src/otg/eqtl_catalogue.py</code> <pre><code>@dataclass\nclass EqtlCatalogueStep:\n    \"\"\"eQTL Catalogue ingestion step.\n\n    Attributes:\n        session (Session): Session object.\n        eqtl_catalogue_paths_imported (str): eQTL Catalogue input files for the harmonised and imported data.\n        eqtl_catalogue_study_index_out (str): Output path for the eQTL Catalogue study index dataset.\n        eqtl_catalogue_summary_stats_out (str): Output path for the eQTL Catalogue summary stats.\n    \"\"\"\n\n    session: Session = MISSING\n\n    eqtl_catalogue_paths_imported: str = MISSING\n    eqtl_catalogue_study_index_out: str = MISSING\n    eqtl_catalogue_summary_stats_out: str = MISSING\n\n    def __post_init__(self: EqtlCatalogueStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Fetch study index.\n        df = self.session.spark.read.option(\"delimiter\", \"\\t\").csv(\n            self.eqtl_catalogue_paths_imported, header=True\n        )\n        # Process partial study index.  At this point, it is not complete because we don't have the gene IDs, which we\n        # will only get once the summary stats are ingested.\n        study_index_df = EqtlCatalogueStudyIndex.from_source(df).df\n\n        # Fetch summary stats.\n        input_filenames = [row.summarystatsLocation for row in study_index_df.collect()]\n        summary_stats_df = (\n            self.session.spark.read.option(\"delimiter\", \"\\t\")\n            .csv(input_filenames, header=True)\n            .repartition(1280)\n        )\n        # Process summary stats.\n        summary_stats_df = EqtlCatalogueSummaryStats.from_source(summary_stats_df).df\n\n        # Add geneId column to the study index.\n        study_index_df = EqtlCatalogueStudyIndex.add_gene_id_column(\n            study_index_df,\n            summary_stats_df,\n        ).df\n\n        # Write study index.\n        study_index_df.write.mode(self.session.write_mode).parquet(\n            self.eqtl_catalogue_study_index_out\n        )\n        # Write summary stats.\n        (\n            summary_stats_df.sortWithinPartitions(\"position\")\n            .write.partitionBy(\"chromosome\")\n            .mode(self.session.write_mode)\n            .parquet(self.eqtl_catalogue_summary_stats_out)\n        )\n</code></pre>"},{"location":"python_api/step/finngen/","title":"FinnGen","text":""},{"location":"python_api/step/finngen/#otg.finngen.FinnGenStep","title":"<code>otg.finngen.FinnGenStep</code>  <code>dataclass</code>","text":"<p>FinnGen ingestion step.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>finngen_study_index_out</code> <code>str</code> <p>Output path for the FinnGen study index dataset.</p> <code>finngen_summary_stats_out</code> <code>str</code> <p>Output path for the FinnGen summary statistics.</p> Source code in <code>src/otg/finngen.py</code> <pre><code>@dataclass\nclass FinnGenStep:\n    \"\"\"FinnGen ingestion step.\n\n    Attributes:\n        session (Session): Session object.\n        finngen_study_index_out (str): Output path for the FinnGen study index dataset.\n        finngen_summary_stats_out (str): Output path for the FinnGen summary statistics.\n    \"\"\"\n\n    session: Session = MISSING\n    finngen_study_index_out: str = MISSING\n    finngen_summary_stats_out: str = MISSING\n\n    def __post_init__(self: FinnGenStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Fetch study index.\n        # Process study index.\n        study_index = FinnGenStudyIndex.from_source(self.session.spark)\n        # Write study index.\n        study_index.df.write.mode(self.session.write_mode).parquet(\n            self.finngen_study_index_out\n        )\n\n        # Fetch summary stats locations\n        input_filenames = [row.summarystatsLocation for row in study_index.df.collect()]\n        # Process summary stats.\n        summary_stats = FinnGenSummaryStats.from_source(\n            self.session.spark, raw_files=input_filenames\n        )\n\n        # Write summary stats.\n        (\n            summary_stats.df.write.partitionBy(\"studyId\")\n            .mode(self.session.write_mode)\n            .parquet(self.finngen_summary_stats_out)\n        )\n</code></pre>"},{"location":"python_api/step/gene_index/","title":"Gene Index","text":""},{"location":"python_api/step/gene_index/#otg.gene_index.GeneIndexStep","title":"<code>otg.gene_index.GeneIndexStep</code>  <code>dataclass</code>","text":"<p>Gene index step.</p> <p>This step generates a gene index dataset from an Open Targets Platform target dataset.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>target_path</code> <code>str</code> <p>Open targets Platform target dataset path.</p> <code>gene_index_path</code> <code>str</code> <p>Output gene index path.</p> Source code in <code>src/otg/gene_index.py</code> <pre><code>@dataclass\nclass GeneIndexStep:\n    \"\"\"Gene index step.\n\n    This step generates a gene index dataset from an Open Targets Platform target dataset.\n\n    Attributes:\n        session (Session): Session object.\n        target_path (str): Open targets Platform target dataset path.\n        gene_index_path (str): Output gene index path.\n    \"\"\"\n\n    session: Session = MISSING\n    target_path: str = MISSING\n    gene_index_path: str = MISSING\n\n    def __post_init__(self: GeneIndexStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Extract\n        platform_target = self.session.spark.read.parquet(self.target_path)\n        # Transform\n        gene_index = OpenTargetsTarget.as_gene_index(platform_target)\n        # Load\n        gene_index.df.write.mode(self.session.write_mode).parquet(self.gene_index_path)\n</code></pre>"},{"location":"python_api/step/gwas_catalog_ingestion/","title":"GWAS Catalog","text":""},{"location":"python_api/step/gwas_catalog_ingestion/#otg.gwas_catalog_ingestion.GWASCatalogIngestionStep","title":"<code>otg.gwas_catalog_ingestion.GWASCatalogIngestionStep</code>  <code>dataclass</code>","text":"<p>GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.</p> <p>!!!note This step currently only processes the GWAS Catalog curated list of top hits.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>catalog_study_files</code> <code>list[str]</code> <p>List of raw GWAS catalog studies file.</p> <code>catalog_ancestry_files</code> <code>list[str]</code> <p>List of raw ancestry annotations files from GWAS Catalog.</p> <code>catalog_sumstats_lut</code> <code>str</code> <p>GWAS Catalog summary statistics lookup table.</p> <code>catalog_associations_file</code> <code>str</code> <p>Raw GWAS catalog associations file.</p> <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> <code>ld_populations</code> <code>list</code> <p>List of populations to include.</p> <code>catalog_studies_out</code> <code>str</code> <p>Output GWAS catalog studies path.</p> <code>catalog_associations_out</code> <code>str</code> <p>Output GWAS catalog associations path.</p> Source code in <code>src/otg/gwas_catalog_ingestion.py</code> <pre><code>@dataclass\nclass GWASCatalogIngestionStep:\n    \"\"\"GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.\n\n    !!!note This step currently only processes the GWAS Catalog curated list of top hits.\n\n    Attributes:\n        session (Session): Session object.\n        catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n        catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.\n        catalog_associations_file (str): Raw GWAS catalog associations file.\n        variant_annotation_path (str): Input variant annotation path.\n        ld_populations (list): List of populations to include.\n        catalog_studies_out (str): Output GWAS catalog studies path.\n        catalog_associations_out (str): Output GWAS catalog associations path.\n    \"\"\"\n\n    session: Session = MISSING\n    catalog_study_files: list[str] = MISSING\n    catalog_ancestry_files: list[str] = MISSING\n    catalog_sumstats_lut: str = MISSING\n    catalog_associations_file: str = MISSING\n    variant_annotation_path: str = MISSING\n    catalog_studies_out: str = MISSING\n    catalog_associations_out: str = MISSING\n\n    def __post_init__(self: GWASCatalogIngestionStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Extract\n        va = VariantAnnotation.from_parquet(self.session, self.variant_annotation_path)\n        catalog_studies = self.session.spark.read.csv(\n            self.catalog_study_files, sep=\"\\t\", header=True\n        )\n        ancestry_lut = self.session.spark.read.csv(\n            self.catalog_ancestry_files, sep=\"\\t\", header=True\n        )\n        sumstats_lut = self.session.spark.read.csv(\n            self.catalog_sumstats_lut, sep=\"\\t\", header=False\n        )\n        catalog_associations = self.session.spark.read.csv(\n            self.catalog_associations_file, sep=\"\\t\", header=True\n        ).persist()\n\n        # Transform\n        study_index, study_locus = GWASCatalogStudySplitter.split(\n            StudyIndexGWASCatalogParser.from_source(\n                catalog_studies, ancestry_lut, sumstats_lut\n            ),\n            GWASCatalogCuratedAssociationsParser.from_source(catalog_associations, va),\n        )\n\n        # Load\n        study_index.df.write.mode(self.session.write_mode).parquet(\n            self.catalog_studies_out\n        )\n        study_locus.df.write.mode(self.session.write_mode).parquet(\n            self.catalog_associations_out\n        )\n</code></pre>"},{"location":"python_api/step/gwas_catalog_sumstat_preprocess/","title":"GWAS Catalog sumstat preprocess","text":""},{"location":"python_api/step/gwas_catalog_sumstat_preprocess/#otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep","title":"<code>otg.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep</code>  <code>dataclass</code>","text":"<p>Step to preprocess GWAS Catalog harmonised summary stats.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>raw_sumstats_path</code> <code>str</code> <p>Input raw GWAS Catalog summary statistics path.</p> <code>out_sumstats_path</code> <code>str</code> <p>Output GWAS Catalog summary statistics path.</p> Source code in <code>src/otg/gwas_catalog_sumstat_preprocess.py</code> <pre><code>@dataclass\nclass GWASCatalogSumstatsPreprocessStep:\n    \"\"\"Step to preprocess GWAS Catalog harmonised summary stats.\n\n    Attributes:\n        session (Session): Session object.\n        raw_sumstats_path (str): Input raw GWAS Catalog summary statistics path.\n        out_sumstats_path (str): Output GWAS Catalog summary statistics path.\n    \"\"\"\n\n    session: Session = MISSING\n    raw_sumstats_path: str = MISSING\n    out_sumstats_path: str = MISSING\n\n    def __post_init__(self: GWASCatalogSumstatsPreprocessStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Extract\n        self.session.logger.info(self.raw_sumstats_path)\n        self.session.logger.info(self.out_sumstats_path)\n\n        # Processing dataset:\n        GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats(\n            self.session.spark, self.raw_sumstats_path\n        ).df.write.mode(self.session.write_mode).parquet(self.out_sumstats_path)\n        self.session.logger.info(\"Processing dataset successfully completed.\")\n</code></pre>"},{"location":"python_api/step/l2g/","title":"Locus-to-gene (L2G)","text":""},{"location":"python_api/step/l2g/#otg.l2g.LocusToGeneStep","title":"<code>otg.l2g.LocusToGeneStep</code>  <code>dataclass</code>","text":"<p>Locus to gene step.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>extended_spark_conf</code> <code>dict[str, str] | None</code> <p>Extended Spark configuration.</p> <code>run_mode</code> <code>str</code> <p>One of \"train\" or \"predict\".</p> <code>wandb_run_name</code> <code>str | None</code> <p>Name of the run to be tracked on W&amp;B.</p> <code>perform_cross_validation</code> <code>bool</code> <p>Whether to perform cross validation.</p> <code>model_path</code> <code>str | None</code> <p>Path to save the model.</p> <code>predictions_path</code> <code>str | None</code> <p>Path to save the predictions.</p> <code>credible_set_path</code> <code>str</code> <p>Path to credible set Parquet files.</p> <code>variant_gene_path</code> <code>str</code> <p>Path to variant to gene Parquet files.</p> <code>colocalisation_path</code> <code>str</code> <p>Path to colocalisation Parquet files.</p> <code>study_index_path</code> <code>str</code> <p>Path to study index Parquet files.</p> <code>study_locus_overlap_path</code> <code>str</code> <p>Path to study locus overlap Parquet files.</p> <code>gold_standard_curation_path</code> <code>str | None</code> <p>Path to gold standard curation JSON files.</p> <code>gene_interactions_path</code> <code>str | None</code> <p>Path to gene interactions Parquet files.</p> <code>features_list</code> <code>list[str]</code> <p>List of features to use.</p> <code>hyperparameters</code> <code>dict</code> <p>Hyperparameters for the model.</p> Source code in <code>src/otg/l2g.py</code> <pre><code>@dataclass\nclass LocusToGeneStep:\n    \"\"\"Locus to gene step.\n\n    Attributes:\n        session (Session): Session object.\n        extended_spark_conf (dict[str, str] | None): Extended Spark configuration.\n        run_mode (str): One of \"train\" or \"predict\".\n        wandb_run_name (str | None): Name of the run to be tracked on W&amp;B.\n        perform_cross_validation (bool): Whether to perform cross validation.\n        model_path (str | None): Path to save the model.\n        predictions_path (str | None): Path to save the predictions.\n        credible_set_path (str): Path to credible set Parquet files.\n        variant_gene_path (str): Path to variant to gene Parquet files.\n        colocalisation_path (str): Path to colocalisation Parquet files.\n        study_index_path (str): Path to study index Parquet files.\n        study_locus_overlap_path (str): Path to study locus overlap Parquet files.\n        gold_standard_curation_path (str | None): Path to gold standard curation JSON files.\n        gene_interactions_path (str | None): Path to gene interactions Parquet files.\n        features_list (list[str]): List of features to use.\n        hyperparameters (dict): Hyperparameters for the model.\n    \"\"\"\n\n    extended_spark_conf: dict[str, str] | None = None\n\n    session: Session = MISSING\n    run_mode: str = MISSING\n    wandb_run_name: str | None = None\n    perform_cross_validation: bool = False\n    model_path: str = MISSING\n    predictions_path: str = MISSING\n    credible_set_path: str = MISSING\n    variant_gene_path: str = MISSING\n    colocalisation_path: str = MISSING\n    study_index_path: str = MISSING\n    study_locus_overlap_path: str = MISSING\n    gold_standard_curation_path: str = MISSING\n    gene_interactions_path: str = MISSING\n    features_list: list[str] = field(\n        default_factory=lambda: [\n            # average distance of all tagging variants to gene TSS\n            \"distanceTssMean\",\n            # # minimum distance of all tagging variants to gene TSS\n            # \"distanceTssMinimum\",\n            # # max clpp for each (study, locus, gene) aggregating over all eQTLs\n            # \"eqtlColocClppLocalMaximum\",\n            # # max clpp for each (study, locus) aggregating over all eQTLs\n            # \"eqtlColocClppNeighborhoodMaximum\",\n            # # max log-likelihood ratio value for each (study, locus, gene) aggregating over all eQTLs\n            # \"eqtlColocLlrLocalMaximum\",\n            # # max log-likelihood ratio value for each (study, locus) aggregating over all eQTLs\n            # \"eqtlColocLlrNeighborhoodMaximum\",\n            # # max clpp for each (study, locus, gene) aggregating over all pQTLs\n            # \"pqtlColocClppLocalMaximum\",\n            # # max clpp for each (study, locus) aggregating over all pQTLs\n            # \"pqtlColocClppNeighborhoodMaximum\",\n            # # max log-likelihood ratio value for each (study, locus, gene) aggregating over all pQTLs\n            # \"pqtlColocLlrLocalMaximum\",\n            # # max log-likelihood ratio value for each (study, locus) aggregating over all pQTLs\n            # \"pqtlColocLlrNeighborhoodMaximum\",\n            # # max clpp for each (study, locus, gene) aggregating over all sQTLs\n            # \"sqtlColocClppLocalMaximum\",\n            # # max clpp for each (study, locus) aggregating over all sQTLs\n            # \"sqtlColocClppNeighborhoodMaximum\",\n            # # max log-likelihood ratio value for each (study, locus, gene) aggregating over all sQTLs\n            # \"sqtlColocLlrLocalMaximum\",\n            # # max log-likelihood ratio value for each (study, locus) aggregating over all sQTLs\n            # \"sqtlColocLlrNeighborhoodMaximum\",\n        ]\n    )\n    hyperparameters: dict[str, Any] = field(\n        default_factory=lambda: {\n            \"max_depth\": 5,\n            \"loss_function\": \"binary:logistic\",\n        }\n    )\n\n    def __post_init__(self: LocusToGeneStep) -&gt; None:\n        \"\"\"Run step.\n\n        Raises:\n            ValueError: if run_mode is not one of \"train\" or \"predict\".\n        \"\"\"\n        print(\"Sci-kit learn version: \", sklearn.__version__)  # noqa: T201\n        if self.run_mode not in [\"train\", \"predict\"]:\n            raise ValueError(\n                f\"run_mode must be one of 'train' or 'predict', got {self.run_mode}\"\n            )\n        # Load common inputs\n        credible_set = StudyLocus.from_parquet(\n            self.session, self.credible_set_path, recursiveFileLookup=True\n        )\n        studies = StudyIndex.from_parquet(\n            self.session, self.study_index_path, recursiveFileLookup=True\n        )\n        v2g = V2G.from_parquet(self.session, self.variant_gene_path)\n        # coloc = Colocalisation.from_parquet(self.session, self.colocalisation_path) # TODO: run step\n\n        if self.run_mode == \"train\":\n            # Process gold standard and L2G features\n            study_locus_overlap = StudyLocusOverlap.from_parquet(\n                self.session, self.study_locus_overlap_path\n            )\n            gs_curation = self.session.spark.read.json(self.gold_standard_curation_path)\n            interactions = self.session.spark.read.parquet(self.gene_interactions_path)\n\n            gold_standards = L2GGoldStandard.from_otg_curation(\n                gold_standard_curation=gs_curation,\n                v2g=v2g,\n                study_locus_overlap=study_locus_overlap,\n                interactions=interactions,\n            )\n\n            fm = L2GFeatureMatrix.generate_features(\n                features_list=self.features_list,\n                study_locus=credible_set,\n                study_index=studies,\n                variant_gene=v2g,\n                # colocalisation=coloc,\n            )\n\n            # Join and fill null values with 0\n            data = L2GFeatureMatrix(\n                _df=fm.df.join(\n                    f.broadcast(\n                        gold_standards.df.drop(\"variantId\", \"studyId\", \"sources\")\n                    ),\n                    on=[\"studyLocusId\", \"geneId\"],\n                    how=\"inner\",\n                ),\n                _schema=L2GFeatureMatrix.get_schema(),\n            ).fill_na()\n\n            # Instantiate classifier\n            estimator = SparkXGBClassifier(\n                eval_metric=\"logloss\",\n                features_col=\"features\",\n                label_col=\"label\",\n                max_depth=5,\n            )\n            l2g_model = LocusToGeneModel(\n                features_list=list(self.features_list), estimator=estimator\n            )\n            if self.perform_cross_validation:\n                # Perform cross validation to extract what are the best hyperparameters\n                cv_folds = self.hyperparameters.get(\"cross_validation_folds\", 5)\n                LocusToGeneTrainer.cross_validate(\n                    l2g_model=l2g_model,\n                    data=data,\n                    num_folds=cv_folds,\n                )\n            else:\n                # Train model\n                LocusToGeneTrainer.train(\n                    data=data,\n                    l2g_model=l2g_model,\n                    features_list=list(self.features_list),\n                    model_path=self.model_path,\n                    evaluate=True,\n                    wandb_run_name=self.wandb_run_name,\n                    **self.hyperparameters,\n                )\n                self.session.logger.info(self.model_path)\n\n        if self.run_mode == \"predict\":\n            if not self.model_path or not self.predictions_path:\n                raise ValueError(\n                    \"model_path and predictions_path must be set for predict mode.\"\n                )\n            predictions = L2GPrediction.from_credible_set(\n                self.model_path,\n                self.features_list,\n                credible_set,\n                studies,\n                v2g,\n                # coloc\n            )\n            predictions.df.write.mode(self.session.write_mode).parquet(\n                self.predictions_path\n            )\n            self.session.logger.info(self.predictions_path)\n</code></pre>"},{"location":"python_api/step/ld_index/","title":"LD Index","text":""},{"location":"python_api/step/ld_index/#otg.ld_index.LDIndexStep","title":"<code>otg.ld_index.LDIndexStep</code>  <code>dataclass</code>","text":"<p>LD index step.</p> <p>This step is resource intensive</p> <p>Suggested params: high memory machine, 5TB of boot disk, no SSDs.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>min_r2</code> <code>float</code> <p>Minimum r2 to consider when considering variants within a window.</p> <code>ld_index_out</code> <code>str</code> <p>Output LD index path.</p> Source code in <code>src/otg/ld_index.py</code> <pre><code>@dataclass\nclass LDIndexStep:\n    \"\"\"LD index step.\n\n    !!! warning \"This step is resource intensive\"\n        Suggested params: high memory machine, 5TB of boot disk, no SSDs.\n\n    Attributes:\n        session (Session): Session object.\n        min_r2 (float): Minimum r2 to consider when considering variants within a window.\n        ld_index_out (str): Output LD index path.\n    \"\"\"\n\n    session: Session = MISSING\n\n    min_r2: float = 0.5\n    ld_index_out: str = MISSING\n\n    def __post_init__(self: LDIndexStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        hl.init(sc=self.session.spark.sparkContext, log=\"/dev/null\")\n        (\n            GnomADLDMatrix()\n            .as_ld_index(self.min_r2)\n            .df.write.partitionBy(\"chromosome\")\n            .mode(self.session.write_mode)\n            .parquet(self.ld_index_out)\n        )\n        self.session.logger.info(self.ld_index_out)\n</code></pre>"},{"location":"python_api/step/pics/","title":"PICS","text":""},{"location":"python_api/step/pics/#otg.pics.PICSStep","title":"<code>otg.pics.PICSStep</code>  <code>dataclass</code>","text":"<p>PICS finemapping of LD-annotated StudyLocus.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>study_locus_ld_annotated_in</code> <code>str</code> <p>Path to Study Locus with the LD information annotated</p> <code>picsed_study_locus_out</code> <code>str</code> <p>Path to Study Locus after running PICS</p> Source code in <code>src/otg/pics.py</code> <pre><code>@dataclass\nclass PICSStep:\n    \"\"\"PICS finemapping of LD-annotated StudyLocus.\n\n    Attributes:\n        session (Session): Session object.\n\n        study_locus_ld_annotated_in (str): Path to Study Locus with the LD information annotated\n        picsed_study_locus_out (str): Path to Study Locus after running PICS\n    \"\"\"\n\n    session: Session = MISSING\n    study_locus_ld_annotated_in: str = MISSING\n    picsed_study_locus_out: str = MISSING\n\n    def __post_init__(self: PICSStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Extract\n        study_locus_ld_annotated = StudyLocus.from_parquet(\n            self.session, self.study_locus_ld_annotated_in\n        )\n        # PICS\n        picsed_sl = PICS.finemap(study_locus_ld_annotated).annotate_credible_sets()\n        # Write\n        picsed_sl.df.write.mode(self.session.write_mode).parquet(\n            self.picsed_study_locus_out\n        )\n</code></pre>"},{"location":"python_api/step/ukbiobank/","title":"UK Biobank","text":""},{"location":"python_api/step/ukbiobank/#otg.ukbiobank.UKBiobankStep","title":"<code>otg.ukbiobank.UKBiobankStep</code>  <code>dataclass</code>","text":"<p>UKBiobank study table ingestion step.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>ukbiobank_manifest</code> <code>str</code> <p>UKBiobank manifest of studies.</p> <code>ukbiobank_study_index_out</code> <code>str</code> <p>Output path for the UKBiobank study index dataset.</p> Source code in <code>src/otg/ukbiobank.py</code> <pre><code>@dataclass\nclass UKBiobankStep:\n    \"\"\"UKBiobank study table ingestion step.\n\n    Attributes:\n        session (Session): Session object.\n        ukbiobank_manifest (str): UKBiobank manifest of studies.\n        ukbiobank_study_index_out (str): Output path for the UKBiobank study index dataset.\n    \"\"\"\n\n    session: Session = MISSING\n    ukbiobank_manifest: str = MISSING\n    ukbiobank_study_index_out: str = MISSING\n\n    def __post_init__(self: UKBiobankStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Read in the UKBiobank manifest tsv file.\n        df = self.session.spark.read.csv(\n            self.ukbiobank_manifest, sep=\"\\t\", header=True, inferSchema=True\n        )\n\n        # Parse the study index data.\n        ukbiobank_study_index = UKBiobankStudyIndex.from_source(df)\n\n        # Write the output.\n        ukbiobank_study_index.df.write.mode(self.session.write_mode).parquet(\n            self.ukbiobank_study_index_out\n        )\n</code></pre>"},{"location":"python_api/step/variant_annotation_step/","title":"Variant Annotation","text":""},{"location":"python_api/step/variant_annotation_step/#otg.variant_annotation.VariantAnnotationStep","title":"<code>otg.variant_annotation.VariantAnnotationStep</code>  <code>dataclass</code>","text":"<p>Variant annotation step.</p> <p>Variant annotation step produces a dataset of the type <code>VariantAnnotation</code> derived from gnomADs <code>gnomad.genomes.vX.X.X.sites.ht</code> Hail's table. This dataset is used to validate variants and as a source of annotation.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>variant_annotation_path</code> <code>str</code> <p>Output variant annotation path.</p> Source code in <code>src/otg/variant_annotation.py</code> <pre><code>@dataclass\nclass VariantAnnotationStep:\n    \"\"\"Variant annotation step.\n\n    Variant annotation step produces a dataset of the type `VariantAnnotation` derived from gnomADs `gnomad.genomes.vX.X.X.sites.ht` Hail's table. This dataset is used to validate variants and as a source of annotation.\n\n    Attributes:\n        session (Session): Session object.\n        variant_annotation_path (str): Output variant annotation path.\n    \"\"\"\n\n    session: Session = MISSING\n    variant_annotation_path: str = MISSING\n\n    def __post_init__(self: VariantAnnotationStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Initialise hail session.\n        hl.init(sc=self.session.spark.sparkContext, log=\"/dev/null\")\n        # Run variant annotation.\n        variant_annotation = GnomADVariants().as_variant_annotation()\n        # Write data partitioned by chromosome and position.\n        (\n            variant_annotation.df.write.mode(self.session.write_mode).parquet(\n                self.variant_annotation_path\n            )\n        )\n</code></pre>"},{"location":"python_api/step/variant_index_step/","title":"Variant Index","text":""},{"location":"python_api/step/variant_index_step/#otg.variant_index.VariantIndexStep","title":"<code>otg.variant_index.VariantIndexStep</code>  <code>dataclass</code>","text":"<p>Run variant index step to only variants in study-locus sets.</p> <p>Using a <code>VariantAnnotation</code> dataset as a reference, this step creates and writes a dataset of the type <code>VariantIndex</code> that includes only variants that have disease-association data with a reduced set of annotations.</p> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> <code>study_locus_path</code> <code>str</code> <p>Input study-locus path.</p> <code>variant_index_path</code> <code>str</code> <p>Output variant index path.</p> Source code in <code>src/otg/variant_index.py</code> <pre><code>@dataclass\nclass VariantIndexStep:\n    \"\"\"Run variant index step to only variants in study-locus sets.\n\n    Using a `VariantAnnotation` dataset as a reference, this step creates and writes a dataset of the type `VariantIndex` that includes only variants that have disease-association data with a reduced set of annotations.\n\n    Attributes:\n        session (Session): Session object.\n        variant_annotation_path (str): Input variant annotation path.\n        study_locus_path (str): Input study-locus path.\n        variant_index_path (str): Output variant index path.\n    \"\"\"\n\n    session: Session = MISSING\n    variant_annotation_path: str = MISSING\n    credible_set_path: str = MISSING\n    variant_index_path: str = MISSING\n\n    def __post_init__(self: VariantIndexStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Extract\n        va = VariantAnnotation.from_parquet(self.session, self.variant_annotation_path)\n        credible_set = StudyLocus.from_parquet(\n            self.session, self.credible_set_path, recursiveFileLookup=True\n        )\n\n        # Transform\n        vi = VariantIndex.from_variant_annotation(va, credible_set)\n\n        (\n            vi.df.write.partitionBy(\"chromosome\")\n            .mode(self.session.write_mode)\n            .parquet(self.variant_index_path)\n        )\n</code></pre>"},{"location":"python_api/step/variant_to_gene_step/","title":"Variant-to-gene","text":""},{"location":"python_api/step/variant_to_gene_step/#otg.v2g.V2GStep","title":"<code>otg.v2g.V2GStep</code>  <code>dataclass</code>","text":"<p>Variant-to-gene (V2G) step.</p> <p>This step aims to generate a dataset that contains multiple pieces of evidence supporting the functional association of specific variants with genes. Some of the evidence types include:</p> <ol> <li>Chromatin interaction experiments, e.g. Promoter Capture Hi-C (PCHi-C).</li> <li>In silico functional predictions, e.g. Variant Effect Predictor (VEP) from Ensembl.</li> <li>Distance between the variant and each gene's canonical transcription start site (TSS).</li> </ol> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>variant_index_path</code> <code>str</code> <p>Input variant index path.</p> <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> <code>gene_index_path</code> <code>str</code> <p>Input gene index path.</p> <code>vep_consequences_path</code> <code>str</code> <p>Input VEP consequences path.</p> <code>liftover_chain_file_path</code> <code>str</code> <p>Path to GRCh37 to GRCh38 chain file.</p> <code>liftover_max_length_difference</code> <code>int</code> <p>Maximum length difference for liftover.</p> <code>max_distance</code> <code>int</code> <p>Maximum distance to consider.</p> <code>approved_biotypes</code> <code>list[str]</code> <p>List of approved biotypes.</p> <code>intervals</code> <code>dict</code> <p>Dictionary of interval sources.</p> <code>v2g_path</code> <code>str</code> <p>Output V2G path.</p> Source code in <code>src/otg/v2g.py</code> <pre><code>@dataclass\nclass V2GStep:\n    \"\"\"Variant-to-gene (V2G) step.\n\n    This step aims to generate a dataset that contains multiple pieces of evidence supporting the functional association of specific variants with genes. Some of the evidence types include:\n\n    1. Chromatin interaction experiments, e.g. Promoter Capture Hi-C (PCHi-C).\n    2. In silico functional predictions, e.g. Variant Effect Predictor (VEP) from Ensembl.\n    3. Distance between the variant and each gene's canonical transcription start site (TSS).\n\n    Attributes:\n        session (Session): Session object.\n        variant_index_path (str): Input variant index path.\n        variant_annotation_path (str): Input variant annotation path.\n        gene_index_path (str): Input gene index path.\n        vep_consequences_path (str): Input VEP consequences path.\n        liftover_chain_file_path (str): Path to GRCh37 to GRCh38 chain file.\n        liftover_max_length_difference: Maximum length difference for liftover.\n        max_distance (int): Maximum distance to consider.\n        approved_biotypes (list[str]): List of approved biotypes.\n        intervals (dict): Dictionary of interval sources.\n        v2g_path (str): Output V2G path.\n    \"\"\"\n\n    session: Session = MISSING\n    variant_index_path: str = MISSING\n    variant_annotation_path: str = MISSING\n    gene_index_path: str = MISSING\n    vep_consequences_path: str = MISSING\n    liftover_chain_file_path: str = MISSING\n    liftover_max_length_difference: int = 100\n    max_distance: int = 500_000\n    approved_biotypes: List[str] = field(\n        default_factory=lambda: [\n            \"protein_coding\",\n            \"3prime_overlapping_ncRNA\",\n            \"antisense\",\n            \"bidirectional_promoter_lncRNA\",\n            \"IG_C_gene\",\n            \"IG_D_gene\",\n            \"IG_J_gene\",\n            \"IG_V_gene\",\n            \"lincRNA\",\n            \"macro_lncRNA\",\n            \"non_coding\",\n            \"sense_intronic\",\n            \"sense_overlapping\",\n        ]\n    )\n    intervals: Dict[str, str] = field(default_factory=dict)\n    v2g_path: str = MISSING\n\n    def __post_init__(self: V2GStep) -&gt; None:\n        \"\"\"Run step.\"\"\"\n        # Read\n        gene_index = GeneIndex.from_parquet(self.session, self.gene_index_path)\n        vi = VariantIndex.from_parquet(self.session, self.variant_index_path).persist()\n        va = VariantAnnotation.from_parquet(self.session, self.variant_annotation_path)\n        vep_consequences = self.session.spark.read.csv(\n            self.vep_consequences_path, sep=\"\\t\", header=True\n        ).select(\n            f.element_at(f.split(\"Accession\", r\"/\"), -1).alias(\n                \"variantFunctionalConsequenceId\"\n            ),\n            f.col(\"Term\").alias(\"label\"),\n            f.col(\"v2g_score\").cast(\"double\").alias(\"score\"),\n        )\n\n        # Transform\n        lift = LiftOverSpark(\n            # lift over variants to hg38\n            self.liftover_chain_file_path,\n            self.liftover_max_length_difference,\n        )\n        gene_index_filtered = gene_index.filter_by_biotypes(\n            # Filter gene index by approved biotypes to define V2G gene universe\n            list(self.approved_biotypes)\n        )\n        va_slimmed = va.filter_by_variant_df(\n            # Variant annotation reduced to the variant index to define V2G variant universe\n            vi.df\n        ).persist()\n        intervals = Intervals(\n            _df=reduce(\n                lambda x, y: x.unionByName(y, allowMissingColumns=True),\n                # create interval instances by parsing each source\n                [\n                    Intervals.from_source(\n                        self.session.spark, source_name, source_path, gene_index, lift\n                    ).df\n                    for source_name, source_path in self.intervals.items()\n                ],\n            ),\n            _schema=Intervals.get_schema(),\n        )\n        v2g_datasets = [\n            va_slimmed.get_distance_to_tss(gene_index_filtered, self.max_distance),\n            va_slimmed.get_most_severe_vep_v2g(vep_consequences, gene_index_filtered),\n            va_slimmed.get_plof_v2g(gene_index_filtered),\n            intervals.v2g(vi),\n        ]\n        v2g = V2G(\n            _df=reduce(\n                lambda x, y: x.unionByName(y, allowMissingColumns=True),\n                [dataset.df for dataset in v2g_datasets],\n            ).repartition(\"chromosome\"),\n            _schema=V2G.get_schema(),\n        )\n\n        # Load\n        (\n            v2g.df.write.partitionBy(\"chromosome\")\n            .mode(self.session.write_mode)\n            .parquet(self.v2g_path)\n        )\n</code></pre>"}]}
\ No newline at end of file
+{"config":{"lang":["en"],"separator":"[\\s\\-]+","pipeline":["stopWordFilter"]},"docs":[{"location":"","title":"Open Targets Gentropy","text":"<p>Open Targets Gentropy is a Python package to facilitate the interpretation and analysis of GWAS and functional genomic studies for target identification. This package contains a toolkit for the harmonisation, statistical analysis and prioritisation of genetic signals to assist drug discovery.</p>"},{"location":"#about-open-targets","title":"About Open Targets","text":"<p>Open Targets is a pre-competitive, public-private partnership that uses human genetics and genomics data to systematically identify and prioritise drug targets. Through large-scale genomic experiments and the development of innovative computational techniques, the partnership aims to help researchers select the best targets for the development of new therapies. For more information, visit the Open Targets website.</p>"},{"location":"installation/","title":"Installation","text":"<p>Note</p> <p>In the early stages of development, we are using Python version 3.10. We recommend using pyenv or similar tools to manage your local Python version. We intend to support more Python versions in the future.</p>"},{"location":"installation/#pypi","title":"Pypi","text":"<p>We recommend installing Open Targets Gentropy using Pypi:</p> <pre><code>pip install gentropy\n</code></pre>"},{"location":"installation/#source","title":"Source","text":"<p>Alternatively, you can install Open Targets Gentropy from source. Check the contributing section for more information.</p>"},{"location":"installation/#uninstall","title":"Uninstall","text":"<pre><code>pip uninstall gentropy -y\n</code></pre> <p>For any issues with the installation, check the troubleshooting section.</p>"},{"location":"roadmap/","title":"Roadmap","text":"<p>The Open Targets core team is working on refactoring Open Targets Genetics, aiming to:</p> <ul> <li>Re-focus the product around Target ID</li> <li>Create a gold standard toolkit for post-GWAS analysis</li> <li>Faster/robust addition of new datasets and datatypes</li> <li>Reduce computational and financial cost</li> </ul> <p>See here for a list of open issues for this project.</p> <p>Schematic diagram representing the drafted process:</p> <p></p>"},{"location":"development/_development/","title":"Development","text":"<p>This section contains various technical information on how to develop and run the code.</p>"},{"location":"development/airflow/","title":"Airflow configuration","text":"<p>This section describes how to set up a local Airflow server which will orchestrate running workflows in Google Cloud Platform. This is useful for testing and debugging, but for production use, it is recommended to run Airflow on a dedicated server.</p>"},{"location":"development/airflow/#install-pre-requisites","title":"Install pre-requisites","text":"<ul> <li>Docker</li> <li>Google Cloud SDK</li> </ul> <p>Warning</p> <p>On macOS, the default amount of memory available for Docker might not be enough to get Airflow up and running. Allocate at least 4GB of memory for the Docker Engine (ideally 8GB). More info</p>"},{"location":"development/airflow/#configure-airflow-access-to-google-cloud-platform","title":"Configure Airflow access to Google Cloud Platform","text":"<p>Warning</p> <p>Run the next two command with the appropriate Google Cloud project ID and service account name to ensure the correct Google default application credentials are set up.</p> <p>Authenticate to Google Cloud:</p> <pre><code>gcloud auth application-default login --project=&lt;PROJECT&gt;\n</code></pre> <p>Create the service account key file that will be used by Airflow to access Google Cloud Platform resources:</p> <pre><code>gcloud iam service-accounts keys create ~/.config/gcloud/service_account_credentials.json --iam-account=&lt;PROJECT&gt;@appspot.gserviceaccount.com\n</code></pre>"},{"location":"development/airflow/#set-up-airflow","title":"Set up Airflow","text":"<p>Change the working directory so that all subsequent commands will work:</p> <pre><code>cd src/airflow\n</code></pre>"},{"location":"development/airflow/#build-docker-image","title":"Build Docker image","text":"<p>Note</p> <p>The custom Dockerfile built by the command below extends the official Airflow Docker Compose YAML. We add support for Google Cloud SDK, Google Dataproc operators, and access to GCP credentials.</p> <pre><code>docker build . --tag extending_airflow:latest\n</code></pre>"},{"location":"development/airflow/#set-airflow-user-id","title":"Set Airflow user ID","text":"<p>Note</p> <p>These commands allow Airflow running inside Docker to access the credentials file which was generated earlier.</p> <pre><code># If any user ID is already specified in .env, remove it.\ngrep -v \"AIRFLOW_UID\" .env &gt; .env.tmp\n# Add the correct user ID.\necho \"AIRFLOW_UID=$(id -u)\" &gt;&gt; .env.tmp\n# Move the file.\nmv .env.tmp .env\n</code></pre>"},{"location":"development/airflow/#initialise","title":"Initialise","text":"<p>Before starting Airflow, initialise the database:</p> <pre><code>docker compose up airflow-init\n</code></pre> <p>Now start all services:</p> <pre><code>docker compose up -d\n</code></pre> <p>Airflow UI will now be available at <code>http://localhost:8080/</code>. Default username and password are both <code>airflow</code>.</p> <p>For additional information on how to use Airflow visit the official documentation.</p>"},{"location":"development/airflow/#cleaning-up","title":"Cleaning up","text":"<p>At any time, you can check the status of your containers with:</p> <pre><code>docker ps\n</code></pre> <p>To stop Airflow, run:</p> <pre><code>docker compose down\n</code></pre> <p>To cleanup the Airflow database, run:</p> <pre><code>docker compose down --volumes --remove-orphans\n</code></pre>"},{"location":"development/airflow/#advanced-configuration","title":"Advanced configuration","text":"<p>More information on running Airflow with Docker Compose can be found in the official docs.</p> <ol> <li>Increase Airflow concurrency. Modify the <code>docker-compose.yaml</code> and add the following to the x-airflow-common \u2192 environment section:</li> </ol> <pre><code>AIRFLOW__CORE__PARALLELISM: 32\nAIRFLOW__CORE__MAX_ACTIVE_TASKS_PER_DAG: 32\nAIRFLOW__SCHEDULER__MAX_TIS_PER_QUERY: 16\nAIRFLOW__CORE__MAX_ACTIVE_RUNS_PER_DAG: 1\n# Also add the following line if you are using CeleryExecutor (by default, LocalExecutor is used).\nAIRFLOW__CELERY__WORKER_CONCURRENCY: 32\n</code></pre> <ol> <li>Additional pip packages. They can be added to the <code>requirements.txt</code> file.</li> </ol>"},{"location":"development/airflow/#troubleshooting","title":"Troubleshooting","text":"<p>Note that when you a a new workflow under <code>dags/</code>, Airflow will not pick that up immediately. By default the filesystem is only scanned for new DAGs every 300s. However, once the DAG is added, updates are applied nearly instantaneously.</p> <p>Also, if you edit the DAG while an instance of it is running, it might cause problems with the run, as Airflow will try to update the tasks and their properties in DAG according to the file changes.</p>"},{"location":"development/contributing/","title":"Contributing guidelines","text":""},{"location":"development/contributing/#one-time-configuration","title":"One-time configuration","text":"<p>The steps in this section only ever need to be done once on any particular system.</p> <p>For Google Cloud configuration:</p> <ol> <li> <p>Install Google Cloud SDK: https://cloud.google.com/sdk/docs/install.</p> </li> <li> <p>Log in to your work Google Account: run <code>gcloud auth login</code> and follow instructions.</p> </li> <li> <p>Obtain Google application credentials: run <code>gcloud auth application-default login</code> and follow instructions.</p> </li> </ol> <p>Check that you have the <code>make</code> utility installed, and if not (which is unlikely), install it using your system package manager.</p> <p>Check that you have <code>java</code> installed.</p>"},{"location":"development/contributing/#environment-configuration","title":"Environment configuration","text":"<p>Run <code>make setup-dev</code> to install/update the necessary packages and activate the development environment. You need to do this every time you open a new shell.</p> <p>It is recommended to use VS Code as an IDE for development.</p>"},{"location":"development/contributing/#how-to-run-the-code","title":"How to run the code","text":"<p>All pipelines in this repository are intended to be run in Google Dataproc. Running them locally is not currently supported.</p> <p>In order to run the code:</p> <ol> <li> <p>Manually edit your local <code>src/airflow/dags/*</code> file and comment out the steps you do not want to run.</p> </li> <li> <p>Manually edit your local <code>pyproject.toml</code> file and modify the version of the code.</p> </li> <li> <p>This must be different from the version used by any other people working on the repository to avoid any deployment conflicts, so it's a good idea to use your name, for example: <code>1.2.3+jdoe</code>.</p> </li> <li>You can also add a brief branch description, for example: <code>1.2.3+jdoe.myfeature</code>.</li> <li>Note that the version must comply with PEP440 conventions, otherwise Poetry will not allow it to be deployed.</li> <li> <p>Do not use underscores or hyphens in your version name. When building the WHL file, they will be automatically converted to dots, which means the file name will no longer match the version and the build will fail. Use dots instead.</p> </li> <li> <p>Manually edit your local <code>src/airflow/dags/common_airflow.py</code> and set <code>OTG_VERSION</code> to the same version as you did in the previous step.</p> </li> <li> <p>Run <code>make build</code>.</p> </li> <li> <p>This will create a bundle containing the neccessary code, configuration and dependencies to run the ETL pipeline, and then upload this bundle to Google Cloud.</p> </li> <li>A version specific subpath is used, so uploading the code will not affect any branches but your own.</li> <li> <p>If there was already a code bundle uploaded with the same version number, it will be replaced.</p> </li> <li> <p>Open Airflow UI and run the DAG.</p> </li> </ol>"},{"location":"development/contributing/#contributing-checklist","title":"Contributing checklist","text":"<p>When making changes, and especially when implementing a new module or feature, it's essential to ensure that all relevant sections of the code base are modified.</p> <ul> <li>[ ] Run <code>make check</code>. This will run the linter and formatter to ensure that the code is compliant with the project conventions.</li> <li>[ ] Develop unit tests for your code and run <code>make test</code>. This will run all unit tests in the repository, including the examples appended in the docstrings of some methods.</li> <li>[ ] Update the configuration if necessary.</li> <li>[ ] Update the documentation and check it with <code>make build-documentation</code>. This will start a local server to browse it (URL will be printed, usually <code>http://127.0.0.1:8000/</code>)</li> </ul> <p>For more details on each of these steps, see the sections below.</p>"},{"location":"development/contributing/#documentation","title":"Documentation","text":"<ul> <li>If during development you had a question which wasn't covered in the documentation, and someone explained it to you, add it to the documentation. The same applies if you encountered any instructions in the documentation which were obsolete or incorrect.</li> <li>Documentation autogeneration expressions start with <code>:::</code>. They will automatically generate sections of the documentation based on class and method docstrings. Be sure to update them for:</li> <li>Dataset definitions in <code>docs/python_api/datasource/STEP</code> (example: <code>docs/python_api/datasource/finngen/study_index.md</code>)</li> <li>Step definition in <code>docs/python_api/step/STEP.md</code> (example: <code>docs/python_api/step/finngen.md</code>)</li> </ul>"},{"location":"development/contributing/#configuration","title":"Configuration","text":"<ul> <li>Input and output paths in <code>config/datasets/gcp.yaml</code></li> <li>Step configuration in <code>config/step/STEP.yaml</code> (example: <code>config/step/finngen.yaml</code>)</li> </ul>"},{"location":"development/contributing/#classes","title":"Classes","text":"<ul> <li>Dataset class in <code>src/gentropy/datasource/STEP</code> (example: <code>src/gentropy/datasource/finngen/study_index.py</code> \u2192 <code>FinnGenStudyIndex</code>)</li> <li>Step main running class in <code>src/gentropy/STEP.py</code> (example: <code>src/gentropy/finngen.py</code>)</li> </ul>"},{"location":"development/contributing/#tests","title":"Tests","text":"<ul> <li>Test study fixture in <code>tests/conftest.py</code> (example: <code>mock_study_index_finngen</code> in that module)</li> <li>Test sample data in <code>tests/data_samples</code> (example: <code>tests/data_samples/finngen_studies_sample.json</code>)</li> <li>Test definition in <code>tests/</code> (example: <code>tests/dataset/test_study_index.py</code> \u2192 <code>test_study_index_finngen_creation</code>)</li> </ul>"},{"location":"development/troubleshooting/","title":"Troubleshooting","text":""},{"location":"development/troubleshooting/#blaslapack","title":"BLAS/LAPACK","text":"<p>If you see errors related to BLAS/LAPACK libraries, see this StackOverflow post for guidance.</p>"},{"location":"development/troubleshooting/#pyenv-and-poetry","title":"Pyenv and Poetry","text":"<p>If you see various errors thrown by Pyenv or Poetry, they can be hard to specifically diagnose and resolve. In this case, it often helps to remove those tools from the system completely. Follow these steps:</p> <ol> <li>Close your currently activated environment, if any: <code>exit</code></li> <li>Uninstall Poetry: <code>curl -sSL https://install.python-poetry.org | python3 - --uninstall</code></li> <li>Clear Poetry cache: <code>rm -rf ~/.cache/pypoetry</code></li> <li>Clear pre-commit cache: <code>rm -rf ~/.cache/pre-commit</code></li> <li>Switch to system Python shell: <code>pyenv shell system</code></li> <li>Edit <code>~/.bashrc</code> to remove the lines related to Pyenv configuration</li> <li>Remove Pyenv configuration and cache: <code>rm -rf ~/.pyenv</code></li> </ol> <p>After that, open a fresh shell session and run <code>make setup-dev</code> again.</p>"},{"location":"development/troubleshooting/#java","title":"Java","text":"<p>Officially, PySpark requires Java version 8 (a.k.a. 1.8) or above to work. However, if you have a very recent version of Java, you may experience issues, as it may introduce breaking changes that PySpark hasn't had time to integrate. For example, as of May 2023, PySpark did not work with Java 20.</p> <p>If you are encountering problems with initialising a Spark session, try using Java 11.</p>"},{"location":"development/troubleshooting/#pre-commit","title":"Pre-commit","text":"<p>If you see an error message thrown by pre-commit, which looks like this (<code>SyntaxError: Unexpected token '?'</code>), followed by a JavaScript traceback, the issue is likely with your system NodeJS version.</p> <p>One solution which can help in this case is to upgrade your system NodeJS version. However, this may not always be possible. For example, Ubuntu repository is several major versions behind the latest version as of July 2023.</p> <p>Another solution which helps is to remove Node, NodeJS, and npm from your system entirely. In this case, pre-commit will not try to rely on a system version of NodeJS and will install its own, suitable one.</p> <p>On Ubuntu, this can be done using <code>sudo apt remove node nodejs npm</code>, followed by <code>sudo apt autoremove</code>. But in some cases, depending on your existing installation, you may need to also manually remove some files. See this StackOverflow answer for guidance.</p> <p>After running these commands, you are advised to open a fresh shell, and then also reinstall Pyenv and Poetry to make sure they pick up the changes (see relevant section above).</p>"},{"location":"development/workflows/","title":"Pipeline workflows","text":"<p>This page describes the high level components of the pipeline, which are organised as Airflow DAGs (directed acyclic graphs).</p>"},{"location":"development/workflows/#note-on-dags-and-dataproc-clusters","title":"Note on DAGs and Dataproc clusters","text":"<p>Each DAG consists of the following general stages:</p> <ol> <li> <p>Create cluster (if it already exists, this step is skipped)</p> </li> <li> <p>Install dependencies on the cluster</p> </li> <li> <p>Run data processing steps for this DAG</p> </li> <li> <p>Delete the cluster</p> </li> </ol> <p>Within a DAG, all data processing steps run on the same Dataproc cluster as separate jobs.</p> <p>There is no need to configure DAGs or steps depending on the size of the input data. Clusters have autoscaling enabled, which means they will increase or decrease the number of worker VMs to accommodate the load.</p>"},{"location":"development/workflows/#dag-1-preprocess","title":"DAG 1: Preprocess","text":"<p>This DAG contains steps which are only supposed to be run once, or very rarely. They ingest external data and apply bespoke transformations specific for each particular data source. The output is normalised according to the data schemas used by the pipeline.</p>"},{"location":"development/workflows/#dag-2-etl","title":"DAG 2: ETL","text":"<p>The ETL DAG takes the inputs of the previous step and performs the main algorithmic processing. This processing is supposed to be data source agnostic.</p>"},{"location":"howto/_howto/","title":"How-to","text":"<p>This page contains a collection of how-to guides for the project.</p> <p>For additional information please visit https://community.opentargets.org/</p>"},{"location":"howto/run_step_in_cli/","title":"Run step in CLI","text":"<p>To run a step in the command line interface (CLI), you need to know the step's name. To list what steps are avaiable in your current environment, simply run <code>gentropy</code> with no arguments. This will list all the steps:</p> <pre><code>You must specify 'step', e.g, step=&lt;OPTION&gt;\nAvailable options:\n        clump\n        colocalisation\n        eqtl_catalogue\n        finngen_studies\n        finngen_sumstat_preprocess\n        gene_index\n        gwas_catalog_ingestion\n        gwas_catalog_sumstat_preprocess\n        ld_index\n        locus_to_gene\n        overlaps\n        pics\n        ukbiobank\n        variant_annotation\n        variant_index\n        variant_to_gene\n\nSet the environment variable HYDRA_FULL_ERROR=1 for a complete stack trace.\n</code></pre> <p>As indicated, you can run a step by specifying the step's name with the <code>step</code> argument. For example, to run the <code>gene_index</code> step, you can run:</p> <pre><code>gentropy step=gene_index\n</code></pre> <p>In most occassions, some mandatory values will be required to run the step. For example, the <code>gene_index</code> step requires the <code>step.target_path</code> and <code>step.gene_index_path</code> argument to be specified. You can complete the necessary arguments by adding them to the command line:</p> <pre><code>gentropy step=gene_index step.target_path=/path/to/target step.gene_index_path=/path/to/gene_index\n</code></pre> <p>You can find more about the available steps in the documentation.</p>"},{"location":"howto/run_step_using_config/","title":"Run step using YAML config","text":"<p>It's possible to parametrise the functionality of a step using a YAML configuration file. This is useful when you want to run a step multiple times with different parameters or simply to avoid having to specify the same parameters every time you run a step.</p> <p>Info</p> <p>The package uses Hydra to handle configuration files. For more information, please visit the Hydra documentation.</p> <p>To run a step using a configuration file, you need to create a configuration file in YAML format.</p> <pre><code>config/\n\u251c\u2500 step/\n\u2502  \u2514\u2500 my_gene_index.md\n\u2514\u2500 my_config.yml\n</code></pre> <p>The configuration file should contain the parameters you want to use to run the step. For example, to run the <code>gene_index</code> step, you need to specify the <code>step.target_path</code> and <code>step.gene_index_path</code> parameters. The configuration file should look like this:</p> my_config.yamlstep/my_gene_index.md <pre><code>defaults:\n    - config\n    - _self_\n</code></pre> <p>This config file will specify that your configuration file will inherit the default configuration (<code>config</code>) and everything provided (<code>_self_</code>) will overwrite the default configuration.</p> <pre><code>defaults:\n    - gene_index\n\ntarget_path: /path/to/target\ngene_index_path: /path/to/gene_index\n</code></pre> <p>This config file will inherit the default configuration for the <code>gene_index</code> step and overwrite the <code>target_path</code> and <code>gene_index_path</code> parameters.</p> <p>Once you have created the configuration file, you can run your own new <code>my_gene_index</code>:</p> <pre><code>gentropy step=my_gene_index --config-dir=config --config-name=my_config\n</code></pre>"},{"location":"python_api/_python_api/","title":"Python API","text":"<p>Open Targets Gentropy is a Python package to facilitate the interpretation and analysis of GWAS and functional genomic studies for target identification. The package contains a toolkit for the harmonisation, statistical analysis and prioritisation of genetic signals to assist drug discovery.</p> <p>The overall architecture of the package distinguishes between:</p> <ul> <li>Data Sources: data sources harmonisation tools</li> <li>Datasets: data model</li> <li>Methods: statistical analysis tools</li> <li>Steps: pipeline steps</li> </ul>"},{"location":"python_api/datasets/_datasets/","title":"Datasets","text":"<p>The Dataset classes define the data model behind Open Targets Gentropy. Every class inherits from the <code>Dataset</code> class and contains a dataframe with a predefined schema that can be found in the respective classes.</p>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset","title":"<code>gentropy.dataset.dataset.Dataset</code>  <code>dataclass</code>","text":"<p>             Bases: <code>ABC</code></p> <p>Open Targets Gentropy Dataset.</p> <p><code>Dataset</code> is a wrapper around a Spark DataFrame with a predefined schema. Schemas for each child dataset are described in the <code>schemas</code> module.</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>@dataclass\nclass Dataset(ABC):\n    \"\"\"Open Targets Gentropy Dataset.\n\n    `Dataset` is a wrapper around a Spark DataFrame with a predefined schema. Schemas for each child dataset are described in the `schemas` module.\n    \"\"\"\n\n    _df: DataFrame\n    _schema: StructType\n\n    def __post_init__(self: Dataset) -&gt; None:\n        \"\"\"Post init.\"\"\"\n        self.validate_schema()\n\n    @property\n    def df(self: Dataset) -&gt; DataFrame:\n        \"\"\"Dataframe included in the Dataset.\n\n        Returns:\n            DataFrame: Dataframe included in the Dataset\n        \"\"\"\n        return self._df\n\n    @df.setter\n    def df(self: Dataset, new_df: DataFrame) -&gt; None:  # noqa: CCE001\n        \"\"\"Dataframe setter.\n\n        Args:\n            new_df (DataFrame): New dataframe to be included in the Dataset\n        \"\"\"\n        self._df: DataFrame = new_df\n        self.validate_schema()\n\n    @property\n    def schema(self: Dataset) -&gt; StructType:\n        \"\"\"Dataframe expected schema.\n\n        Returns:\n            StructType: Dataframe expected schema\n        \"\"\"\n        return self._schema\n\n    @classmethod\n    @abstractmethod\n    def get_schema(cls: type[Self]) -&gt; StructType:\n        \"\"\"Abstract method to get the schema. Must be implemented by child classes.\n\n        Returns:\n            StructType: Schema for the Dataset\n        \"\"\"\n        pass\n\n    @classmethod\n    def from_parquet(\n        cls: type[Self],\n        session: Session,\n        path: str | list[str],\n        **kwargs: bool | float | int | str | None,\n    ) -&gt; Self:\n        \"\"\"Reads parquet into a Dataset with a given schema.\n\n        Args:\n            session (Session): Spark session\n            path (str | list[str]): Path to the parquet dataset\n            **kwargs (bool | float | int | str | None): Additional arguments to pass to spark.read.parquet\n\n        Returns:\n            Self: Dataset with the parquet file contents\n\n        Raises:\n            ValueError: Parquet file is empty\n        \"\"\"\n        schema = cls.get_schema()\n        df = session.read_parquet(path, schema=schema, **kwargs)\n        if df.isEmpty():\n            raise ValueError(f\"Parquet file is empty: {path}\")\n        return cls(_df=df, _schema=schema)\n\n    def validate_schema(self: Dataset) -&gt; None:\n        \"\"\"Validate DataFrame schema against expected class schema.\n\n        Raises:\n            ValueError: DataFrame schema is not valid\n        \"\"\"\n        expected_schema = self._schema\n        expected_fields = flatten_schema(expected_schema)\n        observed_schema = self._df.schema\n        observed_fields = flatten_schema(observed_schema)\n\n        # Unexpected fields in dataset\n        if unexpected_field_names := [\n            x.name\n            for x in observed_fields\n            if x.name not in [y.name for y in expected_fields]\n        ]:\n            raise ValueError(\n                f\"The {unexpected_field_names} fields are not included in DataFrame schema: {expected_fields}\"\n            )\n\n        # Required fields not in dataset\n        required_fields = [x.name for x in expected_schema if not x.nullable]\n        if missing_required_fields := [\n            req\n            for req in required_fields\n            if not any(field.name == req for field in observed_fields)\n        ]:\n            raise ValueError(\n                f\"The {missing_required_fields} fields are required but missing: {required_fields}\"\n            )\n\n        # Fields with duplicated names\n        if duplicated_fields := [\n            x for x in set(observed_fields) if observed_fields.count(x) &gt; 1\n        ]:\n            raise ValueError(\n                f\"The following fields are duplicated in DataFrame schema: {duplicated_fields}\"\n            )\n\n        # Fields with different datatype\n        observed_field_types = {\n            field.name: type(field.dataType) for field in observed_fields\n        }\n        expected_field_types = {\n            field.name: type(field.dataType) for field in expected_fields\n        }\n        if fields_with_different_observed_datatype := [\n            name\n            for name, observed_type in observed_field_types.items()\n            if name in expected_field_types\n            and observed_type != expected_field_types[name]\n        ]:\n            raise ValueError(\n                f\"The following fields present differences in their datatypes: {fields_with_different_observed_datatype}.\"\n            )\n\n    def persist(self: Self) -&gt; Self:\n        \"\"\"Persist in memory the DataFrame included in the Dataset.\n\n        Returns:\n            Self: Persisted Dataset\n        \"\"\"\n        self.df = self._df.persist()\n        return self\n\n    def unpersist(self: Self) -&gt; Self:\n        \"\"\"Remove the persisted DataFrame from memory.\n\n        Returns:\n            Self: Unpersisted Dataset\n        \"\"\"\n        self.df = self._df.unpersist()\n        return self\n\n    def coalesce(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n        \"\"\"Coalesce the DataFrame included in the Dataset.\n\n        Coalescing is efficient for decreasing the number of partitions because it avoids a full shuffle of the data.\n\n        Args:\n            num_partitions (int): Number of partitions to coalesce to\n            **kwargs (Any): Arguments to pass to the coalesce method\n\n        Returns:\n            Self: Coalesced Dataset\n        \"\"\"\n        self.df = self._df.coalesce(num_partitions, **kwargs)\n        return self\n\n    def repartition(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n        \"\"\"Repartition the DataFrame included in the Dataset.\n\n        Repartitioning creates new partitions with data that is distributed evenly.\n\n        Args:\n            num_partitions (int): Number of partitions to repartition to\n            **kwargs (Any): Arguments to pass to the repartition method\n\n        Returns:\n            Self: Repartitioned Dataset\n        \"\"\"\n        self.df = self._df.repartition(num_partitions, **kwargs)\n        return self\n</code></pre>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.df","title":"<code>df: DataFrame</code>  <code>property</code> <code>writable</code>","text":"<p>Dataframe included in the Dataset.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Dataframe included in the Dataset</p>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.schema","title":"<code>schema: StructType</code>  <code>property</code>","text":"<p>Dataframe expected schema.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Dataframe expected schema</p>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.coalesce","title":"<code>coalesce(num_partitions: int, **kwargs: Any) -&gt; Self</code>","text":"<p>Coalesce the DataFrame included in the Dataset.</p> <p>Coalescing is efficient for decreasing the number of partitions because it avoids a full shuffle of the data.</p> <p>Parameters:</p> Name Type Description Default <code>num_partitions</code> <code>int</code> <p>Number of partitions to coalesce to</p> required <code>**kwargs</code> <code>Any</code> <p>Arguments to pass to the coalesce method</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Coalesced Dataset</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>def coalesce(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n    \"\"\"Coalesce the DataFrame included in the Dataset.\n\n    Coalescing is efficient for decreasing the number of partitions because it avoids a full shuffle of the data.\n\n    Args:\n        num_partitions (int): Number of partitions to coalesce to\n        **kwargs (Any): Arguments to pass to the coalesce method\n\n    Returns:\n        Self: Coalesced Dataset\n    \"\"\"\n    self.df = self._df.coalesce(num_partitions, **kwargs)\n    return self\n</code></pre>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.from_parquet","title":"<code>from_parquet(session: Session, path: str | list[str], **kwargs: bool | float | int | str | None) -&gt; Self</code>  <code>classmethod</code>","text":"<p>Reads parquet into a Dataset with a given schema.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Spark session</p> required <code>path</code> <code>str | list[str]</code> <p>Path to the parquet dataset</p> required <code>**kwargs</code> <code>bool | float | int | str | None</code> <p>Additional arguments to pass to spark.read.parquet</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Dataset with the parquet file contents</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>Parquet file is empty</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>@classmethod\ndef from_parquet(\n    cls: type[Self],\n    session: Session,\n    path: str | list[str],\n    **kwargs: bool | float | int | str | None,\n) -&gt; Self:\n    \"\"\"Reads parquet into a Dataset with a given schema.\n\n    Args:\n        session (Session): Spark session\n        path (str | list[str]): Path to the parquet dataset\n        **kwargs (bool | float | int | str | None): Additional arguments to pass to spark.read.parquet\n\n    Returns:\n        Self: Dataset with the parquet file contents\n\n    Raises:\n        ValueError: Parquet file is empty\n    \"\"\"\n    schema = cls.get_schema()\n    df = session.read_parquet(path, schema=schema, **kwargs)\n    if df.isEmpty():\n        raise ValueError(f\"Parquet file is empty: {path}\")\n    return cls(_df=df, _schema=schema)\n</code></pre>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>abstractmethod</code> <code>classmethod</code>","text":"<p>Abstract method to get the schema. Must be implemented by child classes.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the Dataset</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>@classmethod\n@abstractmethod\ndef get_schema(cls: type[Self]) -&gt; StructType:\n    \"\"\"Abstract method to get the schema. Must be implemented by child classes.\n\n    Returns:\n        StructType: Schema for the Dataset\n    \"\"\"\n    pass\n</code></pre>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.persist","title":"<code>persist() -&gt; Self</code>","text":"<p>Persist in memory the DataFrame included in the Dataset.</p> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Persisted Dataset</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>def persist(self: Self) -&gt; Self:\n    \"\"\"Persist in memory the DataFrame included in the Dataset.\n\n    Returns:\n        Self: Persisted Dataset\n    \"\"\"\n    self.df = self._df.persist()\n    return self\n</code></pre>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.repartition","title":"<code>repartition(num_partitions: int, **kwargs: Any) -&gt; Self</code>","text":"<p>Repartition the DataFrame included in the Dataset.</p> <p>Repartitioning creates new partitions with data that is distributed evenly.</p> <p>Parameters:</p> Name Type Description Default <code>num_partitions</code> <code>int</code> <p>Number of partitions to repartition to</p> required <code>**kwargs</code> <code>Any</code> <p>Arguments to pass to the repartition method</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Repartitioned Dataset</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>def repartition(self: Self, num_partitions: int, **kwargs: Any) -&gt; Self:\n    \"\"\"Repartition the DataFrame included in the Dataset.\n\n    Repartitioning creates new partitions with data that is distributed evenly.\n\n    Args:\n        num_partitions (int): Number of partitions to repartition to\n        **kwargs (Any): Arguments to pass to the repartition method\n\n    Returns:\n        Self: Repartitioned Dataset\n    \"\"\"\n    self.df = self._df.repartition(num_partitions, **kwargs)\n    return self\n</code></pre>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.unpersist","title":"<code>unpersist() -&gt; Self</code>","text":"<p>Remove the persisted DataFrame from memory.</p> <p>Returns:</p> Name Type Description <code>Self</code> <code>Self</code> <p>Unpersisted Dataset</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>def unpersist(self: Self) -&gt; Self:\n    \"\"\"Remove the persisted DataFrame from memory.\n\n    Returns:\n        Self: Unpersisted Dataset\n    \"\"\"\n    self.df = self._df.unpersist()\n    return self\n</code></pre>"},{"location":"python_api/datasets/_datasets/#gentropy.dataset.dataset.Dataset.validate_schema","title":"<code>validate_schema() -&gt; None</code>","text":"<p>Validate DataFrame schema against expected class schema.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>DataFrame schema is not valid</p> Source code in <code>src/gentropy/dataset/dataset.py</code> <pre><code>def validate_schema(self: Dataset) -&gt; None:\n    \"\"\"Validate DataFrame schema against expected class schema.\n\n    Raises:\n        ValueError: DataFrame schema is not valid\n    \"\"\"\n    expected_schema = self._schema\n    expected_fields = flatten_schema(expected_schema)\n    observed_schema = self._df.schema\n    observed_fields = flatten_schema(observed_schema)\n\n    # Unexpected fields in dataset\n    if unexpected_field_names := [\n        x.name\n        for x in observed_fields\n        if x.name not in [y.name for y in expected_fields]\n    ]:\n        raise ValueError(\n            f\"The {unexpected_field_names} fields are not included in DataFrame schema: {expected_fields}\"\n        )\n\n    # Required fields not in dataset\n    required_fields = [x.name for x in expected_schema if not x.nullable]\n    if missing_required_fields := [\n        req\n        for req in required_fields\n        if not any(field.name == req for field in observed_fields)\n    ]:\n        raise ValueError(\n            f\"The {missing_required_fields} fields are required but missing: {required_fields}\"\n        )\n\n    # Fields with duplicated names\n    if duplicated_fields := [\n        x for x in set(observed_fields) if observed_fields.count(x) &gt; 1\n    ]:\n        raise ValueError(\n            f\"The following fields are duplicated in DataFrame schema: {duplicated_fields}\"\n        )\n\n    # Fields with different datatype\n    observed_field_types = {\n        field.name: type(field.dataType) for field in observed_fields\n    }\n    expected_field_types = {\n        field.name: type(field.dataType) for field in expected_fields\n    }\n    if fields_with_different_observed_datatype := [\n        name\n        for name, observed_type in observed_field_types.items()\n        if name in expected_field_types\n        and observed_type != expected_field_types[name]\n    ]:\n        raise ValueError(\n            f\"The following fields present differences in their datatypes: {fields_with_different_observed_datatype}.\"\n        )\n</code></pre>"},{"location":"python_api/datasets/colocalisation/","title":"Colocalisation","text":""},{"location":"python_api/datasets/colocalisation/#gentropy.dataset.colocalisation.Colocalisation","title":"<code>gentropy.dataset.colocalisation.Colocalisation</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Colocalisation results for pairs of overlapping study-locus.</p> Source code in <code>src/gentropy/dataset/colocalisation.py</code> <pre><code>@dataclass\nclass Colocalisation(Dataset):\n    \"\"\"Colocalisation results for pairs of overlapping study-locus.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[Colocalisation]) -&gt; StructType:\n        \"\"\"Provides the schema for the Colocalisation dataset.\n\n        Returns:\n            StructType: Schema for the Colocalisation dataset\n        \"\"\"\n        return parse_spark_schema(\"colocalisation.json\")\n</code></pre>"},{"location":"python_api/datasets/colocalisation/#gentropy.dataset.colocalisation.Colocalisation.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the Colocalisation dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the Colocalisation dataset</p> Source code in <code>src/gentropy/dataset/colocalisation.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[Colocalisation]) -&gt; StructType:\n    \"\"\"Provides the schema for the Colocalisation dataset.\n\n    Returns:\n        StructType: Schema for the Colocalisation dataset\n    \"\"\"\n    return parse_spark_schema(\"colocalisation.json\")\n</code></pre>"},{"location":"python_api/datasets/colocalisation/#schema","title":"Schema","text":"<pre><code>root\n |-- leftStudyLocusId: long (nullable = false)\n |-- rightStudyLocusId: long (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- colocalisationMethod: string (nullable = false)\n |-- numberColocalisingVariants: long (nullable = false)\n |-- h0: double (nullable = true)\n |-- h1: double (nullable = true)\n |-- h2: double (nullable = true)\n |-- h3: double (nullable = true)\n |-- h4: double (nullable = true)\n |-- log2h4h3: double (nullable = true)\n |-- clpp: double (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/gene_index/","title":"Gene Index","text":""},{"location":"python_api/datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex","title":"<code>gentropy.dataset.gene_index.GeneIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Gene index dataset.</p> <p>Gene-based annotation.</p> Source code in <code>src/gentropy/dataset/gene_index.py</code> <pre><code>@dataclass\nclass GeneIndex(Dataset):\n    \"\"\"Gene index dataset.\n\n    Gene-based annotation.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[GeneIndex]) -&gt; StructType:\n        \"\"\"Provides the schema for the GeneIndex dataset.\n\n        Returns:\n            StructType: Schema for the GeneIndex dataset\n        \"\"\"\n        return parse_spark_schema(\"gene_index.json\")\n\n    def filter_by_biotypes(self: GeneIndex, biotypes: list[str]) -&gt; GeneIndex:\n        \"\"\"Filter by approved biotypes.\n\n        Args:\n            biotypes (list[str]): List of Ensembl biotypes to keep.\n\n        Returns:\n            GeneIndex: Gene index dataset filtered by biotypes.\n        \"\"\"\n        self.df = self._df.filter(f.col(\"biotype\").isin(biotypes))\n        return self\n\n    def locations_lut(self: GeneIndex) -&gt; DataFrame:\n        \"\"\"Gene location information.\n\n        Returns:\n            DataFrame: Gene LUT including genomic location information.\n        \"\"\"\n        return self.df.select(\n            \"geneId\",\n            \"chromosome\",\n            \"start\",\n            \"end\",\n            \"strand\",\n            \"tss\",\n        )\n\n    def symbols_lut(self: GeneIndex) -&gt; DataFrame:\n        \"\"\"Gene symbol lookup table.\n\n        Pre-processess gene/target dataset to create lookup table of gene symbols, including\n        obsoleted gene symbols.\n\n        Returns:\n            DataFrame: Gene LUT for symbol mapping containing `geneId` and `geneSymbol` columns.\n        \"\"\"\n        return self.df.select(\n            f.explode(\n                f.array_union(f.array(\"approvedSymbol\"), f.col(\"obsoleteSymbols\"))\n            ).alias(\"geneSymbol\"),\n            \"*\",\n        )\n</code></pre>"},{"location":"python_api/datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex.filter_by_biotypes","title":"<code>filter_by_biotypes(biotypes: list[str]) -&gt; GeneIndex</code>","text":"<p>Filter by approved biotypes.</p> <p>Parameters:</p> Name Type Description Default <code>biotypes</code> <code>list[str]</code> <p>List of Ensembl biotypes to keep.</p> required <p>Returns:</p> Name Type Description <code>GeneIndex</code> <code>GeneIndex</code> <p>Gene index dataset filtered by biotypes.</p> Source code in <code>src/gentropy/dataset/gene_index.py</code> <pre><code>def filter_by_biotypes(self: GeneIndex, biotypes: list[str]) -&gt; GeneIndex:\n    \"\"\"Filter by approved biotypes.\n\n    Args:\n        biotypes (list[str]): List of Ensembl biotypes to keep.\n\n    Returns:\n        GeneIndex: Gene index dataset filtered by biotypes.\n    \"\"\"\n    self.df = self._df.filter(f.col(\"biotype\").isin(biotypes))\n    return self\n</code></pre>"},{"location":"python_api/datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the GeneIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the GeneIndex dataset</p> Source code in <code>src/gentropy/dataset/gene_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[GeneIndex]) -&gt; StructType:\n    \"\"\"Provides the schema for the GeneIndex dataset.\n\n    Returns:\n        StructType: Schema for the GeneIndex dataset\n    \"\"\"\n    return parse_spark_schema(\"gene_index.json\")\n</code></pre>"},{"location":"python_api/datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex.locations_lut","title":"<code>locations_lut() -&gt; DataFrame</code>","text":"<p>Gene location information.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Gene LUT including genomic location information.</p> Source code in <code>src/gentropy/dataset/gene_index.py</code> <pre><code>def locations_lut(self: GeneIndex) -&gt; DataFrame:\n    \"\"\"Gene location information.\n\n    Returns:\n        DataFrame: Gene LUT including genomic location information.\n    \"\"\"\n    return self.df.select(\n        \"geneId\",\n        \"chromosome\",\n        \"start\",\n        \"end\",\n        \"strand\",\n        \"tss\",\n    )\n</code></pre>"},{"location":"python_api/datasets/gene_index/#gentropy.dataset.gene_index.GeneIndex.symbols_lut","title":"<code>symbols_lut() -&gt; DataFrame</code>","text":"<p>Gene symbol lookup table.</p> <p>Pre-processess gene/target dataset to create lookup table of gene symbols, including obsoleted gene symbols.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Gene LUT for symbol mapping containing <code>geneId</code> and <code>geneSymbol</code> columns.</p> Source code in <code>src/gentropy/dataset/gene_index.py</code> <pre><code>def symbols_lut(self: GeneIndex) -&gt; DataFrame:\n    \"\"\"Gene symbol lookup table.\n\n    Pre-processess gene/target dataset to create lookup table of gene symbols, including\n    obsoleted gene symbols.\n\n    Returns:\n        DataFrame: Gene LUT for symbol mapping containing `geneId` and `geneSymbol` columns.\n    \"\"\"\n    return self.df.select(\n        f.explode(\n            f.array_union(f.array(\"approvedSymbol\"), f.col(\"obsoleteSymbols\"))\n        ).alias(\"geneSymbol\"),\n        \"*\",\n    )\n</code></pre>"},{"location":"python_api/datasets/gene_index/#schema","title":"Schema","text":"<pre><code>root\n |-- geneId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- approvedSymbol: string (nullable = true)\n |-- biotype: string (nullable = true)\n |-- approvedName: string (nullable = true)\n |-- obsoleteSymbols: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- tss: long (nullable = true)\n |-- start: long (nullable = true)\n |-- end: long (nullable = true)\n |-- strand: integer (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/intervals/","title":"Intervals","text":""},{"location":"python_api/datasets/intervals/#gentropy.dataset.intervals.Intervals","title":"<code>gentropy.dataset.intervals.Intervals</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Intervals dataset links genes to genomic regions based on genome interaction studies.</p> Source code in <code>src/gentropy/dataset/intervals.py</code> <pre><code>@dataclass\nclass Intervals(Dataset):\n    \"\"\"Intervals dataset links genes to genomic regions based on genome interaction studies.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[Intervals]) -&gt; StructType:\n        \"\"\"Provides the schema for the Intervals dataset.\n\n        Returns:\n            StructType: Schema for the Intervals dataset\n        \"\"\"\n        return parse_spark_schema(\"intervals.json\")\n\n    @classmethod\n    def from_source(\n        cls: type[Intervals],\n        spark: SparkSession,\n        source_name: str,\n        source_path: str,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Collect interval data for a particular source.\n\n        Args:\n            spark (SparkSession): Spark session\n            source_name (str): Name of the interval source\n            source_path (str): Path to the interval source file\n            gene_index (GeneIndex): Gene index\n            lift (LiftOverSpark): LiftOverSpark instance to convert coordinats from hg37 to hg38\n\n        Returns:\n            Intervals: Intervals dataset\n\n        Raises:\n            ValueError: If the source name is not recognised\n        \"\"\"\n        from gentropy.datasource.intervals.andersson import IntervalsAndersson\n        from gentropy.datasource.intervals.javierre import IntervalsJavierre\n        from gentropy.datasource.intervals.jung import IntervalsJung\n        from gentropy.datasource.intervals.thurman import IntervalsThurman\n\n        source_to_class = {\n            \"andersson\": IntervalsAndersson,\n            \"javierre\": IntervalsJavierre,\n            \"jung\": IntervalsJung,\n            \"thurman\": IntervalsThurman,\n        }\n\n        if source_name not in source_to_class:\n            raise ValueError(f\"Unknown interval source: {source_name}\")\n\n        source_class = source_to_class[source_name]\n        data = source_class.read(spark, source_path)  # type: ignore\n        return source_class.parse(data, gene_index, lift)  # type: ignore\n\n    def v2g(self: Intervals, variant_index: VariantIndex) -&gt; V2G:\n        \"\"\"Convert intervals into V2G by intersecting with a variant index.\n\n        Args:\n            variant_index (VariantIndex): Variant index dataset\n\n        Returns:\n            V2G: Variant-to-gene evidence dataset\n        \"\"\"\n        return V2G(\n            _df=(\n                self.df.alias(\"interval\")\n                .join(\n                    variant_index.df.selectExpr(\n                        \"chromosome as vi_chromosome\", \"variantId\", \"position\"\n                    ).alias(\"vi\"),\n                    on=[\n                        f.col(\"vi.vi_chromosome\") == f.col(\"interval.chromosome\"),\n                        f.col(\"vi.position\").between(\n                            f.col(\"interval.start\"), f.col(\"interval.end\")\n                        ),\n                    ],\n                    how=\"inner\",\n                )\n                .drop(\"start\", \"end\", \"vi_chromosome\", \"position\")\n            ),\n            _schema=V2G.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasets/intervals/#gentropy.dataset.intervals.Intervals.from_source","title":"<code>from_source(spark: SparkSession, source_name: str, source_path: str, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Collect interval data for a particular source.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>source_name</code> <code>str</code> <p>Name of the interval source</p> required <code>source_path</code> <code>str</code> <p>Path to the interval source file</p> required <code>gene_index</code> <code>GeneIndex</code> <p>Gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance to convert coordinats from hg37 to hg38</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Intervals dataset</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the source name is not recognised</p> Source code in <code>src/gentropy/dataset/intervals.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[Intervals],\n    spark: SparkSession,\n    source_name: str,\n    source_path: str,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Collect interval data for a particular source.\n\n    Args:\n        spark (SparkSession): Spark session\n        source_name (str): Name of the interval source\n        source_path (str): Path to the interval source file\n        gene_index (GeneIndex): Gene index\n        lift (LiftOverSpark): LiftOverSpark instance to convert coordinats from hg37 to hg38\n\n    Returns:\n        Intervals: Intervals dataset\n\n    Raises:\n        ValueError: If the source name is not recognised\n    \"\"\"\n    from gentropy.datasource.intervals.andersson import IntervalsAndersson\n    from gentropy.datasource.intervals.javierre import IntervalsJavierre\n    from gentropy.datasource.intervals.jung import IntervalsJung\n    from gentropy.datasource.intervals.thurman import IntervalsThurman\n\n    source_to_class = {\n        \"andersson\": IntervalsAndersson,\n        \"javierre\": IntervalsJavierre,\n        \"jung\": IntervalsJung,\n        \"thurman\": IntervalsThurman,\n    }\n\n    if source_name not in source_to_class:\n        raise ValueError(f\"Unknown interval source: {source_name}\")\n\n    source_class = source_to_class[source_name]\n    data = source_class.read(spark, source_path)  # type: ignore\n    return source_class.parse(data, gene_index, lift)  # type: ignore\n</code></pre>"},{"location":"python_api/datasets/intervals/#gentropy.dataset.intervals.Intervals.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the Intervals dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the Intervals dataset</p> Source code in <code>src/gentropy/dataset/intervals.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[Intervals]) -&gt; StructType:\n    \"\"\"Provides the schema for the Intervals dataset.\n\n    Returns:\n        StructType: Schema for the Intervals dataset\n    \"\"\"\n    return parse_spark_schema(\"intervals.json\")\n</code></pre>"},{"location":"python_api/datasets/intervals/#gentropy.dataset.intervals.Intervals.v2g","title":"<code>v2g(variant_index: VariantIndex) -&gt; V2G</code>","text":"<p>Convert intervals into V2G by intersecting with a variant index.</p> <p>Parameters:</p> Name Type Description Default <code>variant_index</code> <code>VariantIndex</code> <p>Variant index dataset</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>Variant-to-gene evidence dataset</p> Source code in <code>src/gentropy/dataset/intervals.py</code> <pre><code>def v2g(self: Intervals, variant_index: VariantIndex) -&gt; V2G:\n    \"\"\"Convert intervals into V2G by intersecting with a variant index.\n\n    Args:\n        variant_index (VariantIndex): Variant index dataset\n\n    Returns:\n        V2G: Variant-to-gene evidence dataset\n    \"\"\"\n    return V2G(\n        _df=(\n            self.df.alias(\"interval\")\n            .join(\n                variant_index.df.selectExpr(\n                    \"chromosome as vi_chromosome\", \"variantId\", \"position\"\n                ).alias(\"vi\"),\n                on=[\n                    f.col(\"vi.vi_chromosome\") == f.col(\"interval.chromosome\"),\n                    f.col(\"vi.position\").between(\n                        f.col(\"interval.start\"), f.col(\"interval.end\")\n                    ),\n                ],\n                how=\"inner\",\n            )\n            .drop(\"start\", \"end\", \"vi_chromosome\", \"position\")\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasets/intervals/#schema","title":"Schema","text":"<pre><code>root\n |-- chromosome: string (nullable = false)\n |-- start: string (nullable = false)\n |-- end: string (nullable = false)\n |-- geneId: string (nullable = false)\n |-- resourceScore: double (nullable = true)\n |-- score: double (nullable = true)\n |-- datasourceId: string (nullable = false)\n |-- datatypeId: string (nullable = false)\n |-- pmid: string (nullable = true)\n |-- biofeature: string (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/l2g_feature/","title":"L2G Feature","text":""},{"location":"python_api/datasets/l2g_feature/#gentropy.method.l2g.feature_factory.L2GFeature","title":"<code>gentropy.method.l2g.feature_factory.L2GFeature</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Locus-to-gene feature dataset.</p> Source code in <code>src/gentropy/dataset/l2g_feature.py</code> <pre><code>@dataclass\nclass L2GFeature(Dataset):\n    \"\"\"Locus-to-gene feature dataset.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[L2GFeature]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2GFeature dataset.\n\n        Returns:\n            StructType: Schema for the L2GFeature dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_feature.json\")\n</code></pre>"},{"location":"python_api/datasets/l2g_feature/#gentropy.method.l2g.feature_factory.L2GFeature.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2GFeature dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the L2GFeature dataset</p> Source code in <code>src/gentropy/dataset/l2g_feature.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GFeature]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2GFeature dataset.\n\n    Returns:\n        StructType: Schema for the L2GFeature dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_feature.json\")\n</code></pre>"},{"location":"python_api/datasets/l2g_feature/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- geneId: string (nullable = false)\n |-- featureName: string (nullable = false)\n |-- featureValue: float (nullable = false)\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/","title":"L2G Feature Matrix","text":""},{"location":"python_api/datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix","title":"<code>gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset with features for Locus to Gene prediction.</p> <p>Attributes:</p> Name Type Description <code>features_list</code> <code>list[str] | None</code> <p>List of features to use. If None, all possible features are used.</p> Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code> <pre><code>@dataclass\nclass L2GFeatureMatrix(Dataset):\n    \"\"\"Dataset with features for Locus to Gene prediction.\n\n    Attributes:\n        features_list (list[str] | None): List of features to use. If None, all possible features are used.\n    \"\"\"\n\n    features_list: list[str] | None = None\n\n    def __post_init__(self: L2GFeatureMatrix) -&gt; None:\n        \"\"\"Post-initialisation to set the features list. If not provided, all columns except the fixed ones are used.\"\"\"\n        fixed_cols = [\"studyLocusId\", \"geneId\", \"goldStandardSet\"]\n        self.features_list = self.features_list or [\n            col for col in self._df.columns if col not in fixed_cols\n        ]\n\n    @classmethod\n    def generate_features(\n        cls: Type[L2GFeatureMatrix],\n        features_list: list[str],\n        study_locus: StudyLocus,\n        study_index: StudyIndex,\n        variant_gene: V2G,\n        colocalisation: Colocalisation,\n    ) -&gt; L2GFeatureMatrix:\n        \"\"\"Generate features from the gentropy datasets.\n\n        Args:\n            features_list (list[str]): List of features to generate\n            study_locus (StudyLocus): Study locus dataset\n            study_index (StudyIndex): Study index dataset\n            variant_gene (V2G): Variant to gene dataset\n            colocalisation (Colocalisation): Colocalisation dataset\n\n        Returns:\n            L2GFeatureMatrix: L2G feature matrix dataset\n\n        Raises:\n            ValueError: If the feature matrix is empty\n        \"\"\"\n        if features_dfs := [\n            # Extract features\n            ColocalisationFactory._get_coloc_features(\n                study_locus, study_index, colocalisation\n            ).df,\n            StudyLocusFactory._get_tss_distance_features(study_locus, variant_gene).df,\n            StudyLocusFactory._get_vep_features(study_locus, variant_gene).df,\n        ]:\n            fm = reduce(\n                lambda x, y: x.unionByName(y),\n                features_dfs,\n            )\n        else:\n            raise ValueError(\"No features found\")\n\n        # raise error if the feature matrix is empty\n        return cls(\n            _df=convert_from_long_to_wide(\n                fm, [\"studyLocusId\", \"geneId\"], \"featureName\", \"featureValue\"\n            ),\n            _schema=cls.get_schema(),\n            features_list=features_list,\n        )\n\n    @classmethod\n    def get_schema(cls: type[L2GFeatureMatrix]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2gFeatureMatrix dataset.\n\n        Returns:\n            StructType: Schema for the L2gFeatureMatrix dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_feature_matrix.json\")\n\n    def calculate_feature_missingness_rate(\n        self: L2GFeatureMatrix,\n    ) -&gt; dict[str, float]:\n        \"\"\"Calculate the proportion of missing values in each feature.\n\n        Returns:\n            dict[str, float]: Dictionary of feature names and their missingness rate.\n\n        Raises:\n            ValueError: If no features are found.\n        \"\"\"\n        total_count = self._df.count()\n        if not self.features_list:\n            raise ValueError(\"No features found\")\n\n        return {\n            feature: (\n                self._df.filter(\n                    (self._df[feature].isNull()) | (self._df[feature] == 0)\n                ).count()\n                / total_count\n            )\n            for feature in self.features_list\n        }\n\n    def fill_na(\n        self: L2GFeatureMatrix, value: float = 0.0, subset: list[str] | None = None\n    ) -&gt; L2GFeatureMatrix:\n        \"\"\"Fill missing values in a column with a given value.\n\n        Args:\n            value (float): Value to replace missing values with. Defaults to 0.0.\n            subset (list[str] | None): Subset of columns to consider. Defaults to None.\n\n        Returns:\n            L2GFeatureMatrix: L2G feature matrix dataset\n        \"\"\"\n        self.df = self._df.fillna(value, subset=subset)\n        return self\n\n    def select_features(\n        self: L2GFeatureMatrix, features_list: list[str] | None\n    ) -&gt; L2GFeatureMatrix:\n        \"\"\"Select a subset of features from the feature matrix.\n\n        Args:\n            features_list (list[str] | None): List of features to select\n\n        Returns:\n            L2GFeatureMatrix: L2G feature matrix dataset\n        \"\"\"\n        features_list = features_list or self.features_list\n        fixed_cols = [\"studyLocusId\", \"geneId\", \"goldStandardSet\"]\n        self.df = self._df.select(fixed_cols + features_list)  # type: ignore\n        return self\n\n    def train_test_split(\n        self: L2GFeatureMatrix, fraction: float\n    ) -&gt; tuple[L2GFeatureMatrix, L2GFeatureMatrix]:\n        \"\"\"Split the dataset into training and test sets.\n\n        Args:\n            fraction (float): Fraction of the dataset to use for training\n\n        Returns:\n            tuple[L2GFeatureMatrix, L2GFeatureMatrix]: Training and test datasets\n        \"\"\"\n        train, test = self._df.randomSplit([fraction, 1 - fraction], seed=42)\n        return (\n            L2GFeatureMatrix(\n                _df=train, _schema=L2GFeatureMatrix.get_schema()\n            ).persist(),\n            L2GFeatureMatrix(_df=test, _schema=L2GFeatureMatrix.get_schema()).persist(),\n        )\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.calculate_feature_missingness_rate","title":"<code>calculate_feature_missingness_rate() -&gt; dict[str, float]</code>","text":"<p>Calculate the proportion of missing values in each feature.</p> <p>Returns:</p> Type Description <code>dict[str, float]</code> <p>dict[str, float]: Dictionary of feature names and their missingness rate.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If no features are found.</p> Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code> <pre><code>def calculate_feature_missingness_rate(\n    self: L2GFeatureMatrix,\n) -&gt; dict[str, float]:\n    \"\"\"Calculate the proportion of missing values in each feature.\n\n    Returns:\n        dict[str, float]: Dictionary of feature names and their missingness rate.\n\n    Raises:\n        ValueError: If no features are found.\n    \"\"\"\n    total_count = self._df.count()\n    if not self.features_list:\n        raise ValueError(\"No features found\")\n\n    return {\n        feature: (\n            self._df.filter(\n                (self._df[feature].isNull()) | (self._df[feature] == 0)\n            ).count()\n            / total_count\n        )\n        for feature in self.features_list\n    }\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.fill_na","title":"<code>fill_na(value: float = 0.0, subset: list[str] | None = None) -&gt; L2GFeatureMatrix</code>","text":"<p>Fill missing values in a column with a given value.</p> <p>Parameters:</p> Name Type Description Default <code>value</code> <code>float</code> <p>Value to replace missing values with. Defaults to 0.0.</p> <code>0.0</code> <code>subset</code> <code>list[str] | None</code> <p>Subset of columns to consider. Defaults to None.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>L2GFeatureMatrix</code> <code>L2GFeatureMatrix</code> <p>L2G feature matrix dataset</p> Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code> <pre><code>def fill_na(\n    self: L2GFeatureMatrix, value: float = 0.0, subset: list[str] | None = None\n) -&gt; L2GFeatureMatrix:\n    \"\"\"Fill missing values in a column with a given value.\n\n    Args:\n        value (float): Value to replace missing values with. Defaults to 0.0.\n        subset (list[str] | None): Subset of columns to consider. Defaults to None.\n\n    Returns:\n        L2GFeatureMatrix: L2G feature matrix dataset\n    \"\"\"\n    self.df = self._df.fillna(value, subset=subset)\n    return self\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.generate_features","title":"<code>generate_features(features_list: list[str], study_locus: StudyLocus, study_index: StudyIndex, variant_gene: V2G, colocalisation: Colocalisation) -&gt; L2GFeatureMatrix</code>  <code>classmethod</code>","text":"<p>Generate features from the gentropy datasets.</p> <p>Parameters:</p> Name Type Description Default <code>features_list</code> <code>list[str]</code> <p>List of features to generate</p> required <code>study_locus</code> <code>StudyLocus</code> <p>Study locus dataset</p> required <code>study_index</code> <code>StudyIndex</code> <p>Study index dataset</p> required <code>variant_gene</code> <code>V2G</code> <p>Variant to gene dataset</p> required <code>colocalisation</code> <code>Colocalisation</code> <p>Colocalisation dataset</p> required <p>Returns:</p> Name Type Description <code>L2GFeatureMatrix</code> <code>L2GFeatureMatrix</code> <p>L2G feature matrix dataset</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the feature matrix is empty</p> Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code> <pre><code>@classmethod\ndef generate_features(\n    cls: Type[L2GFeatureMatrix],\n    features_list: list[str],\n    study_locus: StudyLocus,\n    study_index: StudyIndex,\n    variant_gene: V2G,\n    colocalisation: Colocalisation,\n) -&gt; L2GFeatureMatrix:\n    \"\"\"Generate features from the gentropy datasets.\n\n    Args:\n        features_list (list[str]): List of features to generate\n        study_locus (StudyLocus): Study locus dataset\n        study_index (StudyIndex): Study index dataset\n        variant_gene (V2G): Variant to gene dataset\n        colocalisation (Colocalisation): Colocalisation dataset\n\n    Returns:\n        L2GFeatureMatrix: L2G feature matrix dataset\n\n    Raises:\n        ValueError: If the feature matrix is empty\n    \"\"\"\n    if features_dfs := [\n        # Extract features\n        ColocalisationFactory._get_coloc_features(\n            study_locus, study_index, colocalisation\n        ).df,\n        StudyLocusFactory._get_tss_distance_features(study_locus, variant_gene).df,\n        StudyLocusFactory._get_vep_features(study_locus, variant_gene).df,\n    ]:\n        fm = reduce(\n            lambda x, y: x.unionByName(y),\n            features_dfs,\n        )\n    else:\n        raise ValueError(\"No features found\")\n\n    # raise error if the feature matrix is empty\n    return cls(\n        _df=convert_from_long_to_wide(\n            fm, [\"studyLocusId\", \"geneId\"], \"featureName\", \"featureValue\"\n        ),\n        _schema=cls.get_schema(),\n        features_list=features_list,\n    )\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2gFeatureMatrix dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the L2gFeatureMatrix dataset</p> Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GFeatureMatrix]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2gFeatureMatrix dataset.\n\n    Returns:\n        StructType: Schema for the L2gFeatureMatrix dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_feature_matrix.json\")\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.select_features","title":"<code>select_features(features_list: list[str] | None) -&gt; L2GFeatureMatrix</code>","text":"<p>Select a subset of features from the feature matrix.</p> <p>Parameters:</p> Name Type Description Default <code>features_list</code> <code>list[str] | None</code> <p>List of features to select</p> required <p>Returns:</p> Name Type Description <code>L2GFeatureMatrix</code> <code>L2GFeatureMatrix</code> <p>L2G feature matrix dataset</p> Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code> <pre><code>def select_features(\n    self: L2GFeatureMatrix, features_list: list[str] | None\n) -&gt; L2GFeatureMatrix:\n    \"\"\"Select a subset of features from the feature matrix.\n\n    Args:\n        features_list (list[str] | None): List of features to select\n\n    Returns:\n        L2GFeatureMatrix: L2G feature matrix dataset\n    \"\"\"\n    features_list = features_list or self.features_list\n    fixed_cols = [\"studyLocusId\", \"geneId\", \"goldStandardSet\"]\n    self.df = self._df.select(fixed_cols + features_list)  # type: ignore\n    return self\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/#gentropy.dataset.l2g_feature_matrix.L2GFeatureMatrix.train_test_split","title":"<code>train_test_split(fraction: float) -&gt; tuple[L2GFeatureMatrix, L2GFeatureMatrix]</code>","text":"<p>Split the dataset into training and test sets.</p> <p>Parameters:</p> Name Type Description Default <code>fraction</code> <code>float</code> <p>Fraction of the dataset to use for training</p> required <p>Returns:</p> Type Description <code>tuple[L2GFeatureMatrix, L2GFeatureMatrix]</code> <p>tuple[L2GFeatureMatrix, L2GFeatureMatrix]: Training and test datasets</p> Source code in <code>src/gentropy/dataset/l2g_feature_matrix.py</code> <pre><code>def train_test_split(\n    self: L2GFeatureMatrix, fraction: float\n) -&gt; tuple[L2GFeatureMatrix, L2GFeatureMatrix]:\n    \"\"\"Split the dataset into training and test sets.\n\n    Args:\n        fraction (float): Fraction of the dataset to use for training\n\n    Returns:\n        tuple[L2GFeatureMatrix, L2GFeatureMatrix]: Training and test datasets\n    \"\"\"\n    train, test = self._df.randomSplit([fraction, 1 - fraction], seed=42)\n    return (\n        L2GFeatureMatrix(\n            _df=train, _schema=L2GFeatureMatrix.get_schema()\n        ).persist(),\n        L2GFeatureMatrix(_df=test, _schema=L2GFeatureMatrix.get_schema()).persist(),\n    )\n</code></pre>"},{"location":"python_api/datasets/l2g_feature_matrix/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- geneId: string (nullable = false)\n |-- goldStandardSet: string (nullable = true)\n |-- distanceTssMean: float (nullable = true)\n |-- distanceTssMinimum: float (nullable = true)\n |-- vepMaximumNeighborhood: float (nullable = true)\n |-- vepMaximum: float (nullable = true)\n |-- vepMeanNeighborhood: float (nullable = true)\n |-- vepMean: float (nullable = true)\n |-- eqtlColocClppMaximum: float (nullable = true)\n |-- eqtlColocClppMaximumNeighborhood: float (nullable = true)\n |-- eqtlColocLlrMaximum: float (nullable = true)\n |-- eqtlColocLlrMaximumNeighborhood: float (nullable = true)\n |-- pqtlColocClppMaximum: float (nullable = true)\n |-- pqtlColocClppMaximumNeighborhood: float (nullable = true)\n |-- pqtlColocLlrMaximum: float (nullable = true)\n |-- pqtlColocLlrMaximumNeighborhood: float (nullable = true)\n |-- sqtlColocClppMaximum: float (nullable = true)\n |-- sqtlColocClppMaximumNeighborhood: float (nullable = true)\n |-- sqtlColocLlrMaximum: float (nullable = true)\n |-- sqtlColocLlrMaximumNeighborhood: float (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/l2g_gold_standard/","title":"L2G Gold Standard","text":""},{"location":"python_api/datasets/l2g_gold_standard/#gentropy.dataset.l2g_gold_standard.L2GGoldStandard","title":"<code>gentropy.dataset.l2g_gold_standard.L2GGoldStandard</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>L2G gold standard dataset.</p> Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code> <pre><code>@dataclass\nclass L2GGoldStandard(Dataset):\n    \"\"\"L2G gold standard dataset.\"\"\"\n\n    INTERACTION_THRESHOLD = 0.7\n    GS_POSITIVE_LABEL = \"positive\"\n    GS_NEGATIVE_LABEL = \"negative\"\n\n    @classmethod\n    def from_otg_curation(\n        cls: type[L2GGoldStandard],\n        gold_standard_curation: DataFrame,\n        v2g: V2G,\n        study_locus_overlap: StudyLocusOverlap,\n        interactions: DataFrame,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Initialise L2GGoldStandard from source dataset.\n\n        Args:\n            gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from\n            v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n            study_locus_overlap (StudyLocusOverlap): Study locus overlap dataset to remove duplicated loci\n            interactions (DataFrame): Gene-gene interactions dataset to remove negative cases where the gene interacts with a positive gene\n\n        Returns:\n            L2GGoldStandard: L2G Gold Standard dataset\n        \"\"\"\n        from gentropy.datasource.open_targets.l2g_gold_standard import (\n            OpenTargetsL2GGoldStandard,\n        )\n\n        interactions_df = cls.process_gene_interactions(interactions)\n\n        return (\n            OpenTargetsL2GGoldStandard.as_l2g_gold_standard(gold_standard_curation, v2g)\n            # .filter_unique_associations(study_locus_overlap)\n            .remove_false_negatives(interactions_df)\n        )\n\n    @classmethod\n    def get_schema(cls: type[L2GGoldStandard]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2GGoldStandard dataset.\n\n        Returns:\n            StructType: Spark schema for the L2GGoldStandard dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_gold_standard.json\")\n\n    @classmethod\n    def process_gene_interactions(\n        cls: Type[L2GGoldStandard], interactions: DataFrame\n    ) -&gt; DataFrame:\n        \"\"\"Extract top scoring gene-gene interaction from the interactions dataset of the Platform.\n\n        Args:\n            interactions (DataFrame): Gene-gene interactions dataset from the Open Targets Platform\n\n        Returns:\n            DataFrame: Top scoring gene-gene interaction per pair of genes\n\n        Examples:\n            &gt;&gt;&gt; interactions = spark.createDataFrame([(\"gene1\", \"gene2\", 0.8), (\"gene1\", \"gene2\", 0.5), (\"gene2\", \"gene3\", 0.7)], [\"targetA\", \"targetB\", \"scoring\"])\n            &gt;&gt;&gt; L2GGoldStandard.process_gene_interactions(interactions).show()\n            +-------+-------+-----+\n            |geneIdA|geneIdB|score|\n            +-------+-------+-----+\n            |  gene1|  gene2|  0.8|\n            |  gene2|  gene3|  0.7|\n            +-------+-------+-----+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        return get_record_with_maximum_value(\n            interactions,\n            [\"targetA\", \"targetB\"],\n            \"scoring\",\n        ).selectExpr(\n            \"targetA as geneIdA\",\n            \"targetB as geneIdB\",\n            \"scoring as score\",\n        )\n\n    def filter_unique_associations(\n        self: L2GGoldStandard,\n        study_locus_overlap: StudyLocusOverlap,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Refines the gold standard to filter out loci that are not independent.\n\n        Rules:\n        - If two loci point to the same gene, one positive and one negative, and have overlapping variants, we keep the positive one.\n        - If two loci point to the same gene, both positive or negative, and have overlapping variants, we drop one.\n        - If two loci point to different genes, and have overlapping variants, we keep both.\n\n        Args:\n            study_locus_overlap (StudyLocusOverlap): A dataset detailing variants that overlap between StudyLocus.\n\n        Returns:\n            L2GGoldStandard: L2GGoldStandard updated to exclude false negatives and redundant positives.\n        \"\"\"\n        squared_overlaps = study_locus_overlap._convert_to_square_matrix()\n        unique_associations = (\n            self.df.alias(\"left\")\n            # identify all the study loci that point to the same gene\n            .withColumn(\n                \"sl_same_gene\",\n                f.collect_set(\"studyLocusId\").over(Window.partitionBy(\"geneId\")),\n            )\n            # identify all the study loci that have an overlapping variant\n            .join(\n                squared_overlaps.df.alias(\"right\"),\n                (f.col(\"left.studyLocusId\") == f.col(\"right.leftStudyLocusId\"))\n                &amp; (f.col(\"left.variantId\") == f.col(\"right.tagVariantId\")),\n                \"left\",\n            )\n            .withColumn(\n                \"overlaps\",\n                f.when(f.col(\"right.tagVariantId\").isNotNull(), f.lit(True)).otherwise(\n                    f.lit(False)\n                ),\n            )\n            # drop redundant rows: where the variantid overlaps and the gene is \"explained\" by more than one study locus\n            .filter(~((f.size(\"sl_same_gene\") &gt; 1) &amp; (f.col(\"overlaps\") == 1)))\n            .select(*self.df.columns)\n        )\n        return L2GGoldStandard(_df=unique_associations, _schema=self.get_schema())\n\n    def remove_false_negatives(\n        self: L2GGoldStandard,\n        interactions_df: DataFrame,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Refines the gold standard to remove negative gold standard instances where the gene interacts with a positive gene.\n\n        Args:\n            interactions_df (DataFrame): Top scoring gene-gene interaction per pair of genes\n\n        Returns:\n            L2GGoldStandard: A refined set of locus-to-gene associations with increased reliability, having excluded loci that were likely false negatives due to gene-gene interaction confounding.\n        \"\"\"\n        squared_interactions = interactions_df.unionByName(\n            interactions_df.selectExpr(\n                \"geneIdB as geneIdA\", \"geneIdA as geneIdB\", \"score\"\n            )\n        ).filter(f.col(\"score\") &gt; self.INTERACTION_THRESHOLD)\n        df = (\n            self.df.alias(\"left\")\n            .join(\n                # bring gene partners\n                squared_interactions.alias(\"right\"),\n                f.col(\"left.geneId\") == f.col(\"right.geneIdA\"),\n                \"left\",\n            )\n            .withColumnRenamed(\"geneIdB\", \"interactorGeneId\")\n            .join(\n                # bring gold standard status for gene partners\n                self.df.selectExpr(\n                    \"geneId as interactorGeneId\",\n                    \"goldStandardSet as interactorGeneIdGoldStandardSet\",\n                ),\n                \"interactorGeneId\",\n                \"left\",\n            )\n            # remove self-interactions\n            .filter(\n                (f.col(\"geneId\") != f.col(\"interactorGeneId\"))\n                | (f.col(\"interactorGeneId\").isNull())\n            )\n            # remove false negatives\n            .filter(\n                # drop rows where the GS gene is negative but the interactor is a GS positive\n                ~(f.col(\"goldStandardSet\") == \"negative\")\n                &amp; (f.col(\"interactorGeneIdGoldStandardSet\") == \"positive\")\n                |\n                # keep rows where the gene does not interact\n                (f.col(\"interactorGeneId\").isNull())\n            )\n            .select(*self.df.columns)\n            .distinct()\n        )\n        return L2GGoldStandard(_df=df, _schema=self.get_schema())\n</code></pre>"},{"location":"python_api/datasets/l2g_gold_standard/#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.filter_unique_associations","title":"<code>filter_unique_associations(study_locus_overlap: StudyLocusOverlap) -&gt; L2GGoldStandard</code>","text":"<p>Refines the gold standard to filter out loci that are not independent.</p> <p>Rules: - If two loci point to the same gene, one positive and one negative, and have overlapping variants, we keep the positive one. - If two loci point to the same gene, both positive or negative, and have overlapping variants, we drop one. - If two loci point to different genes, and have overlapping variants, we keep both.</p> <p>Parameters:</p> Name Type Description Default <code>study_locus_overlap</code> <code>StudyLocusOverlap</code> <p>A dataset detailing variants that overlap between StudyLocus.</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>L2GGoldStandard updated to exclude false negatives and redundant positives.</p> Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code> <pre><code>def filter_unique_associations(\n    self: L2GGoldStandard,\n    study_locus_overlap: StudyLocusOverlap,\n) -&gt; L2GGoldStandard:\n    \"\"\"Refines the gold standard to filter out loci that are not independent.\n\n    Rules:\n    - If two loci point to the same gene, one positive and one negative, and have overlapping variants, we keep the positive one.\n    - If two loci point to the same gene, both positive or negative, and have overlapping variants, we drop one.\n    - If two loci point to different genes, and have overlapping variants, we keep both.\n\n    Args:\n        study_locus_overlap (StudyLocusOverlap): A dataset detailing variants that overlap between StudyLocus.\n\n    Returns:\n        L2GGoldStandard: L2GGoldStandard updated to exclude false negatives and redundant positives.\n    \"\"\"\n    squared_overlaps = study_locus_overlap._convert_to_square_matrix()\n    unique_associations = (\n        self.df.alias(\"left\")\n        # identify all the study loci that point to the same gene\n        .withColumn(\n            \"sl_same_gene\",\n            f.collect_set(\"studyLocusId\").over(Window.partitionBy(\"geneId\")),\n        )\n        # identify all the study loci that have an overlapping variant\n        .join(\n            squared_overlaps.df.alias(\"right\"),\n            (f.col(\"left.studyLocusId\") == f.col(\"right.leftStudyLocusId\"))\n            &amp; (f.col(\"left.variantId\") == f.col(\"right.tagVariantId\")),\n            \"left\",\n        )\n        .withColumn(\n            \"overlaps\",\n            f.when(f.col(\"right.tagVariantId\").isNotNull(), f.lit(True)).otherwise(\n                f.lit(False)\n            ),\n        )\n        # drop redundant rows: where the variantid overlaps and the gene is \"explained\" by more than one study locus\n        .filter(~((f.size(\"sl_same_gene\") &gt; 1) &amp; (f.col(\"overlaps\") == 1)))\n        .select(*self.df.columns)\n    )\n    return L2GGoldStandard(_df=unique_associations, _schema=self.get_schema())\n</code></pre>"},{"location":"python_api/datasets/l2g_gold_standard/#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.from_otg_curation","title":"<code>from_otg_curation(gold_standard_curation: DataFrame, v2g: V2G, study_locus_overlap: StudyLocusOverlap, interactions: DataFrame) -&gt; L2GGoldStandard</code>  <code>classmethod</code>","text":"<p>Initialise L2GGoldStandard from source dataset.</p> <p>Parameters:</p> Name Type Description Default <code>gold_standard_curation</code> <code>DataFrame</code> <p>Gold standard curation dataframe, extracted from</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset to bring distance between a variant and a gene's TSS</p> required <code>study_locus_overlap</code> <code>StudyLocusOverlap</code> <p>Study locus overlap dataset to remove duplicated loci</p> required <code>interactions</code> <code>DataFrame</code> <p>Gene-gene interactions dataset to remove negative cases where the gene interacts with a positive gene</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>L2G Gold Standard dataset</p> Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef from_otg_curation(\n    cls: type[L2GGoldStandard],\n    gold_standard_curation: DataFrame,\n    v2g: V2G,\n    study_locus_overlap: StudyLocusOverlap,\n    interactions: DataFrame,\n) -&gt; L2GGoldStandard:\n    \"\"\"Initialise L2GGoldStandard from source dataset.\n\n    Args:\n        gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from\n        v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n        study_locus_overlap (StudyLocusOverlap): Study locus overlap dataset to remove duplicated loci\n        interactions (DataFrame): Gene-gene interactions dataset to remove negative cases where the gene interacts with a positive gene\n\n    Returns:\n        L2GGoldStandard: L2G Gold Standard dataset\n    \"\"\"\n    from gentropy.datasource.open_targets.l2g_gold_standard import (\n        OpenTargetsL2GGoldStandard,\n    )\n\n    interactions_df = cls.process_gene_interactions(interactions)\n\n    return (\n        OpenTargetsL2GGoldStandard.as_l2g_gold_standard(gold_standard_curation, v2g)\n        # .filter_unique_associations(study_locus_overlap)\n        .remove_false_negatives(interactions_df)\n    )\n</code></pre>"},{"location":"python_api/datasets/l2g_gold_standard/#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2GGoldStandard dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Spark schema for the L2GGoldStandard dataset</p> Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GGoldStandard]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2GGoldStandard dataset.\n\n    Returns:\n        StructType: Spark schema for the L2GGoldStandard dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_gold_standard.json\")\n</code></pre>"},{"location":"python_api/datasets/l2g_gold_standard/#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.process_gene_interactions","title":"<code>process_gene_interactions(interactions: DataFrame) -&gt; DataFrame</code>  <code>classmethod</code>","text":"<p>Extract top scoring gene-gene interaction from the interactions dataset of the Platform.</p> <p>Parameters:</p> Name Type Description Default <code>interactions</code> <code>DataFrame</code> <p>Gene-gene interactions dataset from the Open Targets Platform</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Top scoring gene-gene interaction per pair of genes</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; interactions = spark.createDataFrame([(\"gene1\", \"gene2\", 0.8), (\"gene1\", \"gene2\", 0.5), (\"gene2\", \"gene3\", 0.7)], [\"targetA\", \"targetB\", \"scoring\"])\n&gt;&gt;&gt; L2GGoldStandard.process_gene_interactions(interactions).show()\n+-------+-------+-----+\n|geneIdA|geneIdB|score|\n+-------+-------+-----+\n|  gene1|  gene2|  0.8|\n|  gene2|  gene3|  0.7|\n+-------+-------+-----+\n</code></pre> Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef process_gene_interactions(\n    cls: Type[L2GGoldStandard], interactions: DataFrame\n) -&gt; DataFrame:\n    \"\"\"Extract top scoring gene-gene interaction from the interactions dataset of the Platform.\n\n    Args:\n        interactions (DataFrame): Gene-gene interactions dataset from the Open Targets Platform\n\n    Returns:\n        DataFrame: Top scoring gene-gene interaction per pair of genes\n\n    Examples:\n        &gt;&gt;&gt; interactions = spark.createDataFrame([(\"gene1\", \"gene2\", 0.8), (\"gene1\", \"gene2\", 0.5), (\"gene2\", \"gene3\", 0.7)], [\"targetA\", \"targetB\", \"scoring\"])\n        &gt;&gt;&gt; L2GGoldStandard.process_gene_interactions(interactions).show()\n        +-------+-------+-----+\n        |geneIdA|geneIdB|score|\n        +-------+-------+-----+\n        |  gene1|  gene2|  0.8|\n        |  gene2|  gene3|  0.7|\n        +-------+-------+-----+\n        &lt;BLANKLINE&gt;\n    \"\"\"\n    return get_record_with_maximum_value(\n        interactions,\n        [\"targetA\", \"targetB\"],\n        \"scoring\",\n    ).selectExpr(\n        \"targetA as geneIdA\",\n        \"targetB as geneIdB\",\n        \"scoring as score\",\n    )\n</code></pre>"},{"location":"python_api/datasets/l2g_gold_standard/#gentropy.dataset.l2g_gold_standard.L2GGoldStandard.remove_false_negatives","title":"<code>remove_false_negatives(interactions_df: DataFrame) -&gt; L2GGoldStandard</code>","text":"<p>Refines the gold standard to remove negative gold standard instances where the gene interacts with a positive gene.</p> <p>Parameters:</p> Name Type Description Default <code>interactions_df</code> <code>DataFrame</code> <p>Top scoring gene-gene interaction per pair of genes</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>A refined set of locus-to-gene associations with increased reliability, having excluded loci that were likely false negatives due to gene-gene interaction confounding.</p> Source code in <code>src/gentropy/dataset/l2g_gold_standard.py</code> <pre><code>def remove_false_negatives(\n    self: L2GGoldStandard,\n    interactions_df: DataFrame,\n) -&gt; L2GGoldStandard:\n    \"\"\"Refines the gold standard to remove negative gold standard instances where the gene interacts with a positive gene.\n\n    Args:\n        interactions_df (DataFrame): Top scoring gene-gene interaction per pair of genes\n\n    Returns:\n        L2GGoldStandard: A refined set of locus-to-gene associations with increased reliability, having excluded loci that were likely false negatives due to gene-gene interaction confounding.\n    \"\"\"\n    squared_interactions = interactions_df.unionByName(\n        interactions_df.selectExpr(\n            \"geneIdB as geneIdA\", \"geneIdA as geneIdB\", \"score\"\n        )\n    ).filter(f.col(\"score\") &gt; self.INTERACTION_THRESHOLD)\n    df = (\n        self.df.alias(\"left\")\n        .join(\n            # bring gene partners\n            squared_interactions.alias(\"right\"),\n            f.col(\"left.geneId\") == f.col(\"right.geneIdA\"),\n            \"left\",\n        )\n        .withColumnRenamed(\"geneIdB\", \"interactorGeneId\")\n        .join(\n            # bring gold standard status for gene partners\n            self.df.selectExpr(\n                \"geneId as interactorGeneId\",\n                \"goldStandardSet as interactorGeneIdGoldStandardSet\",\n            ),\n            \"interactorGeneId\",\n            \"left\",\n        )\n        # remove self-interactions\n        .filter(\n            (f.col(\"geneId\") != f.col(\"interactorGeneId\"))\n            | (f.col(\"interactorGeneId\").isNull())\n        )\n        # remove false negatives\n        .filter(\n            # drop rows where the GS gene is negative but the interactor is a GS positive\n            ~(f.col(\"goldStandardSet\") == \"negative\")\n            &amp; (f.col(\"interactorGeneIdGoldStandardSet\") == \"positive\")\n            |\n            # keep rows where the gene does not interact\n            (f.col(\"interactorGeneId\").isNull())\n        )\n        .select(*self.df.columns)\n        .distinct()\n    )\n    return L2GGoldStandard(_df=df, _schema=self.get_schema())\n</code></pre>"},{"location":"python_api/datasets/l2g_gold_standard/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- variantId: string (nullable = false)\n |-- studyId: string (nullable = false)\n |-- geneId: string (nullable = false)\n |-- goldStandardSet: string (nullable = false)\n |-- sources: array (nullable = true)\n |    |-- element: string (containsNull = true)\n</code></pre>"},{"location":"python_api/datasets/l2g_prediction/","title":"L2G Prediction","text":""},{"location":"python_api/datasets/l2g_prediction/#gentropy.dataset.l2g_prediction.L2GPrediction","title":"<code>gentropy.dataset.l2g_prediction.L2GPrediction</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset that contains the Locus to Gene predictions.</p> <p>It is the result of applying the L2G model on a feature matrix, which contains all the study/locus pairs and their functional annotations. The score column informs the confidence of the prediction that a gene is causal to an association.</p> Source code in <code>src/gentropy/dataset/l2g_prediction.py</code> <pre><code>@dataclass\nclass L2GPrediction(Dataset):\n    \"\"\"Dataset that contains the Locus to Gene predictions.\n\n    It is the result of applying the L2G model on a feature matrix, which contains all\n    the study/locus pairs and their functional annotations. The score column informs the\n    confidence of the prediction that a gene is causal to an association.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[L2GPrediction]) -&gt; StructType:\n        \"\"\"Provides the schema for the L2GPrediction dataset.\n\n        Returns:\n            StructType: Schema for the L2GPrediction dataset\n        \"\"\"\n        return parse_spark_schema(\"l2g_predictions.json\")\n\n    @classmethod\n    def from_credible_set(\n        cls: Type[L2GPrediction],\n        model_path: str,\n        features_list: list[str],\n        study_locus: StudyLocus,\n        study_index: StudyIndex,\n        v2g: V2G,\n        coloc: Colocalisation,\n    ) -&gt; L2GPrediction:\n        \"\"\"Extract L2G predictions for a set of credible sets derived from GWAS.\n\n        Args:\n            model_path (str): Path to the fitted model\n            features_list (list[str]): List of features to use for the model\n            study_locus (StudyLocus): Study locus dataset\n            study_index (StudyIndex): Study index dataset\n            v2g (V2G): Variant to gene dataset\n            coloc (Colocalisation): Colocalisation dataset\n\n        Returns:\n            L2GPrediction: L2G dataset\n        \"\"\"\n        fm = L2GFeatureMatrix.generate_features(\n            features_list=features_list,\n            study_locus=study_locus,\n            study_index=study_index,\n            variant_gene=v2g,\n            colocalisation=coloc,\n        ).fill_na()\n\n        gwas_fm = L2GFeatureMatrix(\n            _df=(\n                fm.df.join(\n                    study_locus.filter_by_study_type(\"gwas\", study_index).df,\n                    on=\"studyLocusId\",\n                )\n            ),\n            _schema=cls.get_schema(),\n        )\n        return L2GPrediction(\n            # Load and apply fitted model\n            _df=(\n                LocusToGeneModel.load_from_disk(\n                    model_path,\n                    features_list=features_list,\n                )\n                .predict(gwas_fm)\n                # the probability of the positive class is the second element inside the probability array\n                # - this is selected as the L2G probability\n                .select(\n                    \"studyLocusId\",\n                    \"geneId\",\n                    vector_to_array(f.col(\"probability\"))[1].alias(\"score\"),\n                )\n            ),\n            _schema=cls.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasets/l2g_prediction/#gentropy.dataset.l2g_prediction.L2GPrediction.from_credible_set","title":"<code>from_credible_set(model_path: str, features_list: list[str], study_locus: StudyLocus, study_index: StudyIndex, v2g: V2G, coloc: Colocalisation) -&gt; L2GPrediction</code>  <code>classmethod</code>","text":"<p>Extract L2G predictions for a set of credible sets derived from GWAS.</p> <p>Parameters:</p> Name Type Description Default <code>model_path</code> <code>str</code> <p>Path to the fitted model</p> required <code>features_list</code> <code>list[str]</code> <p>List of features to use for the model</p> required <code>study_locus</code> <code>StudyLocus</code> <p>Study locus dataset</p> required <code>study_index</code> <code>StudyIndex</code> <p>Study index dataset</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset</p> required <code>coloc</code> <code>Colocalisation</code> <p>Colocalisation dataset</p> required <p>Returns:</p> Name Type Description <code>L2GPrediction</code> <code>L2GPrediction</code> <p>L2G dataset</p> Source code in <code>src/gentropy/dataset/l2g_prediction.py</code> <pre><code>@classmethod\ndef from_credible_set(\n    cls: Type[L2GPrediction],\n    model_path: str,\n    features_list: list[str],\n    study_locus: StudyLocus,\n    study_index: StudyIndex,\n    v2g: V2G,\n    coloc: Colocalisation,\n) -&gt; L2GPrediction:\n    \"\"\"Extract L2G predictions for a set of credible sets derived from GWAS.\n\n    Args:\n        model_path (str): Path to the fitted model\n        features_list (list[str]): List of features to use for the model\n        study_locus (StudyLocus): Study locus dataset\n        study_index (StudyIndex): Study index dataset\n        v2g (V2G): Variant to gene dataset\n        coloc (Colocalisation): Colocalisation dataset\n\n    Returns:\n        L2GPrediction: L2G dataset\n    \"\"\"\n    fm = L2GFeatureMatrix.generate_features(\n        features_list=features_list,\n        study_locus=study_locus,\n        study_index=study_index,\n        variant_gene=v2g,\n        colocalisation=coloc,\n    ).fill_na()\n\n    gwas_fm = L2GFeatureMatrix(\n        _df=(\n            fm.df.join(\n                study_locus.filter_by_study_type(\"gwas\", study_index).df,\n                on=\"studyLocusId\",\n            )\n        ),\n        _schema=cls.get_schema(),\n    )\n    return L2GPrediction(\n        # Load and apply fitted model\n        _df=(\n            LocusToGeneModel.load_from_disk(\n                model_path,\n                features_list=features_list,\n            )\n            .predict(gwas_fm)\n            # the probability of the positive class is the second element inside the probability array\n            # - this is selected as the L2G probability\n            .select(\n                \"studyLocusId\",\n                \"geneId\",\n                vector_to_array(f.col(\"probability\"))[1].alias(\"score\"),\n            )\n        ),\n        _schema=cls.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasets/l2g_prediction/#gentropy.dataset.l2g_prediction.L2GPrediction.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the L2GPrediction dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the L2GPrediction dataset</p> Source code in <code>src/gentropy/dataset/l2g_prediction.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[L2GPrediction]) -&gt; StructType:\n    \"\"\"Provides the schema for the L2GPrediction dataset.\n\n    Returns:\n        StructType: Schema for the L2GPrediction dataset\n    \"\"\"\n    return parse_spark_schema(\"l2g_predictions.json\")\n</code></pre>"},{"location":"python_api/datasets/l2g_prediction/#schema","title":"Schema","text":""},{"location":"python_api/datasets/ld_index/","title":"LD Index","text":""},{"location":"python_api/datasets/ld_index/#gentropy.dataset.ld_index.LDIndex","title":"<code>gentropy.dataset.ld_index.LDIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset containing linkage desequilibrium information between variants.</p> Source code in <code>src/gentropy/dataset/ld_index.py</code> <pre><code>@dataclass\nclass LDIndex(Dataset):\n    \"\"\"Dataset containing linkage desequilibrium information between variants.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[LDIndex]) -&gt; StructType:\n        \"\"\"Provides the schema for the LDIndex dataset.\n\n        Returns:\n            StructType: Schema for the LDIndex dataset\n        \"\"\"\n        return parse_spark_schema(\"ld_index.json\")\n</code></pre>"},{"location":"python_api/datasets/ld_index/#gentropy.dataset.ld_index.LDIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the LDIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the LDIndex dataset</p> Source code in <code>src/gentropy/dataset/ld_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[LDIndex]) -&gt; StructType:\n    \"\"\"Provides the schema for the LDIndex dataset.\n\n    Returns:\n        StructType: Schema for the LDIndex dataset\n    \"\"\"\n    return parse_spark_schema(\"ld_index.json\")\n</code></pre>"},{"location":"python_api/datasets/ld_index/#schema","title":"Schema","text":"<pre><code>root\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- ldSet: array (nullable = false)\n |    |-- element: struct (containsNull = false)\n |    |    |-- tagVariantId: string (nullable = false)\n |    |    |-- rValues: array (nullable = false)\n |    |    |    |-- element: struct (containsNull = false)\n |    |    |    |    |-- population: string (nullable = false)\n |    |    |    |    |-- r: double (nullable = false)\n</code></pre>"},{"location":"python_api/datasets/study_index/","title":"Study Index","text":""},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex","title":"<code>gentropy.dataset.study_index.StudyIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Study index dataset.</p> <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>@dataclass\nclass StudyIndex(Dataset):\n    \"\"\"Study index dataset.\n\n    A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.\n    \"\"\"\n\n    @staticmethod\n    def _aggregate_samples_by_ancestry(merged: Column, ancestry: Column) -&gt; Column:\n        \"\"\"Aggregate sample counts by ancestry in a list of struct colmns.\n\n        Args:\n            merged (Column): A column representing merged data (list of structs).\n            ancestry (Column): The `ancestry` parameter is a column that represents the ancestry of each\n                sample. (a struct)\n\n        Returns:\n            Column: the modified \"merged\" column after aggregating the samples by ancestry.\n        \"\"\"\n        # Iterating over the list of ancestries and adding the sample size if label matches:\n        return f.transform(\n            merged,\n            lambda a: f.when(\n                a.ancestry == ancestry.ancestry,\n                f.struct(\n                    a.ancestry.alias(\"ancestry\"),\n                    (a.sampleSize + ancestry.sampleSize).alias(\"sampleSize\"),\n                ),\n            ).otherwise(a),\n        )\n\n    @staticmethod\n    def _map_ancestries_to_ld_population(gwas_ancestry_label: Column) -&gt; Column:\n        \"\"\"Normalise ancestry column from GWAS studies into reference LD panel based on a pre-defined map.\n\n        This function assumes all possible ancestry categories have a corresponding\n        LD panel in the LD index. It is very important to have the ancestry labels\n        moved to the LD panel map.\n\n        Args:\n            gwas_ancestry_label (Column): A struct column with ancestry label like Finnish,\n                European, African etc. and the corresponding sample size.\n\n        Returns:\n            Column: Struct column with the mapped LD population label and the sample size.\n        \"\"\"\n        # Loading ancestry label to LD population label:\n        json_dict = json.loads(\n            pkg_resources.read_text(\n                data, \"gwas_population_2_LD_panel_map.json\", encoding=\"utf-8\"\n            )\n        )\n        map_expr = f.create_map(*[f.lit(x) for x in chain(*json_dict.items())])\n\n        return f.struct(\n            map_expr[gwas_ancestry_label.ancestry].alias(\"ancestry\"),\n            gwas_ancestry_label.sampleSize.alias(\"sampleSize\"),\n        )\n\n    @classmethod\n    def get_schema(cls: type[StudyIndex]) -&gt; StructType:\n        \"\"\"Provide the schema for the StudyIndex dataset.\n\n        Returns:\n            StructType: The schema of the StudyIndex dataset.\n        \"\"\"\n        return parse_spark_schema(\"study_index.json\")\n\n    @classmethod\n    def aggregate_and_map_ancestries(\n        cls: type[StudyIndex], discovery_samples: Column\n    ) -&gt; Column:\n        \"\"\"Map ancestries to populations in the LD reference and calculate relative sample size.\n\n        Args:\n            discovery_samples (Column): A list of struct column. Has an `ancestry` column and a `sampleSize` columns\n\n        Returns:\n            Column: A list of struct with mapped LD population and their relative sample size.\n        \"\"\"\n        # Map ancestry categories to population labels of the LD index:\n        mapped_ancestries = f.transform(\n            discovery_samples, cls._map_ancestries_to_ld_population\n        )\n\n        # Aggregate sample sizes belonging to the same LD population:\n        aggregated_counts = f.aggregate(\n            mapped_ancestries,\n            f.array_distinct(\n                f.transform(\n                    mapped_ancestries,\n                    lambda x: f.struct(\n                        x.ancestry.alias(\"ancestry\"), f.lit(0.0).alias(\"sampleSize\")\n                    ),\n                )\n            ),\n            cls._aggregate_samples_by_ancestry,\n        )\n        # Getting total sample count:\n        total_sample_count = f.aggregate(\n            aggregated_counts, f.lit(0.0), lambda total, pop: total + pop.sampleSize\n        ).alias(\"sampleSize\")\n\n        # Calculating relative sample size for each LD population:\n        return f.transform(\n            aggregated_counts,\n            lambda ld_population: f.struct(\n                ld_population.ancestry.alias(\"ldPopulation\"),\n                (ld_population.sampleSize / total_sample_count).alias(\n                    \"relativeSampleSize\"\n                ),\n            ),\n        )\n\n    def study_type_lut(self: StudyIndex) -&gt; DataFrame:\n        \"\"\"Return a lookup table of study type.\n\n        Returns:\n            DataFrame: A dataframe containing `studyId` and `studyType` columns.\n        \"\"\"\n        return self.df.select(\"studyId\", \"studyType\")\n\n    def is_qtl(self: StudyIndex) -&gt; Column:\n        \"\"\"Return a boolean column with true values for QTL studies.\n\n        Returns:\n            Column: True if the study is a QTL study.\n        \"\"\"\n        return self.df.studyType.endswith(\"qtl\")\n\n    def is_gwas(self: StudyIndex) -&gt; Column:\n        \"\"\"Return a boolean column with true values for GWAS studies.\n\n        Returns:\n            Column: True if the study is a GWAS study.\n        \"\"\"\n        return self.df.studyType == \"gwas\"\n\n    def has_mapped_trait(self: StudyIndex) -&gt; Column:\n        \"\"\"Return a boolean column indicating if a study has mapped disease.\n\n        Returns:\n            Column: True if the study has mapped disease.\n        \"\"\"\n        return f.size(self.df.traitFromSourceMappedIds) &gt; 0\n\n    def is_quality_flagged(self: StudyIndex) -&gt; Column:\n        \"\"\"Return a boolean column indicating if a study is flagged due to quality issues.\n\n        Returns:\n            Column: True if the study is flagged.\n        \"\"\"\n        # Testing for the presence of the qualityControls column:\n        if \"qualityControls\" not in self.df.columns:\n            return f.lit(False)\n        else:\n            return f.size(self.df.qualityControls) != 0\n\n    def has_summarystats(self: StudyIndex) -&gt; Column:\n        \"\"\"Return a boolean column indicating if a study has harmonized summary statistics.\n\n        Returns:\n            Column: True if the study has harmonized summary statistics.\n        \"\"\"\n        return self.df.hasSumstats\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.aggregate_and_map_ancestries","title":"<code>aggregate_and_map_ancestries(discovery_samples: Column) -&gt; Column</code>  <code>classmethod</code>","text":"<p>Map ancestries to populations in the LD reference and calculate relative sample size.</p> <p>Parameters:</p> Name Type Description Default <code>discovery_samples</code> <code>Column</code> <p>A list of struct column. Has an <code>ancestry</code> column and a <code>sampleSize</code> columns</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>A list of struct with mapped LD population and their relative sample size.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>@classmethod\ndef aggregate_and_map_ancestries(\n    cls: type[StudyIndex], discovery_samples: Column\n) -&gt; Column:\n    \"\"\"Map ancestries to populations in the LD reference and calculate relative sample size.\n\n    Args:\n        discovery_samples (Column): A list of struct column. Has an `ancestry` column and a `sampleSize` columns\n\n    Returns:\n        Column: A list of struct with mapped LD population and their relative sample size.\n    \"\"\"\n    # Map ancestry categories to population labels of the LD index:\n    mapped_ancestries = f.transform(\n        discovery_samples, cls._map_ancestries_to_ld_population\n    )\n\n    # Aggregate sample sizes belonging to the same LD population:\n    aggregated_counts = f.aggregate(\n        mapped_ancestries,\n        f.array_distinct(\n            f.transform(\n                mapped_ancestries,\n                lambda x: f.struct(\n                    x.ancestry.alias(\"ancestry\"), f.lit(0.0).alias(\"sampleSize\")\n                ),\n            )\n        ),\n        cls._aggregate_samples_by_ancestry,\n    )\n    # Getting total sample count:\n    total_sample_count = f.aggregate(\n        aggregated_counts, f.lit(0.0), lambda total, pop: total + pop.sampleSize\n    ).alias(\"sampleSize\")\n\n    # Calculating relative sample size for each LD population:\n    return f.transform(\n        aggregated_counts,\n        lambda ld_population: f.struct(\n            ld_population.ancestry.alias(\"ldPopulation\"),\n            (ld_population.sampleSize / total_sample_count).alias(\n                \"relativeSampleSize\"\n            ),\n        ),\n    )\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provide the schema for the StudyIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>The schema of the StudyIndex dataset.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[StudyIndex]) -&gt; StructType:\n    \"\"\"Provide the schema for the StudyIndex dataset.\n\n    Returns:\n        StructType: The schema of the StudyIndex dataset.\n    \"\"\"\n    return parse_spark_schema(\"study_index.json\")\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.has_mapped_trait","title":"<code>has_mapped_trait() -&gt; Column</code>","text":"<p>Return a boolean column indicating if a study has mapped disease.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>True if the study has mapped disease.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>def has_mapped_trait(self: StudyIndex) -&gt; Column:\n    \"\"\"Return a boolean column indicating if a study has mapped disease.\n\n    Returns:\n        Column: True if the study has mapped disease.\n    \"\"\"\n    return f.size(self.df.traitFromSourceMappedIds) &gt; 0\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.has_summarystats","title":"<code>has_summarystats() -&gt; Column</code>","text":"<p>Return a boolean column indicating if a study has harmonized summary statistics.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>True if the study has harmonized summary statistics.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>def has_summarystats(self: StudyIndex) -&gt; Column:\n    \"\"\"Return a boolean column indicating if a study has harmonized summary statistics.\n\n    Returns:\n        Column: True if the study has harmonized summary statistics.\n    \"\"\"\n    return self.df.hasSumstats\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.is_gwas","title":"<code>is_gwas() -&gt; Column</code>","text":"<p>Return a boolean column with true values for GWAS studies.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>True if the study is a GWAS study.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>def is_gwas(self: StudyIndex) -&gt; Column:\n    \"\"\"Return a boolean column with true values for GWAS studies.\n\n    Returns:\n        Column: True if the study is a GWAS study.\n    \"\"\"\n    return self.df.studyType == \"gwas\"\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.is_qtl","title":"<code>is_qtl() -&gt; Column</code>","text":"<p>Return a boolean column with true values for QTL studies.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>True if the study is a QTL study.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>def is_qtl(self: StudyIndex) -&gt; Column:\n    \"\"\"Return a boolean column with true values for QTL studies.\n\n    Returns:\n        Column: True if the study is a QTL study.\n    \"\"\"\n    return self.df.studyType.endswith(\"qtl\")\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.is_quality_flagged","title":"<code>is_quality_flagged() -&gt; Column</code>","text":"<p>Return a boolean column indicating if a study is flagged due to quality issues.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>True if the study is flagged.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>def is_quality_flagged(self: StudyIndex) -&gt; Column:\n    \"\"\"Return a boolean column indicating if a study is flagged due to quality issues.\n\n    Returns:\n        Column: True if the study is flagged.\n    \"\"\"\n    # Testing for the presence of the qualityControls column:\n    if \"qualityControls\" not in self.df.columns:\n        return f.lit(False)\n    else:\n        return f.size(self.df.qualityControls) != 0\n</code></pre>"},{"location":"python_api/datasets/study_index/#gentropy.dataset.study_index.StudyIndex.study_type_lut","title":"<code>study_type_lut() -&gt; DataFrame</code>","text":"<p>Return a lookup table of study type.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>A dataframe containing <code>studyId</code> and <code>studyType</code> columns.</p> Source code in <code>src/gentropy/dataset/study_index.py</code> <pre><code>def study_type_lut(self: StudyIndex) -&gt; DataFrame:\n    \"\"\"Return a lookup table of study type.\n\n    Returns:\n        DataFrame: A dataframe containing `studyId` and `studyType` columns.\n    \"\"\"\n    return self.df.select(\"studyId\", \"studyType\")\n</code></pre>"},{"location":"python_api/datasets/study_index/#schema","title":"Schema","text":"<pre><code>root\n |-- studyId: string (nullable = false)\n |-- projectId: string (nullable = false)\n |-- studyType: string (nullable = false)\n |-- traitFromSource: string (nullable = false)\n |-- traitFromSourceMappedIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- geneId: string (nullable = true)\n |-- pubmedId: string (nullable = true)\n |-- publicationTitle: string (nullable = true)\n |-- publicationFirstAuthor: string (nullable = true)\n |-- publicationDate: string (nullable = true)\n |-- publicationJournal: string (nullable = true)\n |-- backgroundTraitFromSourceMappedIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- initialSampleSize: string (nullable = true)\n |-- nCases: integer (nullable = true)\n |-- nControls: integer (nullable = true)\n |-- nSamples: integer (nullable = true)\n |-- cohorts: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- ldPopulationStructure: array (nullable = true)\n |    |-- element: struct (containsNull = false)\n |    |    |-- ldPopulation: string (nullable = true)\n |    |    |-- relativeSampleSize: double (nullable = true)\n |-- discoverySamples: array (nullable = true)\n |    |-- element: struct (containsNull = false)\n |    |    |-- sampleSize: integer (nullable = true)\n |    |    |-- ancestry: string (nullable = true)\n |-- replicationSamples: array (nullable = true)\n |    |-- element: struct (containsNull = false)\n |    |    |-- sampleSize: integer (nullable = true)\n |    |    |-- ancestry: string (nullable = true)\n |-- qualityControls: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- analysisFlags: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- summarystatsLocation: string (nullable = true)\n |-- hasSumstats: boolean (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/study_locus/","title":"Study Locus","text":""},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus","title":"<code>gentropy.dataset.study_locus.StudyLocus</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Study-Locus dataset.</p> <p>This dataset captures associations between study/traits and a genetic loci as provided by finemapping methods.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>@dataclass\nclass StudyLocus(Dataset):\n    \"\"\"Study-Locus dataset.\n\n    This dataset captures associations between study/traits and a genetic loci as provided by finemapping methods.\n    \"\"\"\n\n    @staticmethod\n    def _overlapping_peaks(credset_to_overlap: DataFrame) -&gt; DataFrame:\n        \"\"\"Calculate overlapping signals (study-locus) between GWAS-GWAS and GWAS-Molecular trait.\n\n        Args:\n            credset_to_overlap (DataFrame): DataFrame containing at least `studyLocusId`, `studyType`, `chromosome` and `tagVariantId` columns.\n\n        Returns:\n            DataFrame: containing `leftStudyLocusId`, `rightStudyLocusId` and `chromosome` columns.\n        \"\"\"\n        # Reduce columns to the minimum to reduce the size of the dataframe\n        credset_to_overlap = credset_to_overlap.select(\n            \"studyLocusId\", \"studyType\", \"chromosome\", \"tagVariantId\"\n        )\n        return (\n            credset_to_overlap.alias(\"left\")\n            .filter(f.col(\"studyType\") == \"gwas\")\n            # Self join with complex condition. Left it's all gwas and right can be gwas or molecular trait\n            .join(\n                credset_to_overlap.alias(\"right\"),\n                on=[\n                    f.col(\"left.chromosome\") == f.col(\"right.chromosome\"),\n                    f.col(\"left.tagVariantId\") == f.col(\"right.tagVariantId\"),\n                    (f.col(\"right.studyType\") != \"gwas\")\n                    | (f.col(\"left.studyLocusId\") &gt; f.col(\"right.studyLocusId\")),\n                ],\n                how=\"inner\",\n            )\n            .select(\n                f.col(\"left.studyLocusId\").alias(\"leftStudyLocusId\"),\n                f.col(\"right.studyLocusId\").alias(\"rightStudyLocusId\"),\n                f.col(\"left.chromosome\").alias(\"chromosome\"),\n            )\n            .distinct()\n            .repartition(\"chromosome\")\n            .persist()\n        )\n\n    @staticmethod\n    def _align_overlapping_tags(\n        loci_to_overlap: DataFrame, peak_overlaps: DataFrame\n    ) -&gt; StudyLocusOverlap:\n        \"\"\"Align overlapping tags in pairs of overlapping study-locus, keeping all tags in both loci.\n\n        Args:\n            loci_to_overlap (DataFrame): containing `studyLocusId`, `studyType`, `chromosome`, `tagVariantId`, `logBF` and `posteriorProbability` columns.\n            peak_overlaps (DataFrame): containing `leftStudyLocusId`, `rightStudyLocusId` and `chromosome` columns.\n\n        Returns:\n            StudyLocusOverlap: Pairs of overlapping study-locus with aligned tags.\n        \"\"\"\n        # Complete information about all tags in the left study-locus of the overlap\n        stats_cols = [\n            \"logBF\",\n            \"posteriorProbability\",\n            \"beta\",\n            \"pValueMantissa\",\n            \"pValueExponent\",\n        ]\n        overlapping_left = loci_to_overlap.select(\n            f.col(\"chromosome\"),\n            f.col(\"tagVariantId\"),\n            f.col(\"studyLocusId\").alias(\"leftStudyLocusId\"),\n            *[f.col(col).alias(f\"left_{col}\") for col in stats_cols],\n        ).join(peak_overlaps, on=[\"chromosome\", \"leftStudyLocusId\"], how=\"inner\")\n\n        # Complete information about all tags in the right study-locus of the overlap\n        overlapping_right = loci_to_overlap.select(\n            f.col(\"chromosome\"),\n            f.col(\"tagVariantId\"),\n            f.col(\"studyLocusId\").alias(\"rightStudyLocusId\"),\n            *[f.col(col).alias(f\"right_{col}\") for col in stats_cols],\n        ).join(peak_overlaps, on=[\"chromosome\", \"rightStudyLocusId\"], how=\"inner\")\n\n        # Include information about all tag variants in both study-locus aligned by tag variant id\n        overlaps = overlapping_left.join(\n            overlapping_right,\n            on=[\n                \"chromosome\",\n                \"rightStudyLocusId\",\n                \"leftStudyLocusId\",\n                \"tagVariantId\",\n            ],\n            how=\"outer\",\n        ).select(\n            \"leftStudyLocusId\",\n            \"rightStudyLocusId\",\n            \"chromosome\",\n            \"tagVariantId\",\n            f.struct(\n                *[f\"left_{e}\" for e in stats_cols] + [f\"right_{e}\" for e in stats_cols]\n            ).alias(\"statistics\"),\n        )\n        return StudyLocusOverlap(\n            _df=overlaps,\n            _schema=StudyLocusOverlap.get_schema(),\n        )\n\n    @staticmethod\n    def update_quality_flag(\n        qc: Column, flag_condition: Column, flag_text: StudyLocusQualityCheck\n    ) -&gt; Column:\n        \"\"\"Update the provided quality control list with a new flag if condition is met.\n\n        Args:\n            qc (Column): Array column with the current list of qc flags.\n            flag_condition (Column): This is a column of booleans, signing which row should be flagged\n            flag_text (StudyLocusQualityCheck): Text for the new quality control flag\n\n        Returns:\n            Column: Array column with the updated list of qc flags.\n        \"\"\"\n        qc = f.when(qc.isNull(), f.array()).otherwise(qc)\n        return f.when(\n            flag_condition,\n            f.array_union(qc, f.array(f.lit(flag_text.value))),\n        ).otherwise(qc)\n\n    @staticmethod\n    def assign_study_locus_id(study_id_col: Column, variant_id_col: Column) -&gt; Column:\n        \"\"\"Hashes a column with a variant ID and a study ID to extract a consistent studyLocusId.\n\n        Args:\n            study_id_col (Column): column name with a study ID\n            variant_id_col (Column): column name with a variant ID\n\n        Returns:\n            Column: column with a study locus ID\n\n        Examples:\n            &gt;&gt;&gt; df = spark.createDataFrame([(\"GCST000001\", \"1_1000_A_C\"), (\"GCST000002\", \"1_1000_A_C\")]).toDF(\"studyId\", \"variantId\")\n            &gt;&gt;&gt; df.withColumn(\"study_locus_id\", StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\"))).show()\n            +----------+----------+-------------------+\n            |   studyId| variantId|     study_locus_id|\n            +----------+----------+-------------------+\n            |GCST000001|1_1000_A_C|1553357789130151995|\n            |GCST000002|1_1000_A_C|-415050894682709184|\n            +----------+----------+-------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        variant_id_col = f.coalesce(variant_id_col, f.rand().cast(\"string\"))\n        return f.xxhash64(study_id_col, variant_id_col).alias(\"studyLocusId\")\n\n    @classmethod\n    def get_schema(cls: type[StudyLocus]) -&gt; StructType:\n        \"\"\"Provides the schema for the StudyLocus dataset.\n\n        Returns:\n            StructType: schema for the StudyLocus dataset.\n        \"\"\"\n        return parse_spark_schema(\"study_locus.json\")\n\n    def filter_by_study_type(\n        self: StudyLocus, study_type: str, study_index: StudyIndex\n    ) -&gt; StudyLocus:\n        \"\"\"Creates a new StudyLocus dataset filtered by study type.\n\n        Args:\n            study_type (str): Study type to filter for. Can be one of `gwas`, `eqtl`, `pqtl`, `eqtl`.\n            study_index (StudyIndex): Study index to resolve study types.\n\n        Returns:\n            StudyLocus: Filtered study-locus dataset.\n\n        Raises:\n            ValueError: If study type is not supported.\n        \"\"\"\n        if study_type not in [\"gwas\", \"eqtl\", \"pqtl\", \"sqtl\"]:\n            raise ValueError(\n                f\"Study type {study_type} not supported. Supported types are: gwas, eqtl, pqtl, sqtl.\"\n            )\n        new_df = (\n            self.df.join(study_index.study_type_lut(), on=\"studyId\", how=\"inner\")\n            .filter(f.col(\"studyType\") == study_type)\n            .drop(\"studyType\")\n        )\n        return StudyLocus(\n            _df=new_df,\n            _schema=self._schema,\n        )\n\n    def filter_credible_set(\n        self: StudyLocus,\n        credible_interval: CredibleInterval,\n    ) -&gt; StudyLocus:\n        \"\"\"Filter study-locus tag variants based on given credible interval.\n\n        Args:\n            credible_interval (CredibleInterval): Credible interval to filter for.\n\n        Returns:\n            StudyLocus: Filtered study-locus dataset.\n        \"\"\"\n        self.df = self._df.withColumn(\n            \"locus\",\n            f.filter(\n                f.col(\"locus\"),\n                lambda tag: (tag[credible_interval.value]),\n            ),\n        )\n        return self\n\n    def find_overlaps(self: StudyLocus, study_index: StudyIndex) -&gt; StudyLocusOverlap:\n        \"\"\"Calculate overlapping study-locus.\n\n        Find overlapping study-locus that share at least one tagging variant. All GWAS-GWAS and all GWAS-Molecular traits are computed with the Molecular traits always\n        appearing on the right side.\n\n        Args:\n            study_index (StudyIndex): Study index to resolve study types.\n\n        Returns:\n            StudyLocusOverlap: Pairs of overlapping study-locus with aligned tags.\n        \"\"\"\n        loci_to_overlap = (\n            self.df.join(study_index.study_type_lut(), on=\"studyId\", how=\"inner\")\n            .withColumn(\"locus\", f.explode(\"locus\"))\n            .select(\n                \"studyLocusId\",\n                \"studyType\",\n                \"chromosome\",\n                f.col(\"locus.variantId\").alias(\"tagVariantId\"),\n                f.col(\"locus.logBF\").alias(\"logBF\"),\n                f.col(\"locus.posteriorProbability\").alias(\"posteriorProbability\"),\n                f.col(\"locus.pValueMantissa\").alias(\"pValueMantissa\"),\n                f.col(\"locus.pValueExponent\").alias(\"pValueExponent\"),\n                f.col(\"locus.beta\").alias(\"beta\"),\n            )\n            .persist()\n        )\n\n        # overlapping study-locus\n        peak_overlaps = self._overlapping_peaks(loci_to_overlap)\n\n        # study-locus overlap by aligning overlapping variants\n        return self._align_overlapping_tags(loci_to_overlap, peak_overlaps)\n\n    def unique_variants_in_locus(self: StudyLocus) -&gt; DataFrame:\n        \"\"\"All unique variants collected in a `StudyLocus` dataframe.\n\n        Returns:\n            DataFrame: A dataframe containing `variantId` and `chromosome` columns.\n        \"\"\"\n        return (\n            self.df.withColumn(\n                \"variantId\",\n                # Joint array of variants in that studylocus. Locus can be null\n                f.explode(\n                    f.array_union(\n                        f.array(f.col(\"variantId\")),\n                        f.coalesce(f.col(\"locus.variantId\"), f.array()),\n                    )\n                ),\n            )\n            .select(\n                \"variantId\", f.split(f.col(\"variantId\"), \"_\")[0].alias(\"chromosome\")\n            )\n            .distinct()\n        )\n\n    def neglog_pvalue(self: StudyLocus) -&gt; Column:\n        \"\"\"Returns the negative log p-value.\n\n        Returns:\n            Column: Negative log p-value\n        \"\"\"\n        return calculate_neglog_pvalue(\n            self.df.pValueMantissa,\n            self.df.pValueExponent,\n        )\n\n    def annotate_credible_sets(self: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Annotate study-locus dataset with credible set flags.\n\n        Sorts the array in the `locus` column elements by their `posteriorProbability` values in descending order and adds\n        `is95CredibleSet` and `is99CredibleSet` fields to the elements, indicating which are the tagging variants whose cumulative sum\n        of their `posteriorProbability` values is below 0.95 and 0.99, respectively.\n\n        Returns:\n            StudyLocus: including annotation on `is95CredibleSet` and `is99CredibleSet`.\n\n        Raises:\n            ValueError: If `locus` column is not available.\n        \"\"\"\n        if \"locus\" not in self.df.columns:\n            raise ValueError(\"Locus column not available.\")\n\n        self.df = self.df.withColumn(\n            # Sort credible set by posterior probability in descending order\n            \"locus\",\n            f.when(\n                f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n                order_array_of_structs_by_field(\"locus\", \"posteriorProbability\"),\n            ),\n        ).withColumn(\n            # Calculate array of cumulative sums of posterior probabilities to determine which variants are in the 95% and 99% credible sets\n            # and zip the cumulative sums array with the credible set array to add the flags\n            \"locus\",\n            f.when(\n                f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n                f.zip_with(\n                    f.col(\"locus\"),\n                    f.transform(\n                        f.sequence(f.lit(1), f.size(f.col(\"locus\"))),\n                        lambda index: f.aggregate(\n                            f.slice(\n                                # By using `index - 1` we introduce a value of `0.0` in the cumulative sums array. to ensure that the last variant\n                                # that exceeds the 0.95 threshold is included in the cumulative sum, as its probability is necessary to satisfy the threshold.\n                                f.col(\"locus.posteriorProbability\"),\n                                1,\n                                index - 1,\n                            ),\n                            f.lit(0.0),\n                            lambda acc, el: acc + el,\n                        ),\n                    ),\n                    lambda struct_e, acc: struct_e.withField(\n                        CredibleInterval.IS95.value, (acc &lt; 0.95) &amp; acc.isNotNull()\n                    ).withField(\n                        CredibleInterval.IS99.value, (acc &lt; 0.99) &amp; acc.isNotNull()\n                    ),\n                ),\n            ),\n        )\n        return self\n\n    def annotate_ld(\n        self: StudyLocus, study_index: StudyIndex, ld_index: LDIndex\n    ) -&gt; StudyLocus:\n        \"\"\"Annotate LD information to study-locus.\n\n        Args:\n            study_index (StudyIndex): Study index to resolve ancestries.\n            ld_index (LDIndex): LD index to resolve LD information.\n\n        Returns:\n            StudyLocus: Study locus annotated with ld information from LD index.\n        \"\"\"\n        from gentropy.method.ld import LDAnnotator\n\n        return LDAnnotator.ld_annotate(self, study_index, ld_index)\n\n    def clump(self: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Perform LD clumping of the studyLocus.\n\n        Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.\n\n        Returns:\n            StudyLocus: with empty credible sets for linked variants and QC flag.\n        \"\"\"\n        self.df = (\n            self.df.withColumn(\n                \"is_lead_linked\",\n                LDclumping._is_lead_linked(\n                    self.df.studyId,\n                    self.df.variantId,\n                    self.df.pValueExponent,\n                    self.df.pValueMantissa,\n                    self.df.ldSet,\n                ),\n            )\n            .withColumn(\n                \"ldSet\",\n                f.when(f.col(\"is_lead_linked\"), f.array()).otherwise(f.col(\"ldSet\")),\n            )\n            .withColumn(\n                \"qualityControls\",\n                StudyLocus.update_quality_flag(\n                    f.col(\"qualityControls\"),\n                    f.col(\"is_lead_linked\"),\n                    StudyLocusQualityCheck.LD_CLUMPED,\n                ),\n            )\n            .drop(\"is_lead_linked\")\n        )\n        return self\n\n    def _qc_unresolved_ld(\n        self: StudyLocus,\n    ) -&gt; StudyLocus:\n        \"\"\"Flag associations with variants that are not found in the LD reference.\n\n        Returns:\n            StudyLocus: Updated study locus.\n        \"\"\"\n        self.df = self.df.withColumn(\n            \"qualityControls\",\n            self.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.col(\"ldSet\").isNull(),\n                StudyLocusQualityCheck.UNRESOLVED_LD,\n            ),\n        )\n        return self\n\n    def _qc_no_population(self: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Flag associations where the study doesn't have population information to resolve LD.\n\n        Returns:\n            StudyLocus: Updated study locus.\n        \"\"\"\n        # If the tested column is not present, return self unchanged:\n        if \"ldPopulationStructure\" not in self.df.columns:\n            return self\n\n        self.df = self.df.withColumn(\n            \"qualityControls\",\n            self.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.col(\"ldPopulationStructure\").isNull(),\n                StudyLocusQualityCheck.NO_POPULATION,\n            ),\n        )\n        return self\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.annotate_credible_sets","title":"<code>annotate_credible_sets() -&gt; StudyLocus</code>","text":"<p>Annotate study-locus dataset with credible set flags.</p> <p>Sorts the array in the <code>locus</code> column elements by their <code>posteriorProbability</code> values in descending order and adds <code>is95CredibleSet</code> and <code>is99CredibleSet</code> fields to the elements, indicating which are the tagging variants whose cumulative sum of their <code>posteriorProbability</code> values is below 0.95 and 0.99, respectively.</p> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>including annotation on <code>is95CredibleSet</code> and <code>is99CredibleSet</code>.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If <code>locus</code> column is not available.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def annotate_credible_sets(self: StudyLocus) -&gt; StudyLocus:\n    \"\"\"Annotate study-locus dataset with credible set flags.\n\n    Sorts the array in the `locus` column elements by their `posteriorProbability` values in descending order and adds\n    `is95CredibleSet` and `is99CredibleSet` fields to the elements, indicating which are the tagging variants whose cumulative sum\n    of their `posteriorProbability` values is below 0.95 and 0.99, respectively.\n\n    Returns:\n        StudyLocus: including annotation on `is95CredibleSet` and `is99CredibleSet`.\n\n    Raises:\n        ValueError: If `locus` column is not available.\n    \"\"\"\n    if \"locus\" not in self.df.columns:\n        raise ValueError(\"Locus column not available.\")\n\n    self.df = self.df.withColumn(\n        # Sort credible set by posterior probability in descending order\n        \"locus\",\n        f.when(\n            f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n            order_array_of_structs_by_field(\"locus\", \"posteriorProbability\"),\n        ),\n    ).withColumn(\n        # Calculate array of cumulative sums of posterior probabilities to determine which variants are in the 95% and 99% credible sets\n        # and zip the cumulative sums array with the credible set array to add the flags\n        \"locus\",\n        f.when(\n            f.col(\"locus\").isNotNull() &amp; (f.size(f.col(\"locus\")) &gt; 0),\n            f.zip_with(\n                f.col(\"locus\"),\n                f.transform(\n                    f.sequence(f.lit(1), f.size(f.col(\"locus\"))),\n                    lambda index: f.aggregate(\n                        f.slice(\n                            # By using `index - 1` we introduce a value of `0.0` in the cumulative sums array. to ensure that the last variant\n                            # that exceeds the 0.95 threshold is included in the cumulative sum, as its probability is necessary to satisfy the threshold.\n                            f.col(\"locus.posteriorProbability\"),\n                            1,\n                            index - 1,\n                        ),\n                        f.lit(0.0),\n                        lambda acc, el: acc + el,\n                    ),\n                ),\n                lambda struct_e, acc: struct_e.withField(\n                    CredibleInterval.IS95.value, (acc &lt; 0.95) &amp; acc.isNotNull()\n                ).withField(\n                    CredibleInterval.IS99.value, (acc &lt; 0.99) &amp; acc.isNotNull()\n                ),\n            ),\n        ),\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.annotate_ld","title":"<code>annotate_ld(study_index: StudyIndex, ld_index: LDIndex) -&gt; StudyLocus</code>","text":"<p>Annotate LD information to study-locus.</p> <p>Parameters:</p> Name Type Description Default <code>study_index</code> <code>StudyIndex</code> <p>Study index to resolve ancestries.</p> required <code>ld_index</code> <code>LDIndex</code> <p>LD index to resolve LD information.</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Study locus annotated with ld information from LD index.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def annotate_ld(\n    self: StudyLocus, study_index: StudyIndex, ld_index: LDIndex\n) -&gt; StudyLocus:\n    \"\"\"Annotate LD information to study-locus.\n\n    Args:\n        study_index (StudyIndex): Study index to resolve ancestries.\n        ld_index (LDIndex): LD index to resolve LD information.\n\n    Returns:\n        StudyLocus: Study locus annotated with ld information from LD index.\n    \"\"\"\n    from gentropy.method.ld import LDAnnotator\n\n    return LDAnnotator.ld_annotate(self, study_index, ld_index)\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.assign_study_locus_id","title":"<code>assign_study_locus_id(study_id_col: Column, variant_id_col: Column) -&gt; Column</code>  <code>staticmethod</code>","text":"<p>Hashes a column with a variant ID and a study ID to extract a consistent studyLocusId.</p> <p>Parameters:</p> Name Type Description Default <code>study_id_col</code> <code>Column</code> <p>column name with a study ID</p> required <code>variant_id_col</code> <code>Column</code> <p>column name with a variant ID</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>column with a study locus ID</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; df = spark.createDataFrame([(\"GCST000001\", \"1_1000_A_C\"), (\"GCST000002\", \"1_1000_A_C\")]).toDF(\"studyId\", \"variantId\")\n&gt;&gt;&gt; df.withColumn(\"study_locus_id\", StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\"))).show()\n+----------+----------+-------------------+\n|   studyId| variantId|     study_locus_id|\n+----------+----------+-------------------+\n|GCST000001|1_1000_A_C|1553357789130151995|\n|GCST000002|1_1000_A_C|-415050894682709184|\n+----------+----------+-------------------+\n</code></pre> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>@staticmethod\ndef assign_study_locus_id(study_id_col: Column, variant_id_col: Column) -&gt; Column:\n    \"\"\"Hashes a column with a variant ID and a study ID to extract a consistent studyLocusId.\n\n    Args:\n        study_id_col (Column): column name with a study ID\n        variant_id_col (Column): column name with a variant ID\n\n    Returns:\n        Column: column with a study locus ID\n\n    Examples:\n        &gt;&gt;&gt; df = spark.createDataFrame([(\"GCST000001\", \"1_1000_A_C\"), (\"GCST000002\", \"1_1000_A_C\")]).toDF(\"studyId\", \"variantId\")\n        &gt;&gt;&gt; df.withColumn(\"study_locus_id\", StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\"))).show()\n        +----------+----------+-------------------+\n        |   studyId| variantId|     study_locus_id|\n        +----------+----------+-------------------+\n        |GCST000001|1_1000_A_C|1553357789130151995|\n        |GCST000002|1_1000_A_C|-415050894682709184|\n        +----------+----------+-------------------+\n        &lt;BLANKLINE&gt;\n    \"\"\"\n    variant_id_col = f.coalesce(variant_id_col, f.rand().cast(\"string\"))\n    return f.xxhash64(study_id_col, variant_id_col).alias(\"studyLocusId\")\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.clump","title":"<code>clump() -&gt; StudyLocus</code>","text":"<p>Perform LD clumping of the studyLocus.</p> <p>Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.</p> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>with empty credible sets for linked variants and QC flag.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def clump(self: StudyLocus) -&gt; StudyLocus:\n    \"\"\"Perform LD clumping of the studyLocus.\n\n    Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.\n\n    Returns:\n        StudyLocus: with empty credible sets for linked variants and QC flag.\n    \"\"\"\n    self.df = (\n        self.df.withColumn(\n            \"is_lead_linked\",\n            LDclumping._is_lead_linked(\n                self.df.studyId,\n                self.df.variantId,\n                self.df.pValueExponent,\n                self.df.pValueMantissa,\n                self.df.ldSet,\n            ),\n        )\n        .withColumn(\n            \"ldSet\",\n            f.when(f.col(\"is_lead_linked\"), f.array()).otherwise(f.col(\"ldSet\")),\n        )\n        .withColumn(\n            \"qualityControls\",\n            StudyLocus.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.col(\"is_lead_linked\"),\n                StudyLocusQualityCheck.LD_CLUMPED,\n            ),\n        )\n        .drop(\"is_lead_linked\")\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.filter_by_study_type","title":"<code>filter_by_study_type(study_type: str, study_index: StudyIndex) -&gt; StudyLocus</code>","text":"<p>Creates a new StudyLocus dataset filtered by study type.</p> <p>Parameters:</p> Name Type Description Default <code>study_type</code> <code>str</code> <p>Study type to filter for. Can be one of <code>gwas</code>, <code>eqtl</code>, <code>pqtl</code>, <code>eqtl</code>.</p> required <code>study_index</code> <code>StudyIndex</code> <p>Study index to resolve study types.</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Filtered study-locus dataset.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If study type is not supported.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def filter_by_study_type(\n    self: StudyLocus, study_type: str, study_index: StudyIndex\n) -&gt; StudyLocus:\n    \"\"\"Creates a new StudyLocus dataset filtered by study type.\n\n    Args:\n        study_type (str): Study type to filter for. Can be one of `gwas`, `eqtl`, `pqtl`, `eqtl`.\n        study_index (StudyIndex): Study index to resolve study types.\n\n    Returns:\n        StudyLocus: Filtered study-locus dataset.\n\n    Raises:\n        ValueError: If study type is not supported.\n    \"\"\"\n    if study_type not in [\"gwas\", \"eqtl\", \"pqtl\", \"sqtl\"]:\n        raise ValueError(\n            f\"Study type {study_type} not supported. Supported types are: gwas, eqtl, pqtl, sqtl.\"\n        )\n    new_df = (\n        self.df.join(study_index.study_type_lut(), on=\"studyId\", how=\"inner\")\n        .filter(f.col(\"studyType\") == study_type)\n        .drop(\"studyType\")\n    )\n    return StudyLocus(\n        _df=new_df,\n        _schema=self._schema,\n    )\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.filter_credible_set","title":"<code>filter_credible_set(credible_interval: CredibleInterval) -&gt; StudyLocus</code>","text":"<p>Filter study-locus tag variants based on given credible interval.</p> <p>Parameters:</p> Name Type Description Default <code>credible_interval</code> <code>CredibleInterval</code> <p>Credible interval to filter for.</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Filtered study-locus dataset.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def filter_credible_set(\n    self: StudyLocus,\n    credible_interval: CredibleInterval,\n) -&gt; StudyLocus:\n    \"\"\"Filter study-locus tag variants based on given credible interval.\n\n    Args:\n        credible_interval (CredibleInterval): Credible interval to filter for.\n\n    Returns:\n        StudyLocus: Filtered study-locus dataset.\n    \"\"\"\n    self.df = self._df.withColumn(\n        \"locus\",\n        f.filter(\n            f.col(\"locus\"),\n            lambda tag: (tag[credible_interval.value]),\n        ),\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.find_overlaps","title":"<code>find_overlaps(study_index: StudyIndex) -&gt; StudyLocusOverlap</code>","text":"<p>Calculate overlapping study-locus.</p> <p>Find overlapping study-locus that share at least one tagging variant. All GWAS-GWAS and all GWAS-Molecular traits are computed with the Molecular traits always appearing on the right side.</p> <p>Parameters:</p> Name Type Description Default <code>study_index</code> <code>StudyIndex</code> <p>Study index to resolve study types.</p> required <p>Returns:</p> Name Type Description <code>StudyLocusOverlap</code> <code>StudyLocusOverlap</code> <p>Pairs of overlapping study-locus with aligned tags.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def find_overlaps(self: StudyLocus, study_index: StudyIndex) -&gt; StudyLocusOverlap:\n    \"\"\"Calculate overlapping study-locus.\n\n    Find overlapping study-locus that share at least one tagging variant. All GWAS-GWAS and all GWAS-Molecular traits are computed with the Molecular traits always\n    appearing on the right side.\n\n    Args:\n        study_index (StudyIndex): Study index to resolve study types.\n\n    Returns:\n        StudyLocusOverlap: Pairs of overlapping study-locus with aligned tags.\n    \"\"\"\n    loci_to_overlap = (\n        self.df.join(study_index.study_type_lut(), on=\"studyId\", how=\"inner\")\n        .withColumn(\"locus\", f.explode(\"locus\"))\n        .select(\n            \"studyLocusId\",\n            \"studyType\",\n            \"chromosome\",\n            f.col(\"locus.variantId\").alias(\"tagVariantId\"),\n            f.col(\"locus.logBF\").alias(\"logBF\"),\n            f.col(\"locus.posteriorProbability\").alias(\"posteriorProbability\"),\n            f.col(\"locus.pValueMantissa\").alias(\"pValueMantissa\"),\n            f.col(\"locus.pValueExponent\").alias(\"pValueExponent\"),\n            f.col(\"locus.beta\").alias(\"beta\"),\n        )\n        .persist()\n    )\n\n    # overlapping study-locus\n    peak_overlaps = self._overlapping_peaks(loci_to_overlap)\n\n    # study-locus overlap by aligning overlapping variants\n    return self._align_overlapping_tags(loci_to_overlap, peak_overlaps)\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the StudyLocus dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>schema for the StudyLocus dataset.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[StudyLocus]) -&gt; StructType:\n    \"\"\"Provides the schema for the StudyLocus dataset.\n\n    Returns:\n        StructType: schema for the StudyLocus dataset.\n    \"\"\"\n    return parse_spark_schema(\"study_locus.json\")\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.neglog_pvalue","title":"<code>neglog_pvalue() -&gt; Column</code>","text":"<p>Returns the negative log p-value.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>Negative log p-value</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def neglog_pvalue(self: StudyLocus) -&gt; Column:\n    \"\"\"Returns the negative log p-value.\n\n    Returns:\n        Column: Negative log p-value\n    \"\"\"\n    return calculate_neglog_pvalue(\n        self.df.pValueMantissa,\n        self.df.pValueExponent,\n    )\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.unique_variants_in_locus","title":"<code>unique_variants_in_locus() -&gt; DataFrame</code>","text":"<p>All unique variants collected in a <code>StudyLocus</code> dataframe.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>A dataframe containing <code>variantId</code> and <code>chromosome</code> columns.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>def unique_variants_in_locus(self: StudyLocus) -&gt; DataFrame:\n    \"\"\"All unique variants collected in a `StudyLocus` dataframe.\n\n    Returns:\n        DataFrame: A dataframe containing `variantId` and `chromosome` columns.\n    \"\"\"\n    return (\n        self.df.withColumn(\n            \"variantId\",\n            # Joint array of variants in that studylocus. Locus can be null\n            f.explode(\n                f.array_union(\n                    f.array(f.col(\"variantId\")),\n                    f.coalesce(f.col(\"locus.variantId\"), f.array()),\n                )\n            ),\n        )\n        .select(\n            \"variantId\", f.split(f.col(\"variantId\"), \"_\")[0].alias(\"chromosome\")\n        )\n        .distinct()\n    )\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocus.update_quality_flag","title":"<code>update_quality_flag(qc: Column, flag_condition: Column, flag_text: StudyLocusQualityCheck) -&gt; Column</code>  <code>staticmethod</code>","text":"<p>Update the provided quality control list with a new flag if condition is met.</p> <p>Parameters:</p> Name Type Description Default <code>qc</code> <code>Column</code> <p>Array column with the current list of qc flags.</p> required <code>flag_condition</code> <code>Column</code> <p>This is a column of booleans, signing which row should be flagged</p> required <code>flag_text</code> <code>StudyLocusQualityCheck</code> <p>Text for the new quality control flag</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>Array column with the updated list of qc flags.</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>@staticmethod\ndef update_quality_flag(\n    qc: Column, flag_condition: Column, flag_text: StudyLocusQualityCheck\n) -&gt; Column:\n    \"\"\"Update the provided quality control list with a new flag if condition is met.\n\n    Args:\n        qc (Column): Array column with the current list of qc flags.\n        flag_condition (Column): This is a column of booleans, signing which row should be flagged\n        flag_text (StudyLocusQualityCheck): Text for the new quality control flag\n\n    Returns:\n        Column: Array column with the updated list of qc flags.\n    \"\"\"\n    qc = f.when(qc.isNull(), f.array()).otherwise(qc)\n    return f.when(\n        flag_condition,\n        f.array_union(qc, f.array(f.lit(flag_text.value))),\n    ).otherwise(qc)\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.StudyLocusQualityCheck","title":"<code>gentropy.dataset.study_locus.StudyLocusQualityCheck</code>","text":"<p>             Bases: <code>Enum</code></p> <p>Study-Locus quality control options listing concerns on the quality of the association.</p> <p>Attributes:</p> Name Type Description <code>SUBSIGNIFICANT_FLAG</code> <code>str</code> <p>p-value below significance threshold</p> <code>NO_GENOMIC_LOCATION_FLAG</code> <code>str</code> <p>Incomplete genomic mapping</p> <code>COMPOSITE_FLAG</code> <code>str</code> <p>Composite association due to variant x variant interactions</p> <code>VARIANT_INCONSISTENCY_FLAG</code> <code>str</code> <p>Inconsistencies in the reported variants</p> <code>NON_MAPPED_VARIANT_FLAG</code> <code>str</code> <p>Variant not mapped to GnomAd</p> <code>PALINDROMIC_ALLELE_FLAG</code> <code>str</code> <p>Alleles are palindromic - cannot harmonize</p> <code>AMBIGUOUS_STUDY</code> <code>str</code> <p>Association with ambiguous study</p> <code>UNRESOLVED_LD</code> <code>str</code> <p>Variant not found in LD reference</p> <code>LD_CLUMPED</code> <code>str</code> <p>Explained by a more significant variant in high LD (clumped)</p> <code>UNPICSABLE</code> <code>str</code> <p>Unable to calculate PIPs with the provided data</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>class StudyLocusQualityCheck(Enum):\n    \"\"\"Study-Locus quality control options listing concerns on the quality of the association.\n\n    Attributes:\n        SUBSIGNIFICANT_FLAG (str): p-value below significance threshold\n        NO_GENOMIC_LOCATION_FLAG (str): Incomplete genomic mapping\n        COMPOSITE_FLAG (str): Composite association due to variant x variant interactions\n        VARIANT_INCONSISTENCY_FLAG (str): Inconsistencies in the reported variants\n        NON_MAPPED_VARIANT_FLAG (str): Variant not mapped to GnomAd\n        PALINDROMIC_ALLELE_FLAG (str): Alleles are palindromic - cannot harmonize\n        AMBIGUOUS_STUDY (str): Association with ambiguous study\n        UNRESOLVED_LD (str): Variant not found in LD reference\n        LD_CLUMPED (str): Explained by a more significant variant in high LD (clumped)\n        UNPICSABLE (str): Unable to calculate PIPs with the provided data\n    \"\"\"\n\n    SUBSIGNIFICANT_FLAG = \"Subsignificant p-value\"\n    NO_GENOMIC_LOCATION_FLAG = \"Incomplete genomic mapping\"\n    COMPOSITE_FLAG = \"Composite association\"\n    INCONSISTENCY_FLAG = \"Variant inconsistency\"\n    NON_MAPPED_VARIANT_FLAG = \"No mapping in GnomAd\"\n    PALINDROMIC_ALLELE_FLAG = \"Palindrome alleles - cannot harmonize\"\n    AMBIGUOUS_STUDY = \"Association with ambiguous study\"\n    UNRESOLVED_LD = \"Variant not found in LD reference\"\n    LD_CLUMPED = \"Explained by a more significant variant in high LD (clumped)\"\n    NO_POPULATION = \"Study does not have population annotation to resolve LD\"\n    NOT_QUALIFYING_LD_BLOCK = (\n        \"LD block does not contain variants at the required R^2 threshold\"\n    )\n</code></pre>"},{"location":"python_api/datasets/study_locus/#gentropy.dataset.study_locus.CredibleInterval","title":"<code>gentropy.dataset.study_locus.CredibleInterval</code>","text":"<p>             Bases: <code>Enum</code></p> <p>Credible interval enum.</p> <p>Interval within which an unobserved parameter value falls with a particular probability.</p> <p>Attributes:</p> Name Type Description <code>IS95</code> <code>str</code> <p>95% credible interval</p> <code>IS99</code> <code>str</code> <p>99% credible interval</p> Source code in <code>src/gentropy/dataset/study_locus.py</code> <pre><code>class CredibleInterval(Enum):\n    \"\"\"Credible interval enum.\n\n    Interval within which an unobserved parameter value falls with a particular probability.\n\n    Attributes:\n        IS95 (str): 95% credible interval\n        IS99 (str): 99% credible interval\n    \"\"\"\n\n    IS95 = \"is95CredibleSet\"\n    IS99 = \"is99CredibleSet\"\n</code></pre>"},{"location":"python_api/datasets/study_locus/#schema","title":"Schema","text":"<pre><code>root\n |-- studyLocusId: long (nullable = false)\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = true)\n |-- position: integer (nullable = true)\n |-- studyId: string (nullable = false)\n |-- beta: double (nullable = true)\n |-- pValueMantissa: float (nullable = true)\n |-- pValueExponent: integer (nullable = true)\n |-- effectAlleleFrequencyFromSource: float (nullable = true)\n |-- standardError: double (nullable = true)\n |-- subStudyDescription: string (nullable = true)\n |-- qualityControls: array (nullable = true)\n |    |-- element: string (containsNull = false)\n |-- finemappingMethod: string (nullable = true)\n |-- sampleSize: integer (nullable = true)\n |-- ldSet: array (nullable = true)\n |    |-- element: struct (containsNull = true)\n |    |    |-- tagVariantId: string (nullable = true)\n |    |    |-- r2Overall: double (nullable = true)\n |-- locus: array (nullable = true)\n |    |-- element: struct (containsNull = true)\n |    |    |-- is95CredibleSet: boolean (nullable = true)\n |    |    |-- is99CredibleSet: boolean (nullable = true)\n |    |    |-- logBF: double (nullable = true)\n |    |    |-- posteriorProbability: double (nullable = true)\n |    |    |-- variantId: string (nullable = true)\n |    |    |-- pValueMantissa: float (nullable = true)\n |    |    |-- pValueExponent: integer (nullable = true)\n |    |    |-- beta: double (nullable = true)\n |    |    |-- standardError: double (nullable = true)\n |    |    |-- r2Overall: double (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/study_locus_overlap/","title":"Study Locus Overlap","text":""},{"location":"python_api/datasets/study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap","title":"<code>gentropy.dataset.study_locus_overlap.StudyLocusOverlap</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Study-Locus overlap.</p> <p>This dataset captures pairs of overlapping <code>StudyLocus</code>: that is associations whose credible sets share at least one tagging variant.</p> <p>Note</p> <p>This is a helpful dataset for other downstream analyses, such as colocalisation. This dataset will contain the overlapping signals between studyLocus associations once they have been clumped and fine-mapped.</p> Source code in <code>src/gentropy/dataset/study_locus_overlap.py</code> <pre><code>@dataclass\nclass StudyLocusOverlap(Dataset):\n    \"\"\"Study-Locus overlap.\n\n    This dataset captures pairs of overlapping `StudyLocus`: that is associations whose credible sets share at least one tagging variant.\n\n    !!! note\n\n        This is a helpful dataset for other downstream analyses, such as colocalisation. This dataset will contain the overlapping signals between studyLocus associations once they have been clumped and fine-mapped.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[StudyLocusOverlap]) -&gt; StructType:\n        \"\"\"Provides the schema for the StudyLocusOverlap dataset.\n\n        Returns:\n            StructType: Schema for the StudyLocusOverlap dataset\n        \"\"\"\n        return parse_spark_schema(\"study_locus_overlap.json\")\n\n    @classmethod\n    def from_associations(\n        cls: type[StudyLocusOverlap], study_locus: StudyLocus, study_index: StudyIndex\n    ) -&gt; StudyLocusOverlap:\n        \"\"\"Find the overlapping signals in a particular set of associations (StudyLocus dataset).\n\n        Args:\n            study_locus (StudyLocus): Study-locus associations to find the overlapping signals\n            study_index (StudyIndex): Study index to find the overlapping signals\n\n        Returns:\n            StudyLocusOverlap: Study-locus overlap dataset\n        \"\"\"\n        return study_locus.find_overlaps(study_index)\n\n    def _convert_to_square_matrix(self: StudyLocusOverlap) -&gt; StudyLocusOverlap:\n        \"\"\"Convert the dataset to a square matrix.\n\n        Returns:\n            StudyLocusOverlap: Square matrix of the dataset\n        \"\"\"\n        return StudyLocusOverlap(\n            _df=self.df.unionByName(\n                self.df.selectExpr(\n                    \"leftStudyLocusId as rightStudyLocusId\",\n                    \"rightStudyLocusId as leftStudyLocusId\",\n                    \"tagVariantId\",\n                )\n            ).distinct(),\n            _schema=self.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasets/study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.from_associations","title":"<code>from_associations(study_locus: StudyLocus, study_index: StudyIndex) -&gt; StudyLocusOverlap</code>  <code>classmethod</code>","text":"<p>Find the overlapping signals in a particular set of associations (StudyLocus dataset).</p> <p>Parameters:</p> Name Type Description Default <code>study_locus</code> <code>StudyLocus</code> <p>Study-locus associations to find the overlapping signals</p> required <code>study_index</code> <code>StudyIndex</code> <p>Study index to find the overlapping signals</p> required <p>Returns:</p> Name Type Description <code>StudyLocusOverlap</code> <code>StudyLocusOverlap</code> <p>Study-locus overlap dataset</p> Source code in <code>src/gentropy/dataset/study_locus_overlap.py</code> <pre><code>@classmethod\ndef from_associations(\n    cls: type[StudyLocusOverlap], study_locus: StudyLocus, study_index: StudyIndex\n) -&gt; StudyLocusOverlap:\n    \"\"\"Find the overlapping signals in a particular set of associations (StudyLocus dataset).\n\n    Args:\n        study_locus (StudyLocus): Study-locus associations to find the overlapping signals\n        study_index (StudyIndex): Study index to find the overlapping signals\n\n    Returns:\n        StudyLocusOverlap: Study-locus overlap dataset\n    \"\"\"\n    return study_locus.find_overlaps(study_index)\n</code></pre>"},{"location":"python_api/datasets/study_locus_overlap/#gentropy.dataset.study_locus_overlap.StudyLocusOverlap.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the StudyLocusOverlap dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the StudyLocusOverlap dataset</p> Source code in <code>src/gentropy/dataset/study_locus_overlap.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[StudyLocusOverlap]) -&gt; StructType:\n    \"\"\"Provides the schema for the StudyLocusOverlap dataset.\n\n    Returns:\n        StructType: Schema for the StudyLocusOverlap dataset\n    \"\"\"\n    return parse_spark_schema(\"study_locus_overlap.json\")\n</code></pre>"},{"location":"python_api/datasets/study_locus_overlap/#schema","title":"Schema","text":"<pre><code>root\n |-- leftStudyLocusId: long (nullable = false)\n |-- rightStudyLocusId: long (nullable = false)\n |-- chromosome: string (nullable = true)\n |-- tagVariantId: string (nullable = false)\n |-- statistics: struct (nullable = true)\n |    |-- left_pValueMantissa: float (nullable = true)\n |    |-- left_pValueExponent: integer (nullable = true)\n |    |-- right_pValueMantissa: float (nullable = true)\n |    |-- right_pValueExponent: integer (nullable = true)\n |    |-- left_beta: double (nullable = true)\n |    |-- right_beta: double (nullable = true)\n |    |-- left_logBF: double (nullable = true)\n |    |-- right_logBF: double (nullable = true)\n |    |-- left_posteriorProbability: double (nullable = true)\n |    |-- right_posteriorProbability: double (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/summary_statistics/","title":"Summary Statistics","text":""},{"location":"python_api/datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics","title":"<code>gentropy.dataset.summary_statistics.SummaryStatistics</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Summary Statistics dataset.</p> <p>A summary statistics dataset contains all single point statistics resulting from a GWAS.</p> Source code in <code>src/gentropy/dataset/summary_statistics.py</code> <pre><code>@dataclass\nclass SummaryStatistics(Dataset):\n    \"\"\"Summary Statistics dataset.\n\n    A summary statistics dataset contains all single point statistics resulting from a GWAS.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[SummaryStatistics]) -&gt; StructType:\n        \"\"\"Provides the schema for the SummaryStatistics dataset.\n\n        Returns:\n            StructType: Schema for the SummaryStatistics dataset\n        \"\"\"\n        return parse_spark_schema(\"summary_statistics.json\")\n\n    def pvalue_filter(self: SummaryStatistics, pvalue: float) -&gt; SummaryStatistics:\n        \"\"\"Filter summary statistics based on the provided p-value threshold.\n\n        Args:\n            pvalue (float): upper limit of the p-value to be filtered upon.\n\n        Returns:\n            SummaryStatistics: summary statistics object containing single point associations with p-values at least as significant as the provided threshold.\n        \"\"\"\n        # Converting p-value to mantissa and exponent:\n        (mantissa, exponent) = split_pvalue(pvalue)\n\n        # Applying filter:\n        df = self._df.filter(\n            (f.col(\"pValueExponent\") &lt; exponent)\n            | (\n                (f.col(\"pValueExponent\") == exponent)\n                &amp; (f.col(\"pValueMantissa\") &lt;= mantissa)\n            )\n        )\n        return SummaryStatistics(_df=df, _schema=self._schema)\n\n    def window_based_clumping(\n        self: SummaryStatistics,\n        distance: int = 500_000,\n        gwas_significance: float = 5e-8,\n        baseline_significance: float = 0.05,\n        locus_collect_distance: int | None = None,\n    ) -&gt; StudyLocus:\n        \"\"\"Generate study-locus from summary statistics by distance based clumping + collect locus.\n\n        Args:\n            distance (int): Distance in base pairs to be used for clumping. Defaults to 500_000.\n            gwas_significance (float, optional): GWAS significance threshold. Defaults to 5e-8.\n            baseline_significance (float, optional): Baseline significance threshold for inclusion in the locus. Defaults to 0.05.\n            locus_collect_distance (int | None): The distance to collect locus around semi-indices. If not provided, locus is not collected.\n\n        Returns:\n            StudyLocus: Clumped study-locus containing variants based on window.\n        \"\"\"\n        return (\n            WindowBasedClumping.clump_with_locus(\n                self,\n                window_length=distance,\n                p_value_significance=gwas_significance,\n                p_value_baseline=baseline_significance,\n                locus_window_length=locus_collect_distance,\n            )\n            if locus_collect_distance\n            else WindowBasedClumping.clump(\n                self,\n                window_length=distance,\n                p_value_significance=gwas_significance,\n            )\n        )\n\n    def exclude_region(self: SummaryStatistics, region: str) -&gt; SummaryStatistics:\n        \"\"\"Exclude a region from the summary stats dataset.\n\n        Args:\n            region (str): region given in \"chr##:#####-####\" format\n\n        Returns:\n            SummaryStatistics: filtered summary statistics.\n        \"\"\"\n        (chromosome, start_position, end_position) = parse_region(region)\n\n        return SummaryStatistics(\n            _df=(\n                self.df.filter(\n                    ~(\n                        (f.col(\"chromosome\") == chromosome)\n                        &amp; (\n                            (f.col(\"position\") &gt;= start_position)\n                            &amp; (f.col(\"position\") &lt;= end_position)\n                        )\n                    )\n                )\n            ),\n            _schema=SummaryStatistics.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics.exclude_region","title":"<code>exclude_region(region: str) -&gt; SummaryStatistics</code>","text":"<p>Exclude a region from the summary stats dataset.</p> <p>Parameters:</p> Name Type Description Default <code>region</code> <code>str</code> <p>region given in \"chr##:#####-####\" format</p> required <p>Returns:</p> Name Type Description <code>SummaryStatistics</code> <code>SummaryStatistics</code> <p>filtered summary statistics.</p> Source code in <code>src/gentropy/dataset/summary_statistics.py</code> <pre><code>def exclude_region(self: SummaryStatistics, region: str) -&gt; SummaryStatistics:\n    \"\"\"Exclude a region from the summary stats dataset.\n\n    Args:\n        region (str): region given in \"chr##:#####-####\" format\n\n    Returns:\n        SummaryStatistics: filtered summary statistics.\n    \"\"\"\n    (chromosome, start_position, end_position) = parse_region(region)\n\n    return SummaryStatistics(\n        _df=(\n            self.df.filter(\n                ~(\n                    (f.col(\"chromosome\") == chromosome)\n                    &amp; (\n                        (f.col(\"position\") &gt;= start_position)\n                        &amp; (f.col(\"position\") &lt;= end_position)\n                    )\n                )\n            )\n        ),\n        _schema=SummaryStatistics.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the SummaryStatistics dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the SummaryStatistics dataset</p> Source code in <code>src/gentropy/dataset/summary_statistics.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[SummaryStatistics]) -&gt; StructType:\n    \"\"\"Provides the schema for the SummaryStatistics dataset.\n\n    Returns:\n        StructType: Schema for the SummaryStatistics dataset\n    \"\"\"\n    return parse_spark_schema(\"summary_statistics.json\")\n</code></pre>"},{"location":"python_api/datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics.pvalue_filter","title":"<code>pvalue_filter(pvalue: float) -&gt; SummaryStatistics</code>","text":"<p>Filter summary statistics based on the provided p-value threshold.</p> <p>Parameters:</p> Name Type Description Default <code>pvalue</code> <code>float</code> <p>upper limit of the p-value to be filtered upon.</p> required <p>Returns:</p> Name Type Description <code>SummaryStatistics</code> <code>SummaryStatistics</code> <p>summary statistics object containing single point associations with p-values at least as significant as the provided threshold.</p> Source code in <code>src/gentropy/dataset/summary_statistics.py</code> <pre><code>def pvalue_filter(self: SummaryStatistics, pvalue: float) -&gt; SummaryStatistics:\n    \"\"\"Filter summary statistics based on the provided p-value threshold.\n\n    Args:\n        pvalue (float): upper limit of the p-value to be filtered upon.\n\n    Returns:\n        SummaryStatistics: summary statistics object containing single point associations with p-values at least as significant as the provided threshold.\n    \"\"\"\n    # Converting p-value to mantissa and exponent:\n    (mantissa, exponent) = split_pvalue(pvalue)\n\n    # Applying filter:\n    df = self._df.filter(\n        (f.col(\"pValueExponent\") &lt; exponent)\n        | (\n            (f.col(\"pValueExponent\") == exponent)\n            &amp; (f.col(\"pValueMantissa\") &lt;= mantissa)\n        )\n    )\n    return SummaryStatistics(_df=df, _schema=self._schema)\n</code></pre>"},{"location":"python_api/datasets/summary_statistics/#gentropy.dataset.summary_statistics.SummaryStatistics.window_based_clumping","title":"<code>window_based_clumping(distance: int = 500000, gwas_significance: float = 5e-08, baseline_significance: float = 0.05, locus_collect_distance: int | None = None) -&gt; StudyLocus</code>","text":"<p>Generate study-locus from summary statistics by distance based clumping + collect locus.</p> <p>Parameters:</p> Name Type Description Default <code>distance</code> <code>int</code> <p>Distance in base pairs to be used for clumping. Defaults to 500_000.</p> <code>500000</code> <code>gwas_significance</code> <code>float</code> <p>GWAS significance threshold. Defaults to 5e-8.</p> <code>5e-08</code> <code>baseline_significance</code> <code>float</code> <p>Baseline significance threshold for inclusion in the locus. Defaults to 0.05.</p> <code>0.05</code> <code>locus_collect_distance</code> <code>int | None</code> <p>The distance to collect locus around semi-indices. If not provided, locus is not collected.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Clumped study-locus containing variants based on window.</p> Source code in <code>src/gentropy/dataset/summary_statistics.py</code> <pre><code>def window_based_clumping(\n    self: SummaryStatistics,\n    distance: int = 500_000,\n    gwas_significance: float = 5e-8,\n    baseline_significance: float = 0.05,\n    locus_collect_distance: int | None = None,\n) -&gt; StudyLocus:\n    \"\"\"Generate study-locus from summary statistics by distance based clumping + collect locus.\n\n    Args:\n        distance (int): Distance in base pairs to be used for clumping. Defaults to 500_000.\n        gwas_significance (float, optional): GWAS significance threshold. Defaults to 5e-8.\n        baseline_significance (float, optional): Baseline significance threshold for inclusion in the locus. Defaults to 0.05.\n        locus_collect_distance (int | None): The distance to collect locus around semi-indices. If not provided, locus is not collected.\n\n    Returns:\n        StudyLocus: Clumped study-locus containing variants based on window.\n    \"\"\"\n    return (\n        WindowBasedClumping.clump_with_locus(\n            self,\n            window_length=distance,\n            p_value_significance=gwas_significance,\n            p_value_baseline=baseline_significance,\n            locus_window_length=locus_collect_distance,\n        )\n        if locus_collect_distance\n        else WindowBasedClumping.clump(\n            self,\n            window_length=distance,\n            p_value_significance=gwas_significance,\n        )\n    )\n</code></pre>"},{"location":"python_api/datasets/summary_statistics/#schema","title":"Schema","text":"<pre><code>root\n |-- studyId: string (nullable = false)\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- position: integer (nullable = false)\n |-- beta: double (nullable = false)\n |-- sampleSize: integer (nullable = true)\n |-- pValueMantissa: float (nullable = false)\n |-- pValueExponent: integer (nullable = false)\n |-- effectAlleleFrequencyFromSource: float (nullable = true)\n |-- standardError: double (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/","title":"Variant annotation","text":""},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation","title":"<code>gentropy.dataset.variant_annotation.VariantAnnotation</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Dataset with variant-level annotations.</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>@dataclass\nclass VariantAnnotation(Dataset):\n    \"\"\"Dataset with variant-level annotations.\"\"\"\n\n    @classmethod\n    def get_schema(cls: type[VariantAnnotation]) -&gt; StructType:\n        \"\"\"Provides the schema for the VariantAnnotation dataset.\n\n        Returns:\n            StructType: Schema for the VariantAnnotation dataset\n        \"\"\"\n        return parse_spark_schema(\"variant_annotation.json\")\n\n    def max_maf(self: VariantAnnotation) -&gt; Column:\n        \"\"\"Maximum minor allele frequency accross all populations.\n\n        Returns:\n            Column: Maximum minor allele frequency accross all populations.\n        \"\"\"\n        return f.array_max(\n            f.transform(\n                self.df.alleleFrequencies,\n                lambda af: f.when(\n                    af.alleleFrequency &gt; 0.5, 1 - af.alleleFrequency\n                ).otherwise(af.alleleFrequency),\n            )\n        )\n\n    def filter_by_variant_df(\n        self: VariantAnnotation, df: DataFrame\n    ) -&gt; VariantAnnotation:\n        \"\"\"Filter variant annotation dataset by a variant dataframe.\n\n        Args:\n            df (DataFrame): A dataframe of variants\n\n        Returns:\n            VariantAnnotation: A filtered variant annotation dataset\n        \"\"\"\n        self.df = self._df.join(\n            f.broadcast(df.select(\"variantId\", \"chromosome\")),\n            on=[\"variantId\", \"chromosome\"],\n            how=\"inner\",\n        )\n        return self\n\n    def get_transcript_consequence_df(\n        self: VariantAnnotation, gene_index: GeneIndex | None = None\n    ) -&gt; DataFrame:\n        \"\"\"Dataframe of exploded transcript consequences.\n\n        Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n        Args:\n            gene_index (GeneIndex | None): A gene index. Defaults to None.\n\n        Returns:\n            DataFrame: A dataframe exploded by transcript consequences with the columns variantId, chromosome, transcriptConsequence\n        \"\"\"\n        # exploding the array removes records without VEP annotation\n        transript_consequences = self.df.withColumn(\n            \"transcriptConsequence\", f.explode(\"vep.transcriptConsequences\")\n        ).select(\n            \"variantId\",\n            \"chromosome\",\n            \"position\",\n            \"transcriptConsequence\",\n            f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n        )\n        if gene_index:\n            transript_consequences = transript_consequences.join(\n                f.broadcast(gene_index.df),\n                on=[\"chromosome\", \"geneId\"],\n            )\n        return transript_consequences.persist()\n\n    def get_most_severe_vep_v2g(\n        self: VariantAnnotation,\n        vep_consequences: DataFrame,\n        gene_index: GeneIndex,\n    ) -&gt; V2G:\n        \"\"\"Creates a dataset with variant to gene assignments based on VEP's predicted consequence of the transcript.\n\n        Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n        Args:\n            vep_consequences (DataFrame): A dataframe of VEP consequences\n            gene_index (GeneIndex): A gene index to filter by. Defaults to None.\n\n        Returns:\n            V2G: High and medium severity variant to gene assignments\n        \"\"\"\n        return V2G(\n            _df=self.get_transcript_consequence_df(gene_index)\n            .select(\n                \"variantId\",\n                \"chromosome\",\n                f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n                f.explode(\"transcriptConsequence.consequenceTerms\").alias(\"label\"),\n                f.lit(\"vep\").alias(\"datatypeId\"),\n                f.lit(\"variantConsequence\").alias(\"datasourceId\"),\n            )\n            .join(\n                f.broadcast(vep_consequences),\n                on=\"label\",\n                how=\"inner\",\n            )\n            .drop(\"label\")\n            .filter(f.col(\"score\") != 0)\n            # A variant can have multiple predicted consequences on a transcript, the most severe one is selected\n            .transform(\n                lambda df: get_record_with_maximum_value(\n                    df, [\"variantId\", \"geneId\"], \"score\"\n                )\n            ),\n            _schema=V2G.get_schema(),\n        )\n\n    def get_plof_v2g(self: VariantAnnotation, gene_index: GeneIndex) -&gt; V2G:\n        \"\"\"Creates a dataset with variant to gene assignments with a flag indicating if the variant is predicted to be a loss-of-function variant by the LOFTEE algorithm.\n\n        Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n        Args:\n            gene_index (GeneIndex): A gene index to filter by.\n\n        Returns:\n            V2G: variant to gene assignments from the LOFTEE algorithm\n        \"\"\"\n        return V2G(\n            _df=(\n                self.get_transcript_consequence_df(gene_index)\n                .filter(f.col(\"transcriptConsequence.lof\").isNotNull())\n                .withColumn(\n                    \"isHighQualityPlof\",\n                    f.when(f.col(\"transcriptConsequence.lof\") == \"HC\", True).when(\n                        f.col(\"transcriptConsequence.lof\") == \"LC\", False\n                    ),\n                )\n                .withColumn(\n                    \"score\",\n                    f.when(f.col(\"isHighQualityPlof\"), 1.0).when(\n                        ~f.col(\"isHighQualityPlof\"), 0\n                    ),\n                )\n                .select(\n                    \"variantId\",\n                    \"chromosome\",\n                    \"geneId\",\n                    \"isHighQualityPlof\",\n                    f.col(\"score\"),\n                    f.lit(\"vep\").alias(\"datatypeId\"),\n                    f.lit(\"loftee\").alias(\"datasourceId\"),\n                )\n            ),\n            _schema=V2G.get_schema(),\n        )\n\n    def get_distance_to_tss(\n        self: VariantAnnotation,\n        gene_index: GeneIndex,\n        max_distance: int = 500_000,\n    ) -&gt; V2G:\n        \"\"\"Extracts variant to gene assignments for variants falling within a window of a gene's TSS.\n\n        Args:\n            gene_index (GeneIndex): A gene index to filter by.\n            max_distance (int): The maximum distance from the TSS to consider. Defaults to 500_000.\n\n        Returns:\n            V2G: variant to gene assignments with their distance to the TSS\n        \"\"\"\n        return V2G(\n            _df=(\n                self.df.alias(\"variant\")\n                .join(\n                    f.broadcast(gene_index.locations_lut()).alias(\"gene\"),\n                    on=[\n                        f.col(\"variant.chromosome\") == f.col(\"gene.chromosome\"),\n                        f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n                        &lt;= max_distance,\n                    ],\n                    how=\"inner\",\n                )\n                .withColumn(\n                    \"distance\", f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n                )\n                .withColumn(\n                    \"inverse_distance\",\n                    max_distance - f.col(\"distance\"),\n                )\n                .transform(lambda df: normalise_column(df, \"inverse_distance\", \"score\"))\n                .select(\n                    \"variantId\",\n                    f.col(\"variant.chromosome\").alias(\"chromosome\"),\n                    \"distance\",\n                    \"geneId\",\n                    \"score\",\n                    f.lit(\"distance\").alias(\"datatypeId\"),\n                    f.lit(\"canonical_tss\").alias(\"datasourceId\"),\n                )\n            ),\n            _schema=V2G.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation.filter_by_variant_df","title":"<code>filter_by_variant_df(df: DataFrame) -&gt; VariantAnnotation</code>","text":"<p>Filter variant annotation dataset by a variant dataframe.</p> <p>Parameters:</p> Name Type Description Default <code>df</code> <code>DataFrame</code> <p>A dataframe of variants</p> required <p>Returns:</p> Name Type Description <code>VariantAnnotation</code> <code>VariantAnnotation</code> <p>A filtered variant annotation dataset</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>def filter_by_variant_df(\n    self: VariantAnnotation, df: DataFrame\n) -&gt; VariantAnnotation:\n    \"\"\"Filter variant annotation dataset by a variant dataframe.\n\n    Args:\n        df (DataFrame): A dataframe of variants\n\n    Returns:\n        VariantAnnotation: A filtered variant annotation dataset\n    \"\"\"\n    self.df = self._df.join(\n        f.broadcast(df.select(\"variantId\", \"chromosome\")),\n        on=[\"variantId\", \"chromosome\"],\n        how=\"inner\",\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation.get_distance_to_tss","title":"<code>get_distance_to_tss(gene_index: GeneIndex, max_distance: int = 500000) -&gt; V2G</code>","text":"<p>Extracts variant to gene assignments for variants falling within a window of a gene's TSS.</p> <p>Parameters:</p> Name Type Description Default <code>gene_index</code> <code>GeneIndex</code> <p>A gene index to filter by.</p> required <code>max_distance</code> <code>int</code> <p>The maximum distance from the TSS to consider. Defaults to 500_000.</p> <code>500000</code> <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>variant to gene assignments with their distance to the TSS</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>def get_distance_to_tss(\n    self: VariantAnnotation,\n    gene_index: GeneIndex,\n    max_distance: int = 500_000,\n) -&gt; V2G:\n    \"\"\"Extracts variant to gene assignments for variants falling within a window of a gene's TSS.\n\n    Args:\n        gene_index (GeneIndex): A gene index to filter by.\n        max_distance (int): The maximum distance from the TSS to consider. Defaults to 500_000.\n\n    Returns:\n        V2G: variant to gene assignments with their distance to the TSS\n    \"\"\"\n    return V2G(\n        _df=(\n            self.df.alias(\"variant\")\n            .join(\n                f.broadcast(gene_index.locations_lut()).alias(\"gene\"),\n                on=[\n                    f.col(\"variant.chromosome\") == f.col(\"gene.chromosome\"),\n                    f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n                    &lt;= max_distance,\n                ],\n                how=\"inner\",\n            )\n            .withColumn(\n                \"distance\", f.abs(f.col(\"variant.position\") - f.col(\"gene.tss\"))\n            )\n            .withColumn(\n                \"inverse_distance\",\n                max_distance - f.col(\"distance\"),\n            )\n            .transform(lambda df: normalise_column(df, \"inverse_distance\", \"score\"))\n            .select(\n                \"variantId\",\n                f.col(\"variant.chromosome\").alias(\"chromosome\"),\n                \"distance\",\n                \"geneId\",\n                \"score\",\n                f.lit(\"distance\").alias(\"datatypeId\"),\n                f.lit(\"canonical_tss\").alias(\"datasourceId\"),\n            )\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation.get_most_severe_vep_v2g","title":"<code>get_most_severe_vep_v2g(vep_consequences: DataFrame, gene_index: GeneIndex) -&gt; V2G</code>","text":"<p>Creates a dataset with variant to gene assignments based on VEP's predicted consequence of the transcript.</p> <p>Optionally the trancript consequences can be reduced to the universe of a gene index.</p> <p>Parameters:</p> Name Type Description Default <code>vep_consequences</code> <code>DataFrame</code> <p>A dataframe of VEP consequences</p> required <code>gene_index</code> <code>GeneIndex</code> <p>A gene index to filter by. Defaults to None.</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>High and medium severity variant to gene assignments</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>def get_most_severe_vep_v2g(\n    self: VariantAnnotation,\n    vep_consequences: DataFrame,\n    gene_index: GeneIndex,\n) -&gt; V2G:\n    \"\"\"Creates a dataset with variant to gene assignments based on VEP's predicted consequence of the transcript.\n\n    Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n    Args:\n        vep_consequences (DataFrame): A dataframe of VEP consequences\n        gene_index (GeneIndex): A gene index to filter by. Defaults to None.\n\n    Returns:\n        V2G: High and medium severity variant to gene assignments\n    \"\"\"\n    return V2G(\n        _df=self.get_transcript_consequence_df(gene_index)\n        .select(\n            \"variantId\",\n            \"chromosome\",\n            f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n            f.explode(\"transcriptConsequence.consequenceTerms\").alias(\"label\"),\n            f.lit(\"vep\").alias(\"datatypeId\"),\n            f.lit(\"variantConsequence\").alias(\"datasourceId\"),\n        )\n        .join(\n            f.broadcast(vep_consequences),\n            on=\"label\",\n            how=\"inner\",\n        )\n        .drop(\"label\")\n        .filter(f.col(\"score\") != 0)\n        # A variant can have multiple predicted consequences on a transcript, the most severe one is selected\n        .transform(\n            lambda df: get_record_with_maximum_value(\n                df, [\"variantId\", \"geneId\"], \"score\"\n            )\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation.get_plof_v2g","title":"<code>get_plof_v2g(gene_index: GeneIndex) -&gt; V2G</code>","text":"<p>Creates a dataset with variant to gene assignments with a flag indicating if the variant is predicted to be a loss-of-function variant by the LOFTEE algorithm.</p> <p>Optionally the trancript consequences can be reduced to the universe of a gene index.</p> <p>Parameters:</p> Name Type Description Default <code>gene_index</code> <code>GeneIndex</code> <p>A gene index to filter by.</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>variant to gene assignments from the LOFTEE algorithm</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>def get_plof_v2g(self: VariantAnnotation, gene_index: GeneIndex) -&gt; V2G:\n    \"\"\"Creates a dataset with variant to gene assignments with a flag indicating if the variant is predicted to be a loss-of-function variant by the LOFTEE algorithm.\n\n    Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n    Args:\n        gene_index (GeneIndex): A gene index to filter by.\n\n    Returns:\n        V2G: variant to gene assignments from the LOFTEE algorithm\n    \"\"\"\n    return V2G(\n        _df=(\n            self.get_transcript_consequence_df(gene_index)\n            .filter(f.col(\"transcriptConsequence.lof\").isNotNull())\n            .withColumn(\n                \"isHighQualityPlof\",\n                f.when(f.col(\"transcriptConsequence.lof\") == \"HC\", True).when(\n                    f.col(\"transcriptConsequence.lof\") == \"LC\", False\n                ),\n            )\n            .withColumn(\n                \"score\",\n                f.when(f.col(\"isHighQualityPlof\"), 1.0).when(\n                    ~f.col(\"isHighQualityPlof\"), 0\n                ),\n            )\n            .select(\n                \"variantId\",\n                \"chromosome\",\n                \"geneId\",\n                \"isHighQualityPlof\",\n                f.col(\"score\"),\n                f.lit(\"vep\").alias(\"datatypeId\"),\n                f.lit(\"loftee\").alias(\"datasourceId\"),\n            )\n        ),\n        _schema=V2G.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the VariantAnnotation dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the VariantAnnotation dataset</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[VariantAnnotation]) -&gt; StructType:\n    \"\"\"Provides the schema for the VariantAnnotation dataset.\n\n    Returns:\n        StructType: Schema for the VariantAnnotation dataset\n    \"\"\"\n    return parse_spark_schema(\"variant_annotation.json\")\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation.get_transcript_consequence_df","title":"<code>get_transcript_consequence_df(gene_index: GeneIndex | None = None) -&gt; DataFrame</code>","text":"<p>Dataframe of exploded transcript consequences.</p> <p>Optionally the trancript consequences can be reduced to the universe of a gene index.</p> <p>Parameters:</p> Name Type Description Default <code>gene_index</code> <code>GeneIndex | None</code> <p>A gene index. Defaults to None.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>A dataframe exploded by transcript consequences with the columns variantId, chromosome, transcriptConsequence</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>def get_transcript_consequence_df(\n    self: VariantAnnotation, gene_index: GeneIndex | None = None\n) -&gt; DataFrame:\n    \"\"\"Dataframe of exploded transcript consequences.\n\n    Optionally the trancript consequences can be reduced to the universe of a gene index.\n\n    Args:\n        gene_index (GeneIndex | None): A gene index. Defaults to None.\n\n    Returns:\n        DataFrame: A dataframe exploded by transcript consequences with the columns variantId, chromosome, transcriptConsequence\n    \"\"\"\n    # exploding the array removes records without VEP annotation\n    transript_consequences = self.df.withColumn(\n        \"transcriptConsequence\", f.explode(\"vep.transcriptConsequences\")\n    ).select(\n        \"variantId\",\n        \"chromosome\",\n        \"position\",\n        \"transcriptConsequence\",\n        f.col(\"transcriptConsequence.geneId\").alias(\"geneId\"),\n    )\n    if gene_index:\n        transript_consequences = transript_consequences.join(\n            f.broadcast(gene_index.df),\n            on=[\"chromosome\", \"geneId\"],\n        )\n    return transript_consequences.persist()\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#gentropy.dataset.variant_annotation.VariantAnnotation.max_maf","title":"<code>max_maf() -&gt; Column</code>","text":"<p>Maximum minor allele frequency accross all populations.</p> <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>Maximum minor allele frequency accross all populations.</p> Source code in <code>src/gentropy/dataset/variant_annotation.py</code> <pre><code>def max_maf(self: VariantAnnotation) -&gt; Column:\n    \"\"\"Maximum minor allele frequency accross all populations.\n\n    Returns:\n        Column: Maximum minor allele frequency accross all populations.\n    \"\"\"\n    return f.array_max(\n        f.transform(\n            self.df.alleleFrequencies,\n            lambda af: f.when(\n                af.alleleFrequency &gt; 0.5, 1 - af.alleleFrequency\n            ).otherwise(af.alleleFrequency),\n        )\n    )\n</code></pre>"},{"location":"python_api/datasets/variant_annotation/#schema","title":"Schema","text":"<pre><code>root\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- position: integer (nullable = false)\n |-- gnomadVariantId: string (nullable = false)\n |-- referenceAllele: string (nullable = false)\n |-- alternateAllele: string (nullable = false)\n |-- chromosomeB37: string (nullable = true)\n |-- positionB37: integer (nullable = true)\n |-- alleleType: string (nullable = true)\n |-- rsIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n |-- alleleFrequencies: array (nullable = false)\n |    |-- element: struct (containsNull = true)\n |    |    |-- populationName: string (nullable = true)\n |    |    |-- alleleFrequency: double (nullable = true)\n |-- inSilicoPredictors: struct (nullable = false)\n |    |-- cadd: struct (nullable = true)\n |    |    |-- raw: float (nullable = true)\n |    |    |-- phred: float (nullable = true)\n |    |-- revelMax: double (nullable = true)\n |    |-- spliceaiDsMax: float (nullable = true)\n |    |-- pangolinLargestDs: double (nullable = true)\n |    |-- phylop: double (nullable = true)\n |    |-- siftMax: double (nullable = true)\n |    |-- polyphenMax: double (nullable = true)\n |-- vep: struct (nullable = false)\n |    |-- mostSevereConsequence: string (nullable = true)\n |    |-- transcriptConsequences: array (nullable = true)\n |    |    |-- element: struct (containsNull = true)\n |    |    |    |-- aminoAcids: string (nullable = true)\n |    |    |    |-- consequenceTerms: array (nullable = true)\n |    |    |    |    |-- element: string (containsNull = true)\n |    |    |    |-- geneId: string (nullable = true)\n |    |    |    |-- lof: string (nullable = true)\n</code></pre>"},{"location":"python_api/datasets/variant_index/","title":"Variant index","text":""},{"location":"python_api/datasets/variant_index/#gentropy.dataset.variant_index.VariantIndex","title":"<code>gentropy.dataset.variant_index.VariantIndex</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Variant index dataset.</p> <p>Variant index dataset is the result of intersecting the variant annotation dataset with the variants with V2D available information.</p> Source code in <code>src/gentropy/dataset/variant_index.py</code> <pre><code>@dataclass\nclass VariantIndex(Dataset):\n    \"\"\"Variant index dataset.\n\n    Variant index dataset is the result of intersecting the variant annotation dataset with the variants with V2D available information.\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[VariantIndex]) -&gt; StructType:\n        \"\"\"Provides the schema for the VariantIndex dataset.\n\n        Returns:\n            StructType: Schema for the VariantIndex dataset\n        \"\"\"\n        return parse_spark_schema(\"variant_index.json\")\n\n    @classmethod\n    def from_variant_annotation(\n        cls: type[VariantIndex],\n        variant_annotation: VariantAnnotation,\n        study_locus: StudyLocus,\n    ) -&gt; VariantIndex:\n        \"\"\"Initialise VariantIndex from pre-existing variant annotation dataset.\n\n        Args:\n            variant_annotation (VariantAnnotation): Variant annotation dataset\n            study_locus (StudyLocus): Study locus dataset with the variants to intersect with the variant annotation dataset\n\n        Returns:\n            VariantIndex: Variant index dataset\n        \"\"\"\n        unchanged_cols = [\n            \"variantId\",\n            \"chromosome\",\n            \"position\",\n            \"referenceAllele\",\n            \"alternateAllele\",\n            \"chromosomeB37\",\n            \"positionB37\",\n            \"alleleType\",\n            \"alleleFrequencies\",\n            \"inSilicoPredictors\",\n        ]\n        va_slimmed = variant_annotation.filter_by_variant_df(\n            study_locus.unique_variants_in_locus()\n        )\n        return cls(\n            _df=(\n                va_slimmed.df.select(\n                    *unchanged_cols,\n                    f.col(\"vep.mostSevereConsequence\").alias(\"mostSevereConsequence\"),\n                    # filters/rsid are arrays that can be empty, in this case we convert them to null\n                    nullify_empty_array(f.col(\"rsIds\")).alias(\"rsIds\"),\n                )\n                .repartition(400, \"chromosome\")\n                .sortWithinPartitions(\"chromosome\", \"position\")\n            ),\n            _schema=cls.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasets/variant_index/#gentropy.dataset.variant_index.VariantIndex.from_variant_annotation","title":"<code>from_variant_annotation(variant_annotation: VariantAnnotation, study_locus: StudyLocus) -&gt; VariantIndex</code>  <code>classmethod</code>","text":"<p>Initialise VariantIndex from pre-existing variant annotation dataset.</p> <p>Parameters:</p> Name Type Description Default <code>variant_annotation</code> <code>VariantAnnotation</code> <p>Variant annotation dataset</p> required <code>study_locus</code> <code>StudyLocus</code> <p>Study locus dataset with the variants to intersect with the variant annotation dataset</p> required <p>Returns:</p> Name Type Description <code>VariantIndex</code> <code>VariantIndex</code> <p>Variant index dataset</p> Source code in <code>src/gentropy/dataset/variant_index.py</code> <pre><code>@classmethod\ndef from_variant_annotation(\n    cls: type[VariantIndex],\n    variant_annotation: VariantAnnotation,\n    study_locus: StudyLocus,\n) -&gt; VariantIndex:\n    \"\"\"Initialise VariantIndex from pre-existing variant annotation dataset.\n\n    Args:\n        variant_annotation (VariantAnnotation): Variant annotation dataset\n        study_locus (StudyLocus): Study locus dataset with the variants to intersect with the variant annotation dataset\n\n    Returns:\n        VariantIndex: Variant index dataset\n    \"\"\"\n    unchanged_cols = [\n        \"variantId\",\n        \"chromosome\",\n        \"position\",\n        \"referenceAllele\",\n        \"alternateAllele\",\n        \"chromosomeB37\",\n        \"positionB37\",\n        \"alleleType\",\n        \"alleleFrequencies\",\n        \"inSilicoPredictors\",\n    ]\n    va_slimmed = variant_annotation.filter_by_variant_df(\n        study_locus.unique_variants_in_locus()\n    )\n    return cls(\n        _df=(\n            va_slimmed.df.select(\n                *unchanged_cols,\n                f.col(\"vep.mostSevereConsequence\").alias(\"mostSevereConsequence\"),\n                # filters/rsid are arrays that can be empty, in this case we convert them to null\n                nullify_empty_array(f.col(\"rsIds\")).alias(\"rsIds\"),\n            )\n            .repartition(400, \"chromosome\")\n            .sortWithinPartitions(\"chromosome\", \"position\")\n        ),\n        _schema=cls.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasets/variant_index/#gentropy.dataset.variant_index.VariantIndex.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the VariantIndex dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the VariantIndex dataset</p> Source code in <code>src/gentropy/dataset/variant_index.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[VariantIndex]) -&gt; StructType:\n    \"\"\"Provides the schema for the VariantIndex dataset.\n\n    Returns:\n        StructType: Schema for the VariantIndex dataset\n    \"\"\"\n    return parse_spark_schema(\"variant_index.json\")\n</code></pre>"},{"location":"python_api/datasets/variant_index/#schema","title":"Schema","text":"<pre><code>root\n |-- variantId: string (nullable = false)\n |-- chromosome: string (nullable = false)\n |-- position: integer (nullable = false)\n |-- referenceAllele: string (nullable = false)\n |-- alternateAllele: string (nullable = false)\n |-- chromosomeB37: string (nullable = true)\n |-- positionB37: integer (nullable = true)\n |-- alleleType: string (nullable = false)\n |-- alleleFrequencies: array (nullable = false)\n |    |-- element: struct (containsNull = true)\n |    |    |-- populationName: string (nullable = true)\n |    |    |-- alleleFrequency: double (nullable = true)\n |-- inSilicoPredictors: struct (nullable = false)\n |    |-- cadd: struct (nullable = true)\n |    |    |-- raw: float (nullable = true)\n |    |    |-- phred: float (nullable = true)\n |    |-- revelMax: double (nullable = true)\n |    |-- spliceaiDsMax: float (nullable = true)\n |    |-- pangolinLargestDs: double (nullable = true)\n |    |-- phylop: double (nullable = true)\n |    |-- siftMax: double (nullable = true)\n |    |-- polyphenMax: double (nullable = true)\n |-- mostSevereConsequence: string (nullable = true)\n |-- rsIds: array (nullable = true)\n |    |-- element: string (containsNull = true)\n</code></pre>"},{"location":"python_api/datasets/variant_to_gene/","title":"Variant-to-gene","text":""},{"location":"python_api/datasets/variant_to_gene/#gentropy.dataset.v2g.V2G","title":"<code>gentropy.dataset.v2g.V2G</code>  <code>dataclass</code>","text":"<p>             Bases: <code>Dataset</code></p> <p>Variant-to-gene (V2G) evidence dataset.</p> <p>A variant-to-gene (V2G) evidence is understood as any piece of evidence that supports the association of a variant with a likely causal gene. The evidence can sometimes be context-specific and refer to specific <code>biofeatures</code> (e.g. cell types)</p> Source code in <code>src/gentropy/dataset/v2g.py</code> <pre><code>@dataclass\nclass V2G(Dataset):\n    \"\"\"Variant-to-gene (V2G) evidence dataset.\n\n    A variant-to-gene (V2G) evidence is understood as any piece of evidence that supports the association of a variant with a likely causal gene. The evidence can sometimes be context-specific and refer to specific `biofeatures` (e.g. cell types)\n    \"\"\"\n\n    @classmethod\n    def get_schema(cls: type[V2G]) -&gt; StructType:\n        \"\"\"Provides the schema for the V2G dataset.\n\n        Returns:\n            StructType: Schema for the V2G dataset\n        \"\"\"\n        return parse_spark_schema(\"v2g.json\")\n\n    def filter_by_genes(self: V2G, genes: GeneIndex) -&gt; V2G:\n        \"\"\"Filter V2G dataset by genes.\n\n        Args:\n            genes (GeneIndex): Gene index dataset to filter by\n\n        Returns:\n            V2G: V2G dataset filtered by genes\n        \"\"\"\n        self.df = self._df.join(genes.df.select(\"geneId\"), on=\"geneId\", how=\"inner\")\n        return self\n\n    def extract_distance_tss_minimum(self: V2G) -&gt; None:\n        \"\"\"Extract minimum distance to TSS.\"\"\"\n        self.df = self._df.filter(f.col(\"distance\")).withColumn(\n            \"distanceTssMinimum\",\n            f.expr(\"min(distTss) OVER (PARTITION BY studyLocusId)\"),\n        )\n</code></pre>"},{"location":"python_api/datasets/variant_to_gene/#gentropy.dataset.v2g.V2G.extract_distance_tss_minimum","title":"<code>extract_distance_tss_minimum() -&gt; None</code>","text":"<p>Extract minimum distance to TSS.</p> Source code in <code>src/gentropy/dataset/v2g.py</code> <pre><code>def extract_distance_tss_minimum(self: V2G) -&gt; None:\n    \"\"\"Extract minimum distance to TSS.\"\"\"\n    self.df = self._df.filter(f.col(\"distance\")).withColumn(\n        \"distanceTssMinimum\",\n        f.expr(\"min(distTss) OVER (PARTITION BY studyLocusId)\"),\n    )\n</code></pre>"},{"location":"python_api/datasets/variant_to_gene/#gentropy.dataset.v2g.V2G.filter_by_genes","title":"<code>filter_by_genes(genes: GeneIndex) -&gt; V2G</code>","text":"<p>Filter V2G dataset by genes.</p> <p>Parameters:</p> Name Type Description Default <code>genes</code> <code>GeneIndex</code> <p>Gene index dataset to filter by</p> required <p>Returns:</p> Name Type Description <code>V2G</code> <code>V2G</code> <p>V2G dataset filtered by genes</p> Source code in <code>src/gentropy/dataset/v2g.py</code> <pre><code>def filter_by_genes(self: V2G, genes: GeneIndex) -&gt; V2G:\n    \"\"\"Filter V2G dataset by genes.\n\n    Args:\n        genes (GeneIndex): Gene index dataset to filter by\n\n    Returns:\n        V2G: V2G dataset filtered by genes\n    \"\"\"\n    self.df = self._df.join(genes.df.select(\"geneId\"), on=\"geneId\", how=\"inner\")\n    return self\n</code></pre>"},{"location":"python_api/datasets/variant_to_gene/#gentropy.dataset.v2g.V2G.get_schema","title":"<code>get_schema() -&gt; StructType</code>  <code>classmethod</code>","text":"<p>Provides the schema for the V2G dataset.</p> <p>Returns:</p> Name Type Description <code>StructType</code> <code>StructType</code> <p>Schema for the V2G dataset</p> Source code in <code>src/gentropy/dataset/v2g.py</code> <pre><code>@classmethod\ndef get_schema(cls: type[V2G]) -&gt; StructType:\n    \"\"\"Provides the schema for the V2G dataset.\n\n    Returns:\n        StructType: Schema for the V2G dataset\n    \"\"\"\n    return parse_spark_schema(\"v2g.json\")\n</code></pre>"},{"location":"python_api/datasets/variant_to_gene/#schema","title":"Schema","text":"<pre><code>root\n |-- geneId: string (nullable = false)\n |-- variantId: string (nullable = false)\n |-- distance: long (nullable = true)\n |-- chromosome: string (nullable = false)\n |-- datatypeId: string (nullable = false)\n |-- datasourceId: string (nullable = false)\n |-- score: double (nullable = true)\n |-- resourceScore: double (nullable = true)\n |-- pmid: string (nullable = true)\n |-- biofeature: string (nullable = true)\n |-- variantFunctionalConsequenceId: string (nullable = true)\n |-- isHighQualityPlof: boolean (nullable = true)\n</code></pre>"},{"location":"python_api/datasources/_datasources/","title":"Data Sources","text":"<p>This section contains information about the data source harmonisation tools available in Open Targets Gentropy.</p>"},{"location":"python_api/datasources/_datasources/#gwas-study-sources","title":"GWAS study sources","text":"<ol> <li>GWAS Catalog (with or without full summary statistics)</li> <li>FinnGen</li> </ol>"},{"location":"python_api/datasources/_datasources/#molecular-qtls","title":"Molecular QTLs","text":"<ol> <li>GTEx (eQTL catalogue)</li> </ol>"},{"location":"python_api/datasources/_datasources/#interaction-interval-based-experiments","title":"Interaction / Interval-based Experiments","text":"<ol> <li>Intervals-based datasets, informing about the relationships between genetic elements and their functional implications.</li> </ol>"},{"location":"python_api/datasources/_datasources/#variant-annotationvalidation","title":"Variant annotation/validation","text":"<ol> <li>GnomAD v4.0</li> <li>GWAS catalog harmonisation pipeline more info</li> </ol>"},{"location":"python_api/datasources/_datasources/#linkage-desiquilibrium","title":"Linkage desiquilibrium","text":"<ol> <li>GnomAD v2.1.1 LD matrixes (7 ancestries)</li> </ol>"},{"location":"python_api/datasources/_datasources/#locus-to-gene-gold-standard","title":"Locus-to-gene gold standard","text":"<ol> <li>Open Targets training set</li> </ol>"},{"location":"python_api/datasources/_datasources/#gene-annotation","title":"Gene annotation","text":"<ol> <li>Open Targets Platform Target Dataset (derived from Ensembl)</li> </ol>"},{"location":"python_api/datasources/eqtl_catalogue/_eqtl_catalogue/","title":"eQTL Catalogue","text":"<p>The eQTL Catalogue aims to provide uniformly processed gene expression and splicing Quantitative Trait Loci (QTLs) from all available public studies on humans.</p> <p>It serves as the ultimate resource of eQTLs that we use for colocalization and target prioritization.</p> <p>We utilize data from the following study within the eQTL Catalogue:</p> <ol> <li>GTEx v8, 49 tissues</li> </ol>"},{"location":"python_api/datasources/eqtl_catalogue/study_index/","title":"Study Index","text":""},{"location":"python_api/datasources/eqtl_catalogue/study_index/#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex","title":"<code>gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex</code>","text":"<p>Study index dataset from eQTL Catalogue.</p> Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code> <pre><code>class EqtlCatalogueStudyIndex:\n    \"\"\"Study index dataset from eQTL Catalogue.\"\"\"\n\n    study_config = {\n        \"GTEx_V8\": {\n            \"nSamples\": 838,\n            \"initialSampleSize\": \"838 (281 females and 557 males)\",\n            \"discoverySamples\": [\n                {\"sampleSize\": 715, \"ancestry\": \"European American\"},\n                {\"sampleSize\": 103, \"ancestry\": \"African American\"},\n                {\"sampleSize\": 12, \"ancestry\": \"Asian American\"},\n                {\"sampleSize\": 16, \"ancestry\": \"Hispanic or Latino\"},\n            ],\n            \"ldPopulationStructure\": [\n                {\"ldPopulation\": \"nfe\", \"relativeSampleSize\": 0.85},\n                {\"ldPopulation\": \"afr\", \"relativeSampleSize\": 0.12},\n                {\"ldPopulation\": \"eas\", \"relativeSampleSize\": 0.01},\n                {\"ldPopulation\": \"amr\", \"relativeSampleSize\": 0.02},\n            ],\n            \"pubmedId\": \"32913098\",\n            \"publicationTitle\": \"The GTEx Consortium atlas of genetic regulatory effects across human tissues\",\n            \"publicationFirstAuthor\": \"GTEx Consortium\",\n            \"publicationDate\": \"2020-09-11\",\n            \"publicationJournal\": \"Science\",\n        },\n    }\n\n    @classmethod\n    def get_study_attribute(\n        cls: Type[EqtlCatalogueStudyIndex], attribute_key: str\n    ) -&gt; Column:\n        \"\"\"Returns a Column expression that dynamically assigns the attribute based on the study.\n\n        Args:\n            attribute_key (str): The attribute key to assign.\n\n        Returns:\n            Column: The dynamically assigned attribute.\n\n        Raises:\n            ValueError: If the attribute key is not known for the study.\n        \"\"\"\n        study_column = f.col(\"study\")\n        for study, config in cls.study_config.items():\n            attribute_value = config.get(attribute_key)\n            if attribute_value is None:\n                raise ValueError(\n                    f\"Unknown attribute key {attribute_key} for study {study}\"\n                )\n            # Convert list of dicts to array of structs\n            if isinstance(attribute_value, list) and isinstance(\n                attribute_value[0], dict\n            ):\n                struct_fields = [\n                    f.struct(*[f.lit(value).alias(key) for key, value in item.items()])\n                    for item in attribute_value\n                ]\n                attribute_value = f.array(struct_fields)\n            # Convert dict to struct\n            elif isinstance(attribute_value, dict):\n                attribute_value = f.struct(\n                    *[f.lit(value).alias(key) for key, value in attribute_value.items()]\n                )\n        return f.when(study_column == study, attribute_value).alias(attribute_key)\n\n    @classmethod\n    def _all_attributes(cls: Type[EqtlCatalogueStudyIndex]) -&gt; list[Column]:\n        \"\"\"A helper function to return all study index attribute expressions.\n\n        Returns:\n            list[Column]: A list of all study index attribute expressions.\n        \"\"\"\n        study_column = f.col(\"study\")\n\n        static_study_attributes = [\n            study_column.alias(\"projectId\"),\n            f.concat(study_column, f.lit(\"_\"), f.col(\"qtl_group\")).alias(\"studyId\"),\n            f.col(\"ftp_path\").alias(\"summarystatsLocation\"),\n            f.lit(True).alias(\"hasSumstats\"),\n            f.lit(\"eqtl\").alias(\"studyType\"),\n        ]\n        tissue_attributes = [\n            # Human readable tissue label, example: \"Adipose - Subcutaneous\".\n            f.col(\"tissue_label\").alias(\"traitFromSource\"),\n            # Ontology identifier for the tissue, for example: \"UBERON:0001157\".\n            f.array(\n                f.regexp_replace(\n                    f.regexp_replace(\n                        f.col(\"tissue_ontology_id\"),\n                        \"UBER_\",\n                        \"UBERON_\",\n                    ),\n                    \"_\",\n                    \":\",\n                )\n            ).alias(\"traitFromSourceMappedIds\"),\n        ]\n        dynamic_study_attributes = [\n            cls.get_study_attribute(\"nSamples\"),\n            cls.get_study_attribute(\"initialSampleSize\"),\n            cls.get_study_attribute(\"discoverySamples\"),\n            cls.get_study_attribute(\"ldPopulationStructure\"),\n            cls.get_study_attribute(\"pubmedId\"),\n            cls.get_study_attribute(\"publicationTitle\"),\n            cls.get_study_attribute(\"publicationFirstAuthor\"),\n            cls.get_study_attribute(\"publicationDate\"),\n            cls.get_study_attribute(\"publicationJournal\"),\n        ]\n        return static_study_attributes + tissue_attributes + dynamic_study_attributes\n\n    @classmethod\n    def add_gene_to_study_id(\n        cls: type[EqtlCatalogueStudyIndex],\n        study_index_df: DataFrame,\n        summary_stats_df: DataFrame,\n    ) -&gt; StudyIndex:\n        \"\"\"Update the studyId to include gene information from summary statistics. A geneId column is also added.\n\n        While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for\n        an expression of a _particular gene_ in a particular study.  At this stage we have a study index with partial\n        study IDs like \"PROJECT_QTLGROUP\", and a summary statistics object with full study IDs like\n        \"PROJECT_QTLGROUP_GENEID\", so we need to perform a merge and explosion to obtain our final study index.\n\n        Args:\n            study_index_df (DataFrame): preliminary study index for eQTL Catalogue studies.\n            summary_stats_df (DataFrame): summary statistics dataframe for eQTL Catalogue data.\n\n        Returns:\n            StudyIndex: final study index for eQTL Catalogue studies.\n        \"\"\"\n        partial_to_full_study_id = summary_stats_df.select(\n            f.col(\"studyId\").alias(\"fullStudyId\"),  # PROJECT_QTLGROUP_GENEID\n            f.regexp_extract(f.col(\"studyId\"), r\"^(.*)_ENSG\\d+\", 1).alias(\n                \"studyId\"\n            ),  # PROJECT_QTLGROUP\n        ).distinct()\n        study_index_df = (\n            partial_to_full_study_id.join(\n                f.broadcast(study_index_df), \"studyId\", \"inner\"\n            )\n            # Change studyId to fullStudyId\n            .drop(\"studyId\")\n            .withColumnRenamed(\"fullStudyId\", \"studyId\")\n            # Add geneId column\n            .withColumn(\"geneId\", f.regexp_extract(f.col(\"studyId\"), r\"([^_]+)$\", 1))\n        )\n        return StudyIndex(_df=study_index_df, _schema=StudyIndex.get_schema())\n\n    @classmethod\n    def from_source(\n        cls: type[EqtlCatalogueStudyIndex],\n        eqtl_studies: DataFrame,\n    ) -&gt; StudyIndex:\n        \"\"\"Ingest study level metadata from eQTL Catalogue.\n\n        Args:\n            eqtl_studies (DataFrame): ingested but unprocessed eQTL Catalogue studies.\n\n        Returns:\n            StudyIndex: preliminary processed study index for eQTL Catalogue studies.\n        \"\"\"\n        return StudyIndex(\n            _df=eqtl_studies.select(*cls._all_attributes()),\n            _schema=StudyIndex.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/eqtl_catalogue/study_index/#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.add_gene_to_study_id","title":"<code>add_gene_to_study_id(study_index_df: DataFrame, summary_stats_df: DataFrame) -&gt; StudyIndex</code>  <code>classmethod</code>","text":"<p>Update the studyId to include gene information from summary statistics. A geneId column is also added.</p> <p>While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for an expression of a particular gene in a particular study.  At this stage we have a study index with partial study IDs like \"PROJECT_QTLGROUP\", and a summary statistics object with full study IDs like \"PROJECT_QTLGROUP_GENEID\", so we need to perform a merge and explosion to obtain our final study index.</p> <p>Parameters:</p> Name Type Description Default <code>study_index_df</code> <code>DataFrame</code> <p>preliminary study index for eQTL Catalogue studies.</p> required <code>summary_stats_df</code> <code>DataFrame</code> <p>summary statistics dataframe for eQTL Catalogue data.</p> required <p>Returns:</p> Name Type Description <code>StudyIndex</code> <code>StudyIndex</code> <p>final study index for eQTL Catalogue studies.</p> Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code> <pre><code>@classmethod\ndef add_gene_to_study_id(\n    cls: type[EqtlCatalogueStudyIndex],\n    study_index_df: DataFrame,\n    summary_stats_df: DataFrame,\n) -&gt; StudyIndex:\n    \"\"\"Update the studyId to include gene information from summary statistics. A geneId column is also added.\n\n    While the original list contains one entry per tissue, what we consider as a single study is one mini-GWAS for\n    an expression of a _particular gene_ in a particular study.  At this stage we have a study index with partial\n    study IDs like \"PROJECT_QTLGROUP\", and a summary statistics object with full study IDs like\n    \"PROJECT_QTLGROUP_GENEID\", so we need to perform a merge and explosion to obtain our final study index.\n\n    Args:\n        study_index_df (DataFrame): preliminary study index for eQTL Catalogue studies.\n        summary_stats_df (DataFrame): summary statistics dataframe for eQTL Catalogue data.\n\n    Returns:\n        StudyIndex: final study index for eQTL Catalogue studies.\n    \"\"\"\n    partial_to_full_study_id = summary_stats_df.select(\n        f.col(\"studyId\").alias(\"fullStudyId\"),  # PROJECT_QTLGROUP_GENEID\n        f.regexp_extract(f.col(\"studyId\"), r\"^(.*)_ENSG\\d+\", 1).alias(\n            \"studyId\"\n        ),  # PROJECT_QTLGROUP\n    ).distinct()\n    study_index_df = (\n        partial_to_full_study_id.join(\n            f.broadcast(study_index_df), \"studyId\", \"inner\"\n        )\n        # Change studyId to fullStudyId\n        .drop(\"studyId\")\n        .withColumnRenamed(\"fullStudyId\", \"studyId\")\n        # Add geneId column\n        .withColumn(\"geneId\", f.regexp_extract(f.col(\"studyId\"), r\"([^_]+)$\", 1))\n    )\n    return StudyIndex(_df=study_index_df, _schema=StudyIndex.get_schema())\n</code></pre>"},{"location":"python_api/datasources/eqtl_catalogue/study_index/#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.from_source","title":"<code>from_source(eqtl_studies: DataFrame) -&gt; StudyIndex</code>  <code>classmethod</code>","text":"<p>Ingest study level metadata from eQTL Catalogue.</p> <p>Parameters:</p> Name Type Description Default <code>eqtl_studies</code> <code>DataFrame</code> <p>ingested but unprocessed eQTL Catalogue studies.</p> required <p>Returns:</p> Name Type Description <code>StudyIndex</code> <code>StudyIndex</code> <p>preliminary processed study index for eQTL Catalogue studies.</p> Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[EqtlCatalogueStudyIndex],\n    eqtl_studies: DataFrame,\n) -&gt; StudyIndex:\n    \"\"\"Ingest study level metadata from eQTL Catalogue.\n\n    Args:\n        eqtl_studies (DataFrame): ingested but unprocessed eQTL Catalogue studies.\n\n    Returns:\n        StudyIndex: preliminary processed study index for eQTL Catalogue studies.\n    \"\"\"\n    return StudyIndex(\n        _df=eqtl_studies.select(*cls._all_attributes()),\n        _schema=StudyIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/eqtl_catalogue/study_index/#gentropy.datasource.eqtl_catalogue.study_index.EqtlCatalogueStudyIndex.get_study_attribute","title":"<code>get_study_attribute(attribute_key: str) -&gt; Column</code>  <code>classmethod</code>","text":"<p>Returns a Column expression that dynamically assigns the attribute based on the study.</p> <p>Parameters:</p> Name Type Description Default <code>attribute_key</code> <code>str</code> <p>The attribute key to assign.</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>The dynamically assigned attribute.</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the attribute key is not known for the study.</p> Source code in <code>src/gentropy/datasource/eqtl_catalogue/study_index.py</code> <pre><code>@classmethod\ndef get_study_attribute(\n    cls: Type[EqtlCatalogueStudyIndex], attribute_key: str\n) -&gt; Column:\n    \"\"\"Returns a Column expression that dynamically assigns the attribute based on the study.\n\n    Args:\n        attribute_key (str): The attribute key to assign.\n\n    Returns:\n        Column: The dynamically assigned attribute.\n\n    Raises:\n        ValueError: If the attribute key is not known for the study.\n    \"\"\"\n    study_column = f.col(\"study\")\n    for study, config in cls.study_config.items():\n        attribute_value = config.get(attribute_key)\n        if attribute_value is None:\n            raise ValueError(\n                f\"Unknown attribute key {attribute_key} for study {study}\"\n            )\n        # Convert list of dicts to array of structs\n        if isinstance(attribute_value, list) and isinstance(\n            attribute_value[0], dict\n        ):\n            struct_fields = [\n                f.struct(*[f.lit(value).alias(key) for key, value in item.items()])\n                for item in attribute_value\n            ]\n            attribute_value = f.array(struct_fields)\n        # Convert dict to struct\n        elif isinstance(attribute_value, dict):\n            attribute_value = f.struct(\n                *[f.lit(value).alias(key) for key, value in attribute_value.items()]\n            )\n    return f.when(study_column == study, attribute_value).alias(attribute_key)\n</code></pre>"},{"location":"python_api/datasources/eqtl_catalogue/summary_stats/","title":"Summary Stats","text":""},{"location":"python_api/datasources/eqtl_catalogue/summary_stats/#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats","title":"<code>gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats</code>  <code>dataclass</code>","text":"<p>Summary statistics dataset for eQTL Catalogue.</p> Source code in <code>src/gentropy/datasource/eqtl_catalogue/summary_stats.py</code> <pre><code>@dataclass\nclass EqtlCatalogueSummaryStats:\n    \"\"\"Summary statistics dataset for eQTL Catalogue.\"\"\"\n\n    @staticmethod\n    def _full_study_id_regexp() -&gt; Column:\n        \"\"\"Constructs a full study ID from the URI.\n\n        Returns:\n            Column: expression to extract a full study ID from the URI.\n        \"\"\"\n        # Example of a URI which is used for parsing:\n        # \"gs://genetics_etl_python_playground/input/preprocess/eqtl_catalogue/imported/GTEx_V8/ge/Adipose_Subcutaneous.tsv.gz\".\n\n        # Regular expession to extract project ID from URI.  Example: \"GTEx_V8\".\n        _project_id = f.regexp_extract(\n            f.input_file_name(),\n            r\"imported/([^/]+)/.*\",\n            1,\n        )\n        # Regular expression to extract QTL group from URI.  Example: \"Adipose_Subcutaneous\".\n        _qtl_group = f.regexp_extract(f.input_file_name(), r\"([^/]+)\\.tsv\\.gz\", 1)\n        # Extracting gene ID from the column.  Example: \"ENSG00000225630\".\n        _gene_id = f.col(\"gene_id\")\n\n        # We can now construct the full study ID based on all fields.\n        # Example: \"GTEx_V8_Adipose_Subcutaneous_ENSG00000225630\".\n        return f.concat(_project_id, f.lit(\"_\"), _qtl_group, f.lit(\"_\"), _gene_id)\n\n    @classmethod\n    def from_source(\n        cls: type[EqtlCatalogueSummaryStats],\n        summary_stats_df: DataFrame,\n    ) -&gt; SummaryStatistics:\n        \"\"\"Ingests all summary stats for all eQTL Catalogue studies.\n\n        Args:\n            summary_stats_df (DataFrame): an ingested but unprocessed summary statistics dataframe from eQTL Catalogue.\n\n        Returns:\n            SummaryStatistics: a processed summary statistics dataframe for eQTL Catalogue.\n        \"\"\"\n        processed_summary_stats_df = (\n            summary_stats_df.select(\n                # Construct study ID from the appropriate columns.\n                cls._full_study_id_regexp().alias(\"studyId\"),\n                # Add variant information.\n                f.concat_ws(\n                    \"_\",\n                    f.col(\"chromosome\"),\n                    f.col(\"position\"),\n                    f.col(\"ref\"),\n                    f.col(\"alt\"),\n                ).alias(\"variantId\"),\n                f.col(\"chromosome\"),\n                f.col(\"position\").cast(t.IntegerType()),\n                # Parse p-value into mantissa and exponent.\n                *parse_pvalue(f.col(\"pvalue\")),\n                # Add beta, standard error, and allele frequency information.\n                f.col(\"beta\").cast(\"double\"),\n                f.col(\"se\").cast(\"double\").alias(\"standardError\"),\n                f.col(\"maf\").cast(\"float\").alias(\"effectAlleleFrequencyFromSource\"),\n            )\n            # Drop rows which don't have proper position or beta value.\n            .filter(\n                f.col(\"position\").cast(t.IntegerType()).isNotNull()\n                &amp; (f.col(\"beta\") != 0)\n            )\n        )\n\n        # Initialise a summary statistics object.\n        return SummaryStatistics(\n            _df=processed_summary_stats_df,\n            _schema=SummaryStatistics.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/eqtl_catalogue/summary_stats/#gentropy.datasource.eqtl_catalogue.summary_stats.EqtlCatalogueSummaryStats.from_source","title":"<code>from_source(summary_stats_df: DataFrame) -&gt; SummaryStatistics</code>  <code>classmethod</code>","text":"<p>Ingests all summary stats for all eQTL Catalogue studies.</p> <p>Parameters:</p> Name Type Description Default <code>summary_stats_df</code> <code>DataFrame</code> <p>an ingested but unprocessed summary statistics dataframe from eQTL Catalogue.</p> required <p>Returns:</p> Name Type Description <code>SummaryStatistics</code> <code>SummaryStatistics</code> <p>a processed summary statistics dataframe for eQTL Catalogue.</p> Source code in <code>src/gentropy/datasource/eqtl_catalogue/summary_stats.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[EqtlCatalogueSummaryStats],\n    summary_stats_df: DataFrame,\n) -&gt; SummaryStatistics:\n    \"\"\"Ingests all summary stats for all eQTL Catalogue studies.\n\n    Args:\n        summary_stats_df (DataFrame): an ingested but unprocessed summary statistics dataframe from eQTL Catalogue.\n\n    Returns:\n        SummaryStatistics: a processed summary statistics dataframe for eQTL Catalogue.\n    \"\"\"\n    processed_summary_stats_df = (\n        summary_stats_df.select(\n            # Construct study ID from the appropriate columns.\n            cls._full_study_id_regexp().alias(\"studyId\"),\n            # Add variant information.\n            f.concat_ws(\n                \"_\",\n                f.col(\"chromosome\"),\n                f.col(\"position\"),\n                f.col(\"ref\"),\n                f.col(\"alt\"),\n            ).alias(\"variantId\"),\n            f.col(\"chromosome\"),\n            f.col(\"position\").cast(t.IntegerType()),\n            # Parse p-value into mantissa and exponent.\n            *parse_pvalue(f.col(\"pvalue\")),\n            # Add beta, standard error, and allele frequency information.\n            f.col(\"beta\").cast(\"double\"),\n            f.col(\"se\").cast(\"double\").alias(\"standardError\"),\n            f.col(\"maf\").cast(\"float\").alias(\"effectAlleleFrequencyFromSource\"),\n        )\n        # Drop rows which don't have proper position or beta value.\n        .filter(\n            f.col(\"position\").cast(t.IntegerType()).isNotNull()\n            &amp; (f.col(\"beta\") != 0)\n        )\n    )\n\n    # Initialise a summary statistics object.\n    return SummaryStatistics(\n        _df=processed_summary_stats_df,\n        _schema=SummaryStatistics.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/finngen/_finngen/","title":"FinnGen","text":"<p>FinnGen is a research project in genomics and personalized medicine, representing a large public-private partnership. The project has collected and analyzed genome and health data from 500,000 Finnish biobank donors to understand the genetic basis of diseases. FinnGen is now expanding its focus to comprehend the progression and biological mechanisms of diseases. This initiative provides a world-class resource for further breakthroughs in disease prevention, diagnosis, and treatment, offering insights into our genetic makeup.</p> <p>For a comprehensive understanding of the dataset and methods, refer to Kurki et al., 2023.</p>"},{"location":"python_api/datasources/finngen/study_index/","title":"Study Index","text":""},{"location":"python_api/datasources/finngen/study_index/#gentropy.datasource.finngen.study_index.FinnGenStudyIndex","title":"<code>gentropy.datasource.finngen.study_index.FinnGenStudyIndex</code>","text":"<p>Study index dataset from FinnGen.</p> <p>The following information is aggregated/extracted:</p> <ul> <li>Study ID in the special format (e.g. FINNGEN_R10_*)</li> <li>Trait name (for example, Amoebiasis)</li> <li>Number of cases and controls</li> <li>Link to the summary statistics location</li> </ul> <p>Some fields are also populated as constants, such as study type and the initial sample size.</p> Source code in <code>src/gentropy/datasource/finngen/study_index.py</code> <pre><code>class FinnGenStudyIndex:\n    \"\"\"Study index dataset from FinnGen.\n\n    The following information is aggregated/extracted:\n\n    - Study ID in the special format (e.g. FINNGEN_R10_*)\n    - Trait name (for example, Amoebiasis)\n    - Number of cases and controls\n    - Link to the summary statistics location\n\n    Some fields are also populated as constants, such as study type and the initial sample size.\n    \"\"\"\n\n    finngen_phenotype_table_url: str = \"https://r10.finngen.fi/api/phenos\"\n    finngen_release_prefix: str = \"FINNGEN_R10\"\n    finngen_summary_stats_url_prefix: str = (\n        \"gs://finngen-public-data-r10/summary_stats/finngen_R10_\"\n    )\n    finngen_summary_stats_url_suffix: str = \".gz\"\n\n    @classmethod\n    def from_source(\n        cls: type[FinnGenStudyIndex],\n        spark: SparkSession,\n    ) -&gt; StudyIndex:\n        \"\"\"This function ingests study level metadata from FinnGen.\n\n        Args:\n            spark (SparkSession): Spark session object.\n\n        Returns:\n            StudyIndex: Parsed and annotated FinnGen study table.\n        \"\"\"\n        json_data = urlopen(cls.finngen_phenotype_table_url).read().decode(\"utf-8\")\n        rdd = spark.sparkContext.parallelize([json_data])\n        raw_df = spark.read.json(rdd)\n        return StudyIndex(\n            _df=raw_df.select(\n                f.concat(\n                    f.lit(f\"{cls.finngen_release_prefix}_\"), f.col(\"phenocode\")\n                ).alias(\"studyId\"),\n                f.col(\"phenostring\").alias(\"traitFromSource\"),\n                f.col(\"num_cases\").cast(\"integer\").alias(\"nCases\"),\n                f.col(\"num_controls\").cast(\"integer\").alias(\"nControls\"),\n                (f.col(\"num_cases\") + f.col(\"num_controls\"))\n                .cast(\"integer\")\n                .alias(\"nSamples\"),\n                f.lit(cls.finngen_release_prefix).alias(\"projectId\"),\n                f.lit(\"gwas\").alias(\"studyType\"),\n                f.lit(True).alias(\"hasSumstats\"),\n                f.lit(\"377,277 (210,870 females and 166,407 males)\").alias(\n                    \"initialSampleSize\"\n                ),\n                f.array(\n                    f.struct(\n                        f.lit(377277).cast(\"integer\").alias(\"sampleSize\"),\n                        f.lit(\"Finnish\").alias(\"ancestry\"),\n                    )\n                ).alias(\"discoverySamples\"),\n                # Cohort label is consistent with GWAS Catalog curation.\n                f.array(f.lit(\"FinnGen\")).alias(\"cohorts\"),\n                f.concat(\n                    f.lit(cls.finngen_summary_stats_url_prefix),\n                    f.col(\"phenocode\"),\n                    f.lit(cls.finngen_summary_stats_url_suffix),\n                ).alias(\"summarystatsLocation\"),\n            ).withColumn(\n                \"ldPopulationStructure\",\n                StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n            ),\n            _schema=StudyIndex.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/finngen/study_index/#gentropy.datasource.finngen.study_index.FinnGenStudyIndex.from_source","title":"<code>from_source(spark: SparkSession) -&gt; StudyIndex</code>  <code>classmethod</code>","text":"<p>This function ingests study level metadata from FinnGen.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session object.</p> required <p>Returns:</p> Name Type Description <code>StudyIndex</code> <code>StudyIndex</code> <p>Parsed and annotated FinnGen study table.</p> Source code in <code>src/gentropy/datasource/finngen/study_index.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[FinnGenStudyIndex],\n    spark: SparkSession,\n) -&gt; StudyIndex:\n    \"\"\"This function ingests study level metadata from FinnGen.\n\n    Args:\n        spark (SparkSession): Spark session object.\n\n    Returns:\n        StudyIndex: Parsed and annotated FinnGen study table.\n    \"\"\"\n    json_data = urlopen(cls.finngen_phenotype_table_url).read().decode(\"utf-8\")\n    rdd = spark.sparkContext.parallelize([json_data])\n    raw_df = spark.read.json(rdd)\n    return StudyIndex(\n        _df=raw_df.select(\n            f.concat(\n                f.lit(f\"{cls.finngen_release_prefix}_\"), f.col(\"phenocode\")\n            ).alias(\"studyId\"),\n            f.col(\"phenostring\").alias(\"traitFromSource\"),\n            f.col(\"num_cases\").cast(\"integer\").alias(\"nCases\"),\n            f.col(\"num_controls\").cast(\"integer\").alias(\"nControls\"),\n            (f.col(\"num_cases\") + f.col(\"num_controls\"))\n            .cast(\"integer\")\n            .alias(\"nSamples\"),\n            f.lit(cls.finngen_release_prefix).alias(\"projectId\"),\n            f.lit(\"gwas\").alias(\"studyType\"),\n            f.lit(True).alias(\"hasSumstats\"),\n            f.lit(\"377,277 (210,870 females and 166,407 males)\").alias(\n                \"initialSampleSize\"\n            ),\n            f.array(\n                f.struct(\n                    f.lit(377277).cast(\"integer\").alias(\"sampleSize\"),\n                    f.lit(\"Finnish\").alias(\"ancestry\"),\n                )\n            ).alias(\"discoverySamples\"),\n            # Cohort label is consistent with GWAS Catalog curation.\n            f.array(f.lit(\"FinnGen\")).alias(\"cohorts\"),\n            f.concat(\n                f.lit(cls.finngen_summary_stats_url_prefix),\n                f.col(\"phenocode\"),\n                f.lit(cls.finngen_summary_stats_url_suffix),\n            ).alias(\"summarystatsLocation\"),\n        ).withColumn(\n            \"ldPopulationStructure\",\n            StudyIndex.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n        ),\n        _schema=StudyIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/finngen/summary_stats/","title":"Study Index","text":""},{"location":"python_api/datasources/finngen/summary_stats/#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats","title":"<code>gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats</code>  <code>dataclass</code>","text":"<p>Summary statistics dataset for FinnGen.</p> Source code in <code>src/gentropy/datasource/finngen/summary_stats.py</code> <pre><code>@dataclass\nclass FinnGenSummaryStats:\n    \"\"\"Summary statistics dataset for FinnGen.\"\"\"\n\n    raw_schema: t.StructType = StructType(\n        [\n            StructField(\"#chrom\", StringType(), True),\n            StructField(\"pos\", StringType(), True),\n            StructField(\"ref\", StringType(), True),\n            StructField(\"alt\", StringType(), True),\n            StructField(\"rsids\", StringType(), True),\n            StructField(\"nearest_genes\", StringType(), True),\n            StructField(\"pval\", StringType(), True),\n            StructField(\"mlogp\", StringType(), True),\n            StructField(\"beta\", StringType(), True),\n            StructField(\"sebeta\", StringType(), True),\n            StructField(\"af_alt\", StringType(), True),\n            StructField(\"af_alt_cases\", StringType(), True),\n            StructField(\"af_alt_controls\", StringType(), True),\n        ]\n    )\n\n    @classmethod\n    def from_source(\n        cls: type[FinnGenSummaryStats],\n        spark: SparkSession,\n        raw_file: str,\n    ) -&gt; SummaryStatistics:\n        \"\"\"Ingests all summary statst for all FinnGen studies.\n\n        Args:\n            spark (SparkSession): Spark session object.\n            raw_file (str): Path to raw summary statistics .gz files.\n\n        Returns:\n            SummaryStatistics: Processed summary statistics dataset\n        \"\"\"\n        study_id = raw_file.split(\"/\")[-1].split(\".\")[0].upper()\n        processed_summary_stats_df = (\n            spark.read.schema(cls.raw_schema)\n            .option(\"delimiter\", \"\\t\")\n            .csv(raw_file, header=True)\n            # Drop rows which don't have proper position.\n            .filter(f.col(\"pos\").cast(t.IntegerType()).isNotNull())\n            .select(\n                # From the full path, extracts just the filename, and converts to upper case to get the study ID.\n                f.lit(study_id).alias(\"studyId\"),\n                # Add variant information.\n                f.concat_ws(\n                    \"_\",\n                    f.col(\"#chrom\"),\n                    f.col(\"pos\"),\n                    f.col(\"ref\"),\n                    f.col(\"alt\"),\n                ).alias(\"variantId\"),\n                f.col(\"#chrom\").alias(\"chromosome\"),\n                f.col(\"pos\").cast(t.IntegerType()).alias(\"position\"),\n                # Parse p-value into mantissa and exponent.\n                *parse_pvalue(f.col(\"pval\")),\n                # Add beta, standard error, and allele frequency information.\n                f.col(\"beta\").cast(\"double\"),\n                f.col(\"sebeta\").cast(\"double\").alias(\"standardError\"),\n                f.col(\"af_alt\").cast(\"float\").alias(\"effectAlleleFrequencyFromSource\"),\n            )\n            # Calculating the confidence intervals.\n            .filter(\n                f.col(\"pos\").cast(t.IntegerType()).isNotNull() &amp; (f.col(\"beta\") != 0)\n            )\n            # Average ~20Mb partitions with 30 partitions per study\n            .repartitionByRange(30, \"chromosome\", \"position\")\n            .sortWithinPartitions(\"chromosome\", \"position\")\n        )\n\n        # Initializing summary statistics object:\n        return SummaryStatistics(\n            _df=processed_summary_stats_df,\n            _schema=SummaryStatistics.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/finngen/summary_stats/#gentropy.datasource.finngen.summary_stats.FinnGenSummaryStats.from_source","title":"<code>from_source(spark: SparkSession, raw_file: str) -&gt; SummaryStatistics</code>  <code>classmethod</code>","text":"<p>Ingests all summary statst for all FinnGen studies.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session object.</p> required <code>raw_file</code> <code>str</code> <p>Path to raw summary statistics .gz files.</p> required <p>Returns:</p> Name Type Description <code>SummaryStatistics</code> <code>SummaryStatistics</code> <p>Processed summary statistics dataset</p> Source code in <code>src/gentropy/datasource/finngen/summary_stats.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[FinnGenSummaryStats],\n    spark: SparkSession,\n    raw_file: str,\n) -&gt; SummaryStatistics:\n    \"\"\"Ingests all summary statst for all FinnGen studies.\n\n    Args:\n        spark (SparkSession): Spark session object.\n        raw_file (str): Path to raw summary statistics .gz files.\n\n    Returns:\n        SummaryStatistics: Processed summary statistics dataset\n    \"\"\"\n    study_id = raw_file.split(\"/\")[-1].split(\".\")[0].upper()\n    processed_summary_stats_df = (\n        spark.read.schema(cls.raw_schema)\n        .option(\"delimiter\", \"\\t\")\n        .csv(raw_file, header=True)\n        # Drop rows which don't have proper position.\n        .filter(f.col(\"pos\").cast(t.IntegerType()).isNotNull())\n        .select(\n            # From the full path, extracts just the filename, and converts to upper case to get the study ID.\n            f.lit(study_id).alias(\"studyId\"),\n            # Add variant information.\n            f.concat_ws(\n                \"_\",\n                f.col(\"#chrom\"),\n                f.col(\"pos\"),\n                f.col(\"ref\"),\n                f.col(\"alt\"),\n            ).alias(\"variantId\"),\n            f.col(\"#chrom\").alias(\"chromosome\"),\n            f.col(\"pos\").cast(t.IntegerType()).alias(\"position\"),\n            # Parse p-value into mantissa and exponent.\n            *parse_pvalue(f.col(\"pval\")),\n            # Add beta, standard error, and allele frequency information.\n            f.col(\"beta\").cast(\"double\"),\n            f.col(\"sebeta\").cast(\"double\").alias(\"standardError\"),\n            f.col(\"af_alt\").cast(\"float\").alias(\"effectAlleleFrequencyFromSource\"),\n        )\n        # Calculating the confidence intervals.\n        .filter(\n            f.col(\"pos\").cast(t.IntegerType()).isNotNull() &amp; (f.col(\"beta\") != 0)\n        )\n        # Average ~20Mb partitions with 30 partitions per study\n        .repartitionByRange(30, \"chromosome\", \"position\")\n        .sortWithinPartitions(\"chromosome\", \"position\")\n    )\n\n    # Initializing summary statistics object:\n    return SummaryStatistics(\n        _df=processed_summary_stats_df,\n        _schema=SummaryStatistics.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/gnomad/_gnomad/","title":"GnomAD","text":"<p>GnomAD (Genome Aggregation Database) is a comprehensive resource that provides aggregated genomic data from large-scale sequencing projects. It encompasses variants from diverse populations and is widely used for variant annotation and population genetics studies.</p> <p>We use GnomAD v4.0 as a source for variant annotation, offering detailed information about the prevalence and distribution of genetic variants across different populations. This version of GnomAD provides valuable insights into the genomic landscape, aiding in the interpretation of genetic variants and their potential functional implications.</p> <p>Additionally, GnomAD v2.1.1 is utilized as a source for linkage disequilibrium (LD) information.</p>"},{"location":"python_api/datasources/gnomad/gnomad_ld/","title":"LD Matrix","text":""},{"location":"python_api/datasources/gnomad/gnomad_ld/#gentropy.datasource.gnomad.ld.GnomADLDMatrix","title":"<code>gentropy.datasource.gnomad.ld.GnomADLDMatrix</code>  <code>dataclass</code>","text":"<p>Toolset ot interact with GnomAD LD dataset (version: r2.1.1).</p> <p>Datasets are accessed in Hail's native format, as provided by the GnomAD consortium.</p> <p>Attributes:</p> Name Type Description <code>ld_matrix_template</code> <code>str</code> <p>Template for the LD matrix path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm\".</p> <code>ld_index_raw_template</code> <code>str</code> <p>Template for the LD index path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht\".</p> <code>grch37_to_grch38_chain_path</code> <code>str</code> <p>Path to the chain file used to lift over the coordinates. Defaults to \"gs://hail-common/references/grch37_to_grch38.over.chain.gz\".</p> <code>ld_populations</code> <code>list[str]</code> <p>List of populations to use to build the LDIndex. Defaults to [\"afr\", \"amr\", \"asj\", \"eas\", \"fin\", \"nfe\", \"nwe\", \"seu\"].</p> Source code in <code>src/gentropy/datasource/gnomad/ld.py</code> <pre><code>@dataclass\nclass GnomADLDMatrix:\n    \"\"\"Toolset ot interact with GnomAD LD dataset (version: r2.1.1).\n\n    Datasets are accessed in Hail's native format, as provided by the [GnomAD consortium](https://gnomad.broadinstitute.org/downloads/#v2-linkage-disequilibrium).\n\n    Attributes:\n        ld_matrix_template (str): Template for the LD matrix path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm\".\n        ld_index_raw_template (str): Template for the LD index path. Defaults to \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht\".\n        grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates. Defaults to \"gs://hail-common/references/grch37_to_grch38.over.chain.gz\".\n        ld_populations (list[str]): List of populations to use to build the LDIndex. Defaults to [\"afr\", \"amr\", \"asj\", \"eas\", \"fin\", \"nfe\", \"nwe\", \"seu\"].\n    \"\"\"\n\n    ld_matrix_template: str = \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.adj.ld.bm\"\n    ld_index_raw_template: str = \"gs://gcp-public-data--gnomad/release/2.1.1/ld/gnomad.genomes.r2.1.1.{POP}.common.ld.variant_indices.ht\"\n    grch37_to_grch38_chain_path: str = (\n        \"gs://hail-common/references/grch37_to_grch38.over.chain.gz\"\n    )\n    ld_populations: list[str] = field(\n        default_factory=lambda: [\n            \"afr\",  # African-American\n            \"amr\",  # American Admixed/Latino\n            \"asj\",  # Ashkenazi Jewish\n            \"eas\",  # East Asian\n            \"fin\",  # Finnish\n            \"nfe\",  # Non-Finnish European\n            \"nwe\",  # Northwestern European\n            \"seu\",  # Southeastern European\n        ]\n    )\n\n    @staticmethod\n    def _aggregate_ld_index_across_populations(\n        unaggregated_ld_index: DataFrame,\n    ) -&gt; DataFrame:\n        \"\"\"Aggregate LDIndex across populations.\n\n        Args:\n            unaggregated_ld_index (DataFrame): Unaggregate LDIndex index dataframe  each row is a variant pair in a population\n\n        Returns:\n            DataFrame: Aggregated LDIndex index dataframe  each row is a variant with the LD set across populations\n\n        Examples:\n            &gt;&gt;&gt; data = [(\"1.0\", \"var1\", \"X\", \"var1\", \"pop1\"), (\"1.0\", \"X\", \"var2\", \"var2\", \"pop1\"),\n            ...         (\"0.5\", \"var1\", \"X\", \"var2\", \"pop1\"), (\"0.5\", \"var1\", \"X\", \"var2\", \"pop2\"),\n            ...         (\"0.5\", \"var2\", \"X\", \"var1\", \"pop1\"), (\"0.5\", \"X\", \"var2\", \"var1\", \"pop2\")]\n            &gt;&gt;&gt; df = spark.createDataFrame(data, [\"r\", \"variantId\", \"chromosome\", \"tagvariantId\", \"population\"])\n            &gt;&gt;&gt; GnomADLDMatrix._aggregate_ld_index_across_populations(df).printSchema()\n            root\n             |-- variantId: string (nullable = true)\n             |-- chromosome: string (nullable = true)\n             |-- ldSet: array (nullable = false)\n             |    |-- element: struct (containsNull = false)\n             |    |    |-- tagVariantId: string (nullable = true)\n             |    |    |-- rValues: array (nullable = false)\n             |    |    |    |-- element: struct (containsNull = false)\n             |    |    |    |    |-- population: string (nullable = true)\n             |    |    |    |    |-- r: string (nullable = true)\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        return (\n            unaggregated_ld_index\n            # First level of aggregation: get r/population for each variant/tagVariant pair\n            .withColumn(\"r_pop_struct\", f.struct(\"population\", \"r\"))\n            .groupBy(\"chromosome\", \"variantId\", \"tagVariantId\")\n            .agg(\n                f.collect_set(\"r_pop_struct\").alias(\"rValues\"),\n            )\n            # Second level of aggregation: get r/population for each variant\n            .withColumn(\"r_pop_tag_struct\", f.struct(\"tagVariantId\", \"rValues\"))\n            .groupBy(\"variantId\", \"chromosome\")\n            .agg(\n                f.collect_set(\"r_pop_tag_struct\").alias(\"ldSet\"),\n            )\n        )\n\n    @staticmethod\n    def _convert_ld_matrix_to_table(\n        block_matrix: BlockMatrix, min_r2: float\n    ) -&gt; DataFrame:\n        \"\"\"Convert LD matrix to table.\n\n        Args:\n            block_matrix (BlockMatrix): LD matrix\n            min_r2 (float): Minimum r2 value to keep in the table\n\n        Returns:\n            DataFrame: LD matrix as a Spark DataFrame\n        \"\"\"\n        table = block_matrix.entries(keyed=False)\n        return (\n            table.filter(hl.abs(table.entry) &gt;= min_r2**0.5)\n            .to_spark()\n            .withColumnRenamed(\"entry\", \"r\")\n        )\n\n    @staticmethod\n    def _create_ldindex_for_population(\n        population_id: str,\n        ld_matrix_path: str,\n        ld_index_raw_path: str,\n        grch37_to_grch38_chain_path: str,\n        min_r2: float,\n    ) -&gt; DataFrame:\n        \"\"\"Create LDIndex for a specific population.\n\n        Args:\n            population_id (str): Population ID\n            ld_matrix_path (str): Path to the LD matrix\n            ld_index_raw_path (str): Path to the LD index\n            grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates\n            min_r2 (float): Minimum r2 value to keep in the table\n\n        Returns:\n            DataFrame: LDIndex for a specific population\n        \"\"\"\n        # Prepare LD Block matrix\n        ld_matrix = GnomADLDMatrix._convert_ld_matrix_to_table(\n            BlockMatrix.read(ld_matrix_path), min_r2\n        )\n\n        # Prepare table with variant indices\n        ld_index = GnomADLDMatrix._process_variant_indices(\n            hl.read_table(ld_index_raw_path),\n            grch37_to_grch38_chain_path,\n        )\n\n        return GnomADLDMatrix._resolve_variant_indices(ld_index, ld_matrix).select(\n            \"*\",\n            f.lit(population_id).alias(\"population\"),\n        )\n\n    @staticmethod\n    def _process_variant_indices(\n        ld_index_raw: hl.Table, grch37_to_grch38_chain_path: str\n    ) -&gt; DataFrame:\n        \"\"\"Creates a look up table between variants and their coordinates in the LD Matrix.\n\n        !!! info \"Gnomad's LD Matrix and Index are based on GRCh37 coordinates. This function will lift over the coordinates to GRCh38 to build the lookup table.\"\n\n        Args:\n            ld_index_raw (hl.Table): LD index table from GnomAD\n            grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates\n\n        Returns:\n            DataFrame: Look up table between variants in build hg38 and their coordinates in the LD Matrix\n        \"\"\"\n        ld_index_38 = _liftover_loci(\n            ld_index_raw, grch37_to_grch38_chain_path, \"GRCh38\"\n        )\n\n        return (\n            ld_index_38.to_spark()\n            # Filter out variants where the liftover failed\n            .filter(f.col(\"`locus_GRCh38.position`\").isNotNull())\n            .withColumn(\n                \"chromosome\", f.regexp_replace(\"`locus_GRCh38.contig`\", \"chr\", \"\")\n            )\n            .withColumn(\n                \"position\",\n                convert_gnomad_position_to_ensembl(\n                    f.col(\"`locus_GRCh38.position`\"),\n                    f.col(\"`alleles`\").getItem(0),\n                    f.col(\"`alleles`\").getItem(1),\n                ),\n            )\n            .select(\n                \"chromosome\",\n                \"position\",\n                f.concat_ws(\n                    \"_\",\n                    f.col(\"chromosome\"),\n                    f.col(\"position\"),\n                    f.col(\"`alleles`\").getItem(0),\n                    f.col(\"`alleles`\").getItem(1),\n                ).alias(\"variantId\"),\n                f.col(\"idx\"),\n            )\n            # Filter out ambiguous liftover results: multiple indices for the same variant\n            .withColumn(\"count\", f.count(\"*\").over(Window.partitionBy([\"variantId\"])))\n            .filter(f.col(\"count\") == 1)\n            .drop(\"count\")\n        )\n\n    @staticmethod\n    def _resolve_variant_indices(\n        ld_index: DataFrame, ld_matrix: DataFrame\n    ) -&gt; DataFrame:\n        \"\"\"Resolve the `i` and `j` indices of the block matrix to variant IDs (build 38).\n\n        Args:\n            ld_index (DataFrame): Dataframe with resolved variant indices\n            ld_matrix (DataFrame): Dataframe with the filtered LD matrix\n\n        Returns:\n            DataFrame: Dataframe with variant IDs instead of `i` and `j` indices\n        \"\"\"\n        ld_index_i = ld_index.selectExpr(\n            \"idx as i\", \"variantId as variantId_i\", \"chromosome\"\n        )\n        ld_index_j = ld_index.selectExpr(\"idx as j\", \"variantId as variantId_j\")\n        return (\n            ld_matrix.join(ld_index_i, on=\"i\", how=\"inner\")\n            .join(ld_index_j, on=\"j\", how=\"inner\")\n            .drop(\"i\", \"j\")\n        )\n\n    @staticmethod\n    def _transpose_ld_matrix(ld_matrix: DataFrame) -&gt; DataFrame:\n        \"\"\"Transpose LD matrix to a square matrix format.\n\n        Args:\n            ld_matrix (DataFrame): Triangular LD matrix converted to a Spark DataFrame\n\n        Returns:\n            DataFrame: Square LD matrix without diagonal duplicates\n\n        Examples:\n            &gt;&gt;&gt; df = spark.createDataFrame(\n            ...     [\n            ...         (1, 1, 1.0, \"1\", \"AFR\"),\n            ...         (1, 2, 0.5, \"1\", \"AFR\"),\n            ...         (2, 2, 1.0, \"1\", \"AFR\"),\n            ...     ],\n            ...     [\"variantId_i\", \"variantId_j\", \"r\", \"chromosome\", \"population\"],\n            ... )\n            &gt;&gt;&gt; GnomADLDMatrix._transpose_ld_matrix(df).show()\n            +-----------+-----------+---+----------+----------+\n            |variantId_i|variantId_j|  r|chromosome|population|\n            +-----------+-----------+---+----------+----------+\n            |          1|          2|0.5|         1|       AFR|\n            |          1|          1|1.0|         1|       AFR|\n            |          2|          1|0.5|         1|       AFR|\n            |          2|          2|1.0|         1|       AFR|\n            +-----------+-----------+---+----------+----------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        ld_matrix_transposed = ld_matrix.selectExpr(\n            \"variantId_i as variantId_j\",\n            \"variantId_j as variantId_i\",\n            \"r\",\n            \"chromosome\",\n            \"population\",\n        )\n        return ld_matrix.filter(\n            f.col(\"variantId_i\") != f.col(\"variantId_j\")\n        ).unionByName(ld_matrix_transposed)\n\n    def as_ld_index(\n        self: GnomADLDMatrix,\n        min_r2: float,\n    ) -&gt; LDIndex:\n        \"\"\"Create LDIndex dataset aggregating the LD information across a set of populations.\n\n        **The basic steps to generate the LDIndex are:**\n\n        1. Convert LD matrix to a Spark DataFrame.\n        2. Resolve the matrix indices to variant IDs by lifting over the coordinates to GRCh38.\n        3. Aggregate the LD information across populations.\n\n        Args:\n            min_r2 (float): Minimum r2 value to keep in the table\n\n        Returns:\n            LDIndex: LDIndex dataset\n        \"\"\"\n        ld_indices_unaggregated = []\n        for pop in self.ld_populations:\n            try:\n                ld_matrix_path = self.ld_matrix_template.format(POP=pop)\n                ld_index_raw_path = self.ld_index_raw_template.format(POP=pop)\n                pop_ld_index = self._create_ldindex_for_population(\n                    pop,\n                    ld_matrix_path,\n                    ld_index_raw_path.format(pop),\n                    self.grch37_to_grch38_chain_path,\n                    min_r2,\n                )\n                ld_indices_unaggregated.append(pop_ld_index)\n            except Exception as e:\n                print(f\"Failed to create LDIndex for population {pop}: {e}\")  # noqa: T201\n                sys.exit(1)\n\n        ld_index_unaggregated = (\n            GnomADLDMatrix._transpose_ld_matrix(\n                reduce(lambda df1, df2: df1.unionByName(df2), ld_indices_unaggregated)\n            )\n            .withColumnRenamed(\"variantId_i\", \"variantId\")\n            .withColumnRenamed(\"variantId_j\", \"tagVariantId\")\n        )\n        return LDIndex(\n            _df=self._aggregate_ld_index_across_populations(ld_index_unaggregated),\n            _schema=LDIndex.get_schema(),\n        )\n\n    def get_ld_variants(\n        self: GnomADLDMatrix,\n        gnomad_ancestry: str,\n        chromosome: str,\n        start: int,\n        end: int,\n    ) -&gt; DataFrame | None:\n        \"\"\"Return melted LD table with resolved variant id based on ancestry and genomic location.\n\n        Args:\n            gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe`\n            chromosome (str): chromosome label\n            start (int): window upper bound\n            end (int): window lower bound\n\n        Returns:\n            DataFrame | None: LD table with resolved variant id based on ancestry and genomic location\n        \"\"\"\n        # Extracting locus:\n        ld_index_df = (\n            self._process_variant_indices(\n                hl.read_table(self.ld_index_raw_template.format(POP=gnomad_ancestry)),\n                self.grch37_to_grch38_chain_path,\n            )\n            .filter(\n                (f.col(\"chromosome\") == chromosome)\n                &amp; (f.col(\"position\") &gt;= start)\n                &amp; (f.col(\"position\") &lt;= end)\n            )\n            .select(\"chromosome\", \"position\", \"variantId\", \"idx\")\n            .persist()\n        )\n\n        if ld_index_df.limit(1).count() == 0:\n            # If the returned slice from the ld index is empty, return None\n            return None\n\n        # Compute start and end indices\n        start_index = get_value_from_row(\n            get_top_ranked_in_window(\n                ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").asc())\n            ).collect()[0],\n            \"idx\",\n        )\n        end_index = get_value_from_row(\n            get_top_ranked_in_window(\n                ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").desc())\n            ).collect()[0],\n            \"idx\",\n        )\n\n        return self._extract_square_matrix(\n            ld_index_df, gnomad_ancestry, start_index, end_index\n        )\n\n    def _extract_square_matrix(\n        self: GnomADLDMatrix,\n        ld_index_df: DataFrame,\n        gnomad_ancestry: str,\n        start_index: int,\n        end_index: int,\n    ) -&gt; DataFrame:\n        \"\"\"Return LD square matrix for a region where coordinates are normalised.\n\n        Args:\n            ld_index_df (DataFrame): Look up table between a variantId and its index in the LD matrix\n            gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe`\n            start_index (int): start index of the slice\n            end_index (int): end index of the slice\n\n        Returns:\n            DataFrame: square LD matrix resolved to variants.\n        \"\"\"\n        return (\n            self.get_ld_matrix_slice(\n                gnomad_ancestry, start_index=start_index, end_index=end_index\n            )\n            .join(\n                ld_index_df.select(\n                    f.col(\"idx\").alias(\"idx_i\"),\n                    f.col(\"variantId\").alias(\"variantId_i\"),\n                ),\n                on=\"idx_i\",\n                how=\"inner\",\n            )\n            .join(\n                ld_index_df.select(\n                    f.col(\"idx\").alias(\"idx_j\"),\n                    f.col(\"variantId\").alias(\"variantId_j\"),\n                ),\n                on=\"idx_j\",\n                how=\"inner\",\n            )\n            .select(\"variantId_i\", \"variantId_j\", \"r\")\n        )\n\n    def get_ld_matrix_slice(\n        self: GnomADLDMatrix,\n        gnomad_ancestry: str,\n        start_index: int,\n        end_index: int,\n    ) -&gt; DataFrame:\n        \"\"\"Extract a slice of the LD matrix based on the provided ancestry and stop and end indices.\n\n        - The half matrix is completed into a full square.\n        - The returned indices are adjusted based on the start index.\n\n        Args:\n            gnomad_ancestry (str): LD population label eg. `nfe`\n            start_index (int): start index of the slice\n            end_index (int): end index of the slice\n\n        Returns:\n            DataFrame: square slice of the LD matrix melted as dataframe with idx_i, idx_j and r columns\n        \"\"\"\n        # Extracting block matrix slice:\n        half_matrix = BlockMatrix.read(\n            self.ld_matrix_template.format(POP=gnomad_ancestry)\n        ).filter(range(start_index, end_index + 1), range(start_index, end_index + 1))\n\n        # Return converted Dataframe:\n        return (\n            (half_matrix + half_matrix.T)\n            .entries()\n            .to_spark()\n            .select(\n                (f.col(\"i\") + start_index).alias(\"idx_i\"),\n                (f.col(\"j\") + start_index).alias(\"idx_j\"),\n                f.when(f.col(\"i\") == f.col(\"j\"), f.col(\"entry\") / 2)\n                .otherwise(f.col(\"entry\"))\n                .alias(\"r\"),\n            )\n        )\n</code></pre>"},{"location":"python_api/datasources/gnomad/gnomad_ld/#gentropy.datasource.gnomad.ld.GnomADLDMatrix.as_ld_index","title":"<code>as_ld_index(min_r2: float) -&gt; LDIndex</code>","text":"<p>Create LDIndex dataset aggregating the LD information across a set of populations.</p> <p>The basic steps to generate the LDIndex are:</p> <ol> <li>Convert LD matrix to a Spark DataFrame.</li> <li>Resolve the matrix indices to variant IDs by lifting over the coordinates to GRCh38.</li> <li>Aggregate the LD information across populations.</li> </ol> <p>Parameters:</p> Name Type Description Default <code>min_r2</code> <code>float</code> <p>Minimum r2 value to keep in the table</p> required <p>Returns:</p> Name Type Description <code>LDIndex</code> <code>LDIndex</code> <p>LDIndex dataset</p> Source code in <code>src/gentropy/datasource/gnomad/ld.py</code> <pre><code>def as_ld_index(\n    self: GnomADLDMatrix,\n    min_r2: float,\n) -&gt; LDIndex:\n    \"\"\"Create LDIndex dataset aggregating the LD information across a set of populations.\n\n    **The basic steps to generate the LDIndex are:**\n\n    1. Convert LD matrix to a Spark DataFrame.\n    2. Resolve the matrix indices to variant IDs by lifting over the coordinates to GRCh38.\n    3. Aggregate the LD information across populations.\n\n    Args:\n        min_r2 (float): Minimum r2 value to keep in the table\n\n    Returns:\n        LDIndex: LDIndex dataset\n    \"\"\"\n    ld_indices_unaggregated = []\n    for pop in self.ld_populations:\n        try:\n            ld_matrix_path = self.ld_matrix_template.format(POP=pop)\n            ld_index_raw_path = self.ld_index_raw_template.format(POP=pop)\n            pop_ld_index = self._create_ldindex_for_population(\n                pop,\n                ld_matrix_path,\n                ld_index_raw_path.format(pop),\n                self.grch37_to_grch38_chain_path,\n                min_r2,\n            )\n            ld_indices_unaggregated.append(pop_ld_index)\n        except Exception as e:\n            print(f\"Failed to create LDIndex for population {pop}: {e}\")  # noqa: T201\n            sys.exit(1)\n\n    ld_index_unaggregated = (\n        GnomADLDMatrix._transpose_ld_matrix(\n            reduce(lambda df1, df2: df1.unionByName(df2), ld_indices_unaggregated)\n        )\n        .withColumnRenamed(\"variantId_i\", \"variantId\")\n        .withColumnRenamed(\"variantId_j\", \"tagVariantId\")\n    )\n    return LDIndex(\n        _df=self._aggregate_ld_index_across_populations(ld_index_unaggregated),\n        _schema=LDIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/gnomad/gnomad_ld/#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_matrix_slice","title":"<code>get_ld_matrix_slice(gnomad_ancestry: str, start_index: int, end_index: int) -&gt; DataFrame</code>","text":"<p>Extract a slice of the LD matrix based on the provided ancestry and stop and end indices.</p> <ul> <li>The half matrix is completed into a full square.</li> <li>The returned indices are adjusted based on the start index.</li> </ul> <p>Parameters:</p> Name Type Description Default <code>gnomad_ancestry</code> <code>str</code> <p>LD population label eg. <code>nfe</code></p> required <code>start_index</code> <code>int</code> <p>start index of the slice</p> required <code>end_index</code> <code>int</code> <p>end index of the slice</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>square slice of the LD matrix melted as dataframe with idx_i, idx_j and r columns</p> Source code in <code>src/gentropy/datasource/gnomad/ld.py</code> <pre><code>def get_ld_matrix_slice(\n    self: GnomADLDMatrix,\n    gnomad_ancestry: str,\n    start_index: int,\n    end_index: int,\n) -&gt; DataFrame:\n    \"\"\"Extract a slice of the LD matrix based on the provided ancestry and stop and end indices.\n\n    - The half matrix is completed into a full square.\n    - The returned indices are adjusted based on the start index.\n\n    Args:\n        gnomad_ancestry (str): LD population label eg. `nfe`\n        start_index (int): start index of the slice\n        end_index (int): end index of the slice\n\n    Returns:\n        DataFrame: square slice of the LD matrix melted as dataframe with idx_i, idx_j and r columns\n    \"\"\"\n    # Extracting block matrix slice:\n    half_matrix = BlockMatrix.read(\n        self.ld_matrix_template.format(POP=gnomad_ancestry)\n    ).filter(range(start_index, end_index + 1), range(start_index, end_index + 1))\n\n    # Return converted Dataframe:\n    return (\n        (half_matrix + half_matrix.T)\n        .entries()\n        .to_spark()\n        .select(\n            (f.col(\"i\") + start_index).alias(\"idx_i\"),\n            (f.col(\"j\") + start_index).alias(\"idx_j\"),\n            f.when(f.col(\"i\") == f.col(\"j\"), f.col(\"entry\") / 2)\n            .otherwise(f.col(\"entry\"))\n            .alias(\"r\"),\n        )\n    )\n</code></pre>"},{"location":"python_api/datasources/gnomad/gnomad_ld/#gentropy.datasource.gnomad.ld.GnomADLDMatrix.get_ld_variants","title":"<code>get_ld_variants(gnomad_ancestry: str, chromosome: str, start: int, end: int) -&gt; DataFrame | None</code>","text":"<p>Return melted LD table with resolved variant id based on ancestry and genomic location.</p> <p>Parameters:</p> Name Type Description Default <code>gnomad_ancestry</code> <code>str</code> <p>GnomAD major ancestry label eg. <code>nfe</code></p> required <code>chromosome</code> <code>str</code> <p>chromosome label</p> required <code>start</code> <code>int</code> <p>window upper bound</p> required <code>end</code> <code>int</code> <p>window lower bound</p> required <p>Returns:</p> Type Description <code>DataFrame | None</code> <p>DataFrame | None: LD table with resolved variant id based on ancestry and genomic location</p> Source code in <code>src/gentropy/datasource/gnomad/ld.py</code> <pre><code>def get_ld_variants(\n    self: GnomADLDMatrix,\n    gnomad_ancestry: str,\n    chromosome: str,\n    start: int,\n    end: int,\n) -&gt; DataFrame | None:\n    \"\"\"Return melted LD table with resolved variant id based on ancestry and genomic location.\n\n    Args:\n        gnomad_ancestry (str): GnomAD major ancestry label eg. `nfe`\n        chromosome (str): chromosome label\n        start (int): window upper bound\n        end (int): window lower bound\n\n    Returns:\n        DataFrame | None: LD table with resolved variant id based on ancestry and genomic location\n    \"\"\"\n    # Extracting locus:\n    ld_index_df = (\n        self._process_variant_indices(\n            hl.read_table(self.ld_index_raw_template.format(POP=gnomad_ancestry)),\n            self.grch37_to_grch38_chain_path,\n        )\n        .filter(\n            (f.col(\"chromosome\") == chromosome)\n            &amp; (f.col(\"position\") &gt;= start)\n            &amp; (f.col(\"position\") &lt;= end)\n        )\n        .select(\"chromosome\", \"position\", \"variantId\", \"idx\")\n        .persist()\n    )\n\n    if ld_index_df.limit(1).count() == 0:\n        # If the returned slice from the ld index is empty, return None\n        return None\n\n    # Compute start and end indices\n    start_index = get_value_from_row(\n        get_top_ranked_in_window(\n            ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").asc())\n        ).collect()[0],\n        \"idx\",\n    )\n    end_index = get_value_from_row(\n        get_top_ranked_in_window(\n            ld_index_df, Window.partitionBy().orderBy(f.col(\"position\").desc())\n        ).collect()[0],\n        \"idx\",\n    )\n\n    return self._extract_square_matrix(\n        ld_index_df, gnomad_ancestry, start_index, end_index\n    )\n</code></pre>"},{"location":"python_api/datasources/gnomad/gnomad_variants/","title":"Variants","text":""},{"location":"python_api/datasources/gnomad/gnomad_variants/#gentropy.datasource.gnomad.variants.GnomADVariants","title":"<code>gentropy.datasource.gnomad.variants.GnomADVariants</code>  <code>dataclass</code>","text":"<p>GnomAD variants included in the GnomAD genomes dataset.</p> <p>Attributes:</p> Name Type Description <code>gnomad_genomes</code> <code>str</code> <p>Path to gnomAD genomes hail table. Defaults to gnomAD's 4.0 release.</p> <code>chain_hail_38_37</code> <code>str</code> <p>Path to GRCh38 to GRCh37 chain file. Defaults to Hail's chain file.</p> <code>populations</code> <code>list[str]</code> <p>List of populations to include. Defaults to all populations.</p> Source code in <code>src/gentropy/datasource/gnomad/variants.py</code> <pre><code>@dataclass\nclass GnomADVariants:\n    \"\"\"GnomAD variants included in the GnomAD genomes dataset.\n\n    Attributes:\n        gnomad_genomes (str): Path to gnomAD genomes hail table. Defaults to gnomAD's 4.0 release.\n        chain_hail_38_37 (str): Path to GRCh38 to GRCh37 chain file. Defaults to Hail's chain file.\n        populations (list[str]): List of populations to include. Defaults to all populations.\n    \"\"\"\n\n    gnomad_genomes: str = \"gs://gcp-public-data--gnomad/release/4.0/ht/genomes/gnomad.genomes.v4.0.sites.ht/\"\n    chain_hail_38_37: str = \"gs://hail-common/references/grch38_to_grch37.over.chain.gz\"\n    populations: list[str] = field(\n        default_factory=lambda: [\n            \"afr\",  # African-American\n            \"amr\",  # American Admixed/Latino\n            \"ami\",  # Amish ancestry\n            \"asj\",  # Ashkenazi Jewish\n            \"eas\",  # East Asian\n            \"fin\",  # Finnish\n            \"nfe\",  # Non-Finnish European\n            \"mid\",  # Middle Eastern\n            \"sas\",  # South Asian\n            \"remaining\",  # Other\n        ]\n    )\n\n    @staticmethod\n    def _convert_gnomad_position_to_ensembl_hail(\n        position: Int32Expression,\n        reference: StringExpression,\n        alternate: StringExpression,\n    ) -&gt; Int32Expression:\n        \"\"\"Convert GnomAD variant position to Ensembl variant position in hail table.\n\n        For indels (the reference or alternate allele is longer than 1), then adding 1 to the position, for SNPs, the position is unchanged.\n        More info about the problem: https://www.biostars.org/p/84686/\n\n        Args:\n            position (Int32Expression): Position of the variant in the GnomAD genome.\n            reference (StringExpression): The reference allele.\n            alternate (StringExpression): The alternate allele\n\n        Returns:\n            Int32Expression: The position of the variant according to Ensembl genome.\n        \"\"\"\n        return hl.if_else(\n            (reference.length() &gt; 1) | (alternate.length() &gt; 1), position + 1, position\n        )\n\n    def as_variant_annotation(self: GnomADVariants) -&gt; VariantAnnotation:\n        \"\"\"Generate variant annotation dataset from gnomAD.\n\n        Some relevant modifications to the original dataset are:\n\n        1. The transcript consequences features provided by VEP are filtered to only refer to the Ensembl canonical transcript.\n        2. Genome coordinates are liftovered from GRCh38 to GRCh37 to keep as annotation.\n        3. Field names are converted to camel case to follow the convention.\n\n        Returns:\n            VariantAnnotation: Variant annotation dataset\n        \"\"\"\n        # Load variants dataset\n        ht = hl.read_table(\n            self.gnomad_genomes,\n            _load_refs=False,\n        )\n\n        # Liftover\n        grch37 = hl.get_reference(\"GRCh37\")\n        grch38 = hl.get_reference(\"GRCh38\")\n        grch38.add_liftover(self.chain_hail_38_37, grch37)\n\n        # Drop non biallelic variants\n        ht = ht.filter(ht.alleles.length() == 2)\n        # Liftover\n        ht = ht.annotate(locus_GRCh37=hl.liftover(ht.locus, \"GRCh37\"))\n        # Select relevant fields and nested records to create class\n        return VariantAnnotation(\n            _df=(\n                ht.select(\n                    gnomadVariantId=hl.str(\"-\").join(\n                        [\n                            ht.locus.contig.replace(\"chr\", \"\"),\n                            hl.str(ht.locus.position),\n                            ht.alleles[0],\n                            ht.alleles[1],\n                        ]\n                    ),\n                    chromosome=ht.locus.contig.replace(\"chr\", \"\"),\n                    position=GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                        ht.locus.position, ht.alleles[0], ht.alleles[1]\n                    ),\n                    variantId=hl.str(\"_\").join(\n                        [\n                            ht.locus.contig.replace(\"chr\", \"\"),\n                            hl.str(\n                                GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                                    ht.locus.position, ht.alleles[0], ht.alleles[1]\n                                )\n                            ),\n                            ht.alleles[0],\n                            ht.alleles[1],\n                        ]\n                    ),\n                    chromosomeB37=ht.locus_GRCh37.contig.replace(\"chr\", \"\"),\n                    positionB37=ht.locus_GRCh37.position,\n                    referenceAllele=ht.alleles[0],\n                    alternateAllele=ht.alleles[1],\n                    rsIds=ht.rsid,\n                    alleleType=ht.allele_info.allele_type,\n                    alleleFrequencies=hl.set(\n                        [f\"{pop}_adj\" for pop in self.populations]\n                    ).map(\n                        lambda p: hl.struct(\n                            populationName=p,\n                            alleleFrequency=ht.freq[ht.globals.freq_index_dict[p]].AF,\n                        )\n                    ),\n                    vep=hl.struct(\n                        mostSevereConsequence=ht.vep.most_severe_consequence,\n                        transcriptConsequences=hl.map(\n                            lambda x: hl.struct(\n                                aminoAcids=x.amino_acids,\n                                consequenceTerms=x.consequence_terms,\n                                geneId=x.gene_id,\n                                lof=x.lof,\n                            ),\n                            # Only keeping canonical transcripts\n                            ht.vep.transcript_consequences.filter(\n                                lambda x: (x.canonical == 1)\n                                &amp; (x.gene_symbol_source == \"HGNC\")\n                            ),\n                        ),\n                    ),\n                    inSilicoPredictors=hl.struct(\n                        cadd=hl.struct(\n                            phred=ht.in_silico_predictors.cadd.phred,\n                            raw=ht.in_silico_predictors.cadd.raw_score,\n                        ),\n                        revelMax=ht.in_silico_predictors.revel_max,\n                        spliceaiDsMax=ht.in_silico_predictors.spliceai_ds_max,\n                        pangolinLargestDs=ht.in_silico_predictors.pangolin_largest_ds,\n                        phylop=ht.in_silico_predictors.phylop,\n                        siftMax=ht.in_silico_predictors.sift_max,\n                        polyphenMax=ht.in_silico_predictors.polyphen_max,\n                    ),\n                )\n                .key_by(\"chromosome\", \"position\")\n                .drop(\"locus\", \"alleles\")\n                .select_globals()\n                .to_spark(flatten=False)\n            ),\n            _schema=VariantAnnotation.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/gnomad/gnomad_variants/#gentropy.datasource.gnomad.variants.GnomADVariants.as_variant_annotation","title":"<code>as_variant_annotation() -&gt; VariantAnnotation</code>","text":"<p>Generate variant annotation dataset from gnomAD.</p> <p>Some relevant modifications to the original dataset are:</p> <ol> <li>The transcript consequences features provided by VEP are filtered to only refer to the Ensembl canonical transcript.</li> <li>Genome coordinates are liftovered from GRCh38 to GRCh37 to keep as annotation.</li> <li>Field names are converted to camel case to follow the convention.</li> </ol> <p>Returns:</p> Name Type Description <code>VariantAnnotation</code> <code>VariantAnnotation</code> <p>Variant annotation dataset</p> Source code in <code>src/gentropy/datasource/gnomad/variants.py</code> <pre><code>def as_variant_annotation(self: GnomADVariants) -&gt; VariantAnnotation:\n    \"\"\"Generate variant annotation dataset from gnomAD.\n\n    Some relevant modifications to the original dataset are:\n\n    1. The transcript consequences features provided by VEP are filtered to only refer to the Ensembl canonical transcript.\n    2. Genome coordinates are liftovered from GRCh38 to GRCh37 to keep as annotation.\n    3. Field names are converted to camel case to follow the convention.\n\n    Returns:\n        VariantAnnotation: Variant annotation dataset\n    \"\"\"\n    # Load variants dataset\n    ht = hl.read_table(\n        self.gnomad_genomes,\n        _load_refs=False,\n    )\n\n    # Liftover\n    grch37 = hl.get_reference(\"GRCh37\")\n    grch38 = hl.get_reference(\"GRCh38\")\n    grch38.add_liftover(self.chain_hail_38_37, grch37)\n\n    # Drop non biallelic variants\n    ht = ht.filter(ht.alleles.length() == 2)\n    # Liftover\n    ht = ht.annotate(locus_GRCh37=hl.liftover(ht.locus, \"GRCh37\"))\n    # Select relevant fields and nested records to create class\n    return VariantAnnotation(\n        _df=(\n            ht.select(\n                gnomadVariantId=hl.str(\"-\").join(\n                    [\n                        ht.locus.contig.replace(\"chr\", \"\"),\n                        hl.str(ht.locus.position),\n                        ht.alleles[0],\n                        ht.alleles[1],\n                    ]\n                ),\n                chromosome=ht.locus.contig.replace(\"chr\", \"\"),\n                position=GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                    ht.locus.position, ht.alleles[0], ht.alleles[1]\n                ),\n                variantId=hl.str(\"_\").join(\n                    [\n                        ht.locus.contig.replace(\"chr\", \"\"),\n                        hl.str(\n                            GnomADVariants._convert_gnomad_position_to_ensembl_hail(\n                                ht.locus.position, ht.alleles[0], ht.alleles[1]\n                            )\n                        ),\n                        ht.alleles[0],\n                        ht.alleles[1],\n                    ]\n                ),\n                chromosomeB37=ht.locus_GRCh37.contig.replace(\"chr\", \"\"),\n                positionB37=ht.locus_GRCh37.position,\n                referenceAllele=ht.alleles[0],\n                alternateAllele=ht.alleles[1],\n                rsIds=ht.rsid,\n                alleleType=ht.allele_info.allele_type,\n                alleleFrequencies=hl.set(\n                    [f\"{pop}_adj\" for pop in self.populations]\n                ).map(\n                    lambda p: hl.struct(\n                        populationName=p,\n                        alleleFrequency=ht.freq[ht.globals.freq_index_dict[p]].AF,\n                    )\n                ),\n                vep=hl.struct(\n                    mostSevereConsequence=ht.vep.most_severe_consequence,\n                    transcriptConsequences=hl.map(\n                        lambda x: hl.struct(\n                            aminoAcids=x.amino_acids,\n                            consequenceTerms=x.consequence_terms,\n                            geneId=x.gene_id,\n                            lof=x.lof,\n                        ),\n                        # Only keeping canonical transcripts\n                        ht.vep.transcript_consequences.filter(\n                            lambda x: (x.canonical == 1)\n                            &amp; (x.gene_symbol_source == \"HGNC\")\n                        ),\n                    ),\n                ),\n                inSilicoPredictors=hl.struct(\n                    cadd=hl.struct(\n                        phred=ht.in_silico_predictors.cadd.phred,\n                        raw=ht.in_silico_predictors.cadd.raw_score,\n                    ),\n                    revelMax=ht.in_silico_predictors.revel_max,\n                    spliceaiDsMax=ht.in_silico_predictors.spliceai_ds_max,\n                    pangolinLargestDs=ht.in_silico_predictors.pangolin_largest_ds,\n                    phylop=ht.in_silico_predictors.phylop,\n                    siftMax=ht.in_silico_predictors.sift_max,\n                    polyphenMax=ht.in_silico_predictors.polyphen_max,\n                ),\n            )\n            .key_by(\"chromosome\", \"position\")\n            .drop(\"locus\", \"alleles\")\n            .select_globals()\n            .to_spark(flatten=False)\n        ),\n        _schema=VariantAnnotation.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/_gwas_catalog/","title":"GWAS Catalog","text":"GWAS Catalog <p>The GWAS Catalog is a comprehensive resource that aims to provide a curated collection of Genome-Wide Association Studies (GWAS) (including harmonized full GWAS summary statistics) across various traits and diseases in humans.</p> <p>It serves as a valuable repository of genetic associations identified in diverse populations, offering insights into the genetic basis of complex traits and diseases.</p> <p>We rely on the GWAS Catalog for a rich source of genetic associations, utilizing the data for analysis and interpretation.</p> <p>For detailed information on specific genetic associations, their significance, and associated studies, refer to the GWAS Catalog.</p> <p>Within our analyses, we leverage two different types of studies from the GWAS Catalog:</p> <ol> <li> <p>Studies with (full) GWAS summary stats</p> </li> <li> <p>Studies with top hits only - GWAS curated studies</p> </li> </ol>"},{"location":"python_api/datasources/gwas_catalog/associations/","title":"Associations","text":""},{"location":"python_api/datasources/gwas_catalog/associations/#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser","title":"<code>gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser</code>  <code>dataclass</code>","text":"<p>GWAS Catalog curated associations parser.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code> <pre><code>@dataclass\nclass GWASCatalogCuratedAssociationsParser:\n    \"\"\"GWAS Catalog curated associations parser.\"\"\"\n\n    @staticmethod\n    def _parse_pvalue(pvalue: Column) -&gt; tuple[Column, Column]:\n        \"\"\"Parse p-value column.\n\n        Args:\n            pvalue (Column): p-value [string]\n\n        Returns:\n            tuple[Column, Column]: p-value mantissa and exponent\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [(\"1.0\"), (\"0.5\"), (\"1E-20\"), (\"3E-3\"), (\"1E-1000\")]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StringType())\n            &gt;&gt;&gt; df.select('value',*GWASCatalogCuratedAssociationsParser._parse_pvalue(f.col('value'))).show()\n            +-------+--------------+--------------+\n            |  value|pValueMantissa|pValueExponent|\n            +-------+--------------+--------------+\n            |    1.0|           1.0|             1|\n            |    0.5|           0.5|             1|\n            |  1E-20|           1.0|           -20|\n            |   3E-3|           3.0|            -3|\n            |1E-1000|           1.0|         -1000|\n            +-------+--------------+--------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        split = f.split(pvalue, \"E\")\n        return split.getItem(0).cast(\"float\").alias(\"pValueMantissa\"), f.coalesce(\n            split.getItem(1).cast(\"integer\"), f.lit(1)\n        ).alias(\"pValueExponent\")\n\n    @staticmethod\n    def _normalise_pvaluetext(p_value_text: Column) -&gt; Column:\n        \"\"\"Normalised p-value text column to a standardised format.\n\n        For cases where there is no mapping, the value is set to null.\n\n        Args:\n            p_value_text (Column): `pValueText` column from GWASCatalog\n\n        Returns:\n            Column: Array column after using GWAS Catalog mappings. There might be multiple mappings for a single p-value text.\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [(\"European Ancestry\"), (\"African ancestry\"), (\"Alzheimer\u2019s Disease\"), (\"(progression)\"), (\"\"), (None)]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StringType())\n            &gt;&gt;&gt; df.withColumn('normalised', GWASCatalogCuratedAssociationsParser._normalise_pvaluetext(f.col('value'))).show()\n            +-------------------+----------+\n            |              value|normalised|\n            +-------------------+----------+\n            |  European Ancestry|      [EA]|\n            |   African ancestry|      [AA]|\n            |Alzheimer\u2019s Disease|      [AD]|\n            |      (progression)|      null|\n            |                   |      null|\n            |               null|      null|\n            +-------------------+----------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # GWAS Catalog to p-value mapping\n        json_dict = json.loads(\n            pkg_resources.read_text(data, \"gwas_pValueText_map.json\", encoding=\"utf-8\")\n        )\n        map_expr = f.create_map(*[f.lit(x) for x in chain(*json_dict.items())])\n\n        splitted_col = f.split(f.regexp_replace(p_value_text, r\"[\\(\\)]\", \"\"), \",\")\n        mapped_col = f.transform(splitted_col, lambda x: map_expr[x])\n        return f.when(f.forall(mapped_col, lambda x: x.isNull()), None).otherwise(\n            mapped_col\n        )\n\n    @staticmethod\n    def _normalise_risk_allele(risk_allele: Column) -&gt; Column:\n        \"\"\"Normalised risk allele column to a standardised format.\n\n        If multiple risk alleles are present, the first one is returned.\n\n        Args:\n            risk_allele (Column): `riskAllele` column from GWASCatalog\n\n        Returns:\n            Column: mapped using GWAS Catalog mapping\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [(\"rs1234-A-G\"), (\"rs1234-A\"), (\"rs1234-A; rs1235-G\")]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StringType())\n            &gt;&gt;&gt; df.withColumn('normalised', GWASCatalogCuratedAssociationsParser._normalise_risk_allele(f.col('value'))).show()\n            +------------------+----------+\n            |             value|normalised|\n            +------------------+----------+\n            |        rs1234-A-G|         A|\n            |          rs1234-A|         A|\n            |rs1234-A; rs1235-G|         A|\n            +------------------+----------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # GWAS Catalog to risk allele mapping\n        return f.split(f.split(risk_allele, \"; \").getItem(0), \"-\").getItem(1)\n\n    @staticmethod\n    def _collect_rsids(\n        snp_id: Column, snp_id_current: Column, risk_allele: Column\n    ) -&gt; Column:\n        \"\"\"It takes three columns, and returns an array of distinct values from those columns.\n\n        Args:\n            snp_id (Column): The original snp id from the GWAS catalog.\n            snp_id_current (Column): The current snp id field is just a number at the moment (stored as a string). Adding 'rs' prefix if looks good.\n            risk_allele (Column): The risk allele for the SNP.\n\n        Returns:\n            Column: An array of distinct values.\n        \"\"\"\n        # The current snp id field is just a number at the moment (stored as a string). Adding 'rs' prefix if looks good.\n        snp_id_current = f.when(\n            snp_id_current.rlike(\"^[0-9]*$\"),\n            f.format_string(\"rs%s\", snp_id_current),\n        )\n        # Cleaning risk allele:\n        risk_allele = f.split(risk_allele, \"-\").getItem(0)\n\n        # Collecting all values:\n        return f.array_distinct(f.array(snp_id, snp_id_current, risk_allele))\n\n    @staticmethod\n    def _map_to_variant_annotation_variants(\n        gwas_associations: DataFrame, variant_annotation: VariantAnnotation\n    ) -&gt; DataFrame:\n        \"\"\"Add variant metadata in associations.\n\n        Args:\n            gwas_associations (DataFrame): raw GWAS Catalog associations\n            variant_annotation (VariantAnnotation): variant annotation dataset\n\n        Returns:\n            DataFrame: GWAS Catalog associations data including `variantId`, `referenceAllele`,\n            `alternateAllele`, `chromosome`, `position` with variant metadata\n        \"\"\"\n        # Subset of GWAS Catalog associations required for resolving variant IDs:\n        gwas_associations_subset = gwas_associations.select(\n            \"studyLocusId\",\n            f.col(\"CHR_ID\").alias(\"chromosome\"),\n            f.col(\"CHR_POS\").cast(IntegerType()).alias(\"position\"),\n            # List of all SNPs associated with the variant\n            GWASCatalogCuratedAssociationsParser._collect_rsids(\n                f.split(f.col(\"SNPS\"), \"; \").getItem(0),\n                f.col(\"SNP_ID_CURRENT\"),\n                f.split(f.col(\"STRONGEST SNP-RISK ALLELE\"), \"; \").getItem(0),\n            ).alias(\"rsIdsGwasCatalog\"),\n            GWASCatalogCuratedAssociationsParser._normalise_risk_allele(\n                f.col(\"STRONGEST SNP-RISK ALLELE\")\n            ).alias(\"riskAllele\"),\n        )\n\n        # Subset of variant annotation required for GWAS Catalog annotations:\n        va_subset = variant_annotation.df.select(\n            \"variantId\",\n            \"chromosome\",\n            \"position\",\n            f.col(\"rsIds\").alias(\"rsIdsGnomad\"),\n            \"referenceAllele\",\n            \"alternateAllele\",\n            \"alleleFrequencies\",\n            variant_annotation.max_maf().alias(\"maxMaf\"),\n        ).join(\n            f.broadcast(\n                gwas_associations_subset.select(\"chromosome\", \"position\").distinct()\n            ),\n            on=[\"chromosome\", \"position\"],\n            how=\"inner\",\n        )\n\n        # Semi-resolved ids (still contains duplicates when conclusion was not possible to make\n        # based on rsIds or allele concordance)\n        filtered_associations = (\n            gwas_associations_subset.join(\n                f.broadcast(va_subset),\n                on=[\"chromosome\", \"position\"],\n                how=\"left\",\n            )\n            .withColumn(\n                \"rsIdFilter\",\n                GWASCatalogCuratedAssociationsParser._flag_mappings_to_retain(\n                    f.col(\"studyLocusId\"),\n                    GWASCatalogCuratedAssociationsParser._compare_rsids(\n                        f.col(\"rsIdsGnomad\"), f.col(\"rsIdsGwasCatalog\")\n                    ),\n                ),\n            )\n            .withColumn(\n                \"concordanceFilter\",\n                GWASCatalogCuratedAssociationsParser._flag_mappings_to_retain(\n                    f.col(\"studyLocusId\"),\n                    GWASCatalogCuratedAssociationsParser._check_concordance(\n                        f.col(\"riskAllele\"),\n                        f.col(\"referenceAllele\"),\n                        f.col(\"alternateAllele\"),\n                    ),\n                ),\n            )\n            .filter(\n                # Filter out rows where GWAS Catalog rsId does not match with GnomAD rsId,\n                # but there is corresponding variant for the same association\n                f.col(\"rsIdFilter\")\n                # or filter out rows where GWAS Catalog alleles are not concordant with GnomAD alleles,\n                # but there is corresponding variant for the same association\n                | f.col(\"concordanceFilter\")\n            )\n        )\n\n        # Keep only highest maxMaf variant per studyLocusId\n        fully_mapped_associations = get_record_with_maximum_value(\n            filtered_associations, grouping_col=\"studyLocusId\", sorting_col=\"maxMaf\"\n        ).select(\n            \"studyLocusId\",\n            \"variantId\",\n            \"referenceAllele\",\n            \"alternateAllele\",\n            \"chromosome\",\n            \"position\",\n        )\n\n        return gwas_associations.join(\n            fully_mapped_associations, on=\"studyLocusId\", how=\"left\"\n        )\n\n    @staticmethod\n    def _compare_rsids(gnomad: Column, gwas: Column) -&gt; Column:\n        \"\"\"If the intersection of the two arrays is greater than 0, return True, otherwise return False.\n\n        Args:\n            gnomad (Column): rsids from gnomad\n            gwas (Column): rsids from the GWAS Catalog\n\n        Returns:\n            Column: A boolean column that is true if the GnomAD rsIDs can be found in the GWAS rsIDs.\n\n        Examples:\n            &gt;&gt;&gt; d = [\n            ...    (1, [\"rs123\", \"rs523\"], [\"rs123\"]),\n            ...    (2, [], [\"rs123\"]),\n            ...    (3, [\"rs123\", \"rs523\"], []),\n            ...    (4, [], []),\n            ... ]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, ['associationId', 'gnomad', 'gwas'])\n            &gt;&gt;&gt; df.withColumn(\"rsid_matches\", GWASCatalogCuratedAssociationsParser._compare_rsids(f.col(\"gnomad\"),f.col('gwas'))).show()\n            +-------------+--------------+-------+------------+\n            |associationId|        gnomad|   gwas|rsid_matches|\n            +-------------+--------------+-------+------------+\n            |            1|[rs123, rs523]|[rs123]|        true|\n            |            2|            []|[rs123]|       false|\n            |            3|[rs123, rs523]|     []|       false|\n            |            4|            []|     []|       false|\n            +-------------+--------------+-------+------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return f.when(f.size(f.array_intersect(gnomad, gwas)) &gt; 0, True).otherwise(\n            False\n        )\n\n    @staticmethod\n    def _flag_mappings_to_retain(\n        association_id: Column, filter_column: Column\n    ) -&gt; Column:\n        \"\"\"Flagging mappings to drop for each association.\n\n        Some associations have multiple mappings. Some has matching rsId others don't. We only\n        want to drop the non-matching mappings, when a matching is available for the given association.\n        This logic can be generalised for other measures eg. allele concordance.\n\n        Args:\n            association_id (Column): association identifier column\n            filter_column (Column): boolean col indicating to keep a mapping\n\n        Returns:\n            Column: A column with a boolean value.\n\n        Examples:\n        &gt;&gt;&gt; d = [\n        ...    (1, False),\n        ...    (1, False),\n        ...    (2, False),\n        ...    (2, True),\n        ...    (3, True),\n        ...    (3, True),\n        ... ]\n        &gt;&gt;&gt; df = spark.createDataFrame(d, ['associationId', 'filter'])\n        &gt;&gt;&gt; df.withColumn(\"isConcordant\", GWASCatalogCuratedAssociationsParser._flag_mappings_to_retain(f.col(\"associationId\"),f.col('filter'))).show()\n        +-------------+------+------------+\n        |associationId|filter|isConcordant|\n        +-------------+------+------------+\n        |            1| false|        true|\n        |            1| false|        true|\n        |            2| false|       false|\n        |            2|  true|        true|\n        |            3|  true|        true|\n        |            3|  true|        true|\n        +-------------+------+------------+\n        &lt;BLANKLINE&gt;\n\n        \"\"\"\n        w = Window.partitionBy(association_id)\n\n        # Generating a boolean column informing if the filter column contains true anywhere for the association:\n        aggregated_filter = f.when(\n            f.array_contains(f.collect_set(filter_column).over(w), True), True\n        ).otherwise(False)\n\n        # Generate a filter column:\n        return f.when(aggregated_filter &amp; (~filter_column), False).otherwise(True)\n\n    @staticmethod\n    def _check_concordance(\n        risk_allele: Column, reference_allele: Column, alternate_allele: Column\n    ) -&gt; Column:\n        \"\"\"A function to check if the risk allele is concordant with the alt or ref allele.\n\n        If the risk allele is the same as the reference or alternate allele, or if the reverse complement of\n        the risk allele is the same as the reference or alternate allele, then the allele is concordant.\n        If no mapping is available (ref/alt is null), the function returns True.\n\n        Args:\n            risk_allele (Column): The allele that is associated with the risk of the disease.\n            reference_allele (Column): The reference allele from the GWAS catalog\n            alternate_allele (Column): The alternate allele of the variant.\n\n        Returns:\n            Column: A boolean column that is True if the risk allele is the same as the reference or alternate allele,\n            or if the reverse complement of the risk allele is the same as the reference or alternate allele.\n\n        Examples:\n            &gt;&gt;&gt; d = [\n            ...     ('A', 'A', 'G'),\n            ...     ('A', 'T', 'G'),\n            ...     ('A', 'C', 'G'),\n            ...     ('A', 'A', '?'),\n            ...     (None, None, 'A'),\n            ... ]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, ['riskAllele', 'referenceAllele', 'alternateAllele'])\n            &gt;&gt;&gt; df.withColumn(\"isConcordant\", GWASCatalogCuratedAssociationsParser._check_concordance(f.col(\"riskAllele\"),f.col('referenceAllele'), f.col('alternateAllele'))).show()\n            +----------+---------------+---------------+------------+\n            |riskAllele|referenceAllele|alternateAllele|isConcordant|\n            +----------+---------------+---------------+------------+\n            |         A|              A|              G|        true|\n            |         A|              T|              G|        true|\n            |         A|              C|              G|       false|\n            |         A|              A|              ?|        true|\n            |      null|           null|              A|        true|\n            +----------+---------------+---------------+------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # Calculating the reverse complement of the risk allele:\n        risk_allele_reverse_complement = f.when(\n            risk_allele.rlike(r\"^[ACTG]+$\"),\n            f.reverse(f.translate(risk_allele, \"ACTG\", \"TGAC\")),\n        ).otherwise(risk_allele)\n\n        # OK, is the risk allele or the reverse complent is the same as the mapped alleles:\n        return (\n            f.when(\n                (risk_allele == reference_allele) | (risk_allele == alternate_allele),\n                True,\n            )\n            # If risk allele is found on the negative strand:\n            .when(\n                (risk_allele_reverse_complement == reference_allele)\n                | (risk_allele_reverse_complement == alternate_allele),\n                True,\n            )\n            # If risk allele is ambiguous, still accepted: &lt; This condition could be reconsidered\n            .when(risk_allele == \"?\", True)\n            # If the association could not be mapped we keep it:\n            .when(reference_allele.isNull(), True)\n            # Allele is discordant:\n            .otherwise(False)\n        )\n\n    @staticmethod\n    def _get_reverse_complement(allele_col: Column) -&gt; Column:\n        \"\"\"A function to return the reverse complement of an allele column.\n\n        It takes a string and returns the reverse complement of that string if it's a DNA sequence,\n        otherwise it returns the original string. Assumes alleles in upper case.\n\n        Args:\n            allele_col (Column): The column containing the allele to reverse complement.\n\n        Returns:\n            Column: A column that is the reverse complement of the allele column.\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"allele\": 'A'}, {\"allele\": 'T'},{\"allele\": 'G'}, {\"allele\": 'C'},{\"allele\": 'AC'}, {\"allele\": 'GTaatc'},{\"allele\": '?'}, {\"allele\": None}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"revcom_allele\", GWASCatalogCuratedAssociationsParser._get_reverse_complement(f.col(\"allele\"))).show()\n            +------+-------------+\n            |allele|revcom_allele|\n            +------+-------------+\n            |     A|            T|\n            |     T|            A|\n            |     G|            C|\n            |     C|            G|\n            |    AC|           GT|\n            |GTaatc|       GATTAC|\n            |     ?|            ?|\n            |  null|         null|\n            +------+-------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        allele_col = f.upper(allele_col)\n        return f.when(\n            allele_col.rlike(\"[ACTG]+\"),\n            f.reverse(f.translate(allele_col, \"ACTG\", \"TGAC\")),\n        ).otherwise(allele_col)\n\n    @staticmethod\n    def _effect_needs_harmonisation(\n        risk_allele: Column, reference_allele: Column\n    ) -&gt; Column:\n        \"\"\"A function to check if the effect allele needs to be harmonised.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Effect allele column\n\n        Returns:\n            Column: A boolean column indicating if the effect allele needs to be harmonised.\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"risk\": 'A', \"reference\": 'A'}, {\"risk\": 'A', \"reference\": 'T'}, {\"risk\": 'AT', \"reference\": 'TA'}, {\"risk\": 'AT', \"reference\": 'AT'}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"needs_harmonisation\", GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(f.col(\"risk\"), f.col(\"reference\"))).show()\n            +---------+----+-------------------+\n            |reference|risk|needs_harmonisation|\n            +---------+----+-------------------+\n            |        A|   A|               true|\n            |        T|   A|               true|\n            |       TA|  AT|              false|\n            |       AT|  AT|               true|\n            +---------+----+-------------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return (risk_allele == reference_allele) | (\n            risk_allele\n            == GWASCatalogCuratedAssociationsParser._get_reverse_complement(\n                reference_allele\n            )\n        )\n\n    @staticmethod\n    def _are_alleles_palindromic(\n        reference_allele: Column, alternate_allele: Column\n    ) -&gt; Column:\n        \"\"\"A function to check if the alleles are palindromic.\n\n        Args:\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n\n        Returns:\n            Column: A boolean column indicating if the alleles are palindromic.\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"reference\": 'A', \"alternate\": 'T'}, {\"reference\": 'AT', \"alternate\": 'AG'}, {\"reference\": 'AT', \"alternate\": 'AT'}, {\"reference\": 'CATATG', \"alternate\": 'CATATG'}, {\"reference\": '-', \"alternate\": None}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"is_palindromic\", GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(f.col(\"reference\"), f.col(\"alternate\"))).show()\n            +---------+---------+--------------+\n            |alternate|reference|is_palindromic|\n            +---------+---------+--------------+\n            |        T|        A|          true|\n            |       AG|       AT|         false|\n            |       AT|       AT|          true|\n            |   CATATG|   CATATG|          true|\n            |     null|        -|         false|\n            +---------+---------+--------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        revcomp = GWASCatalogCuratedAssociationsParser._get_reverse_complement(\n            alternate_allele\n        )\n        return (\n            f.when(reference_allele == revcomp, True)\n            .when(revcomp.isNull(), False)\n            .otherwise(False)\n        )\n\n    @staticmethod\n    def _harmonise_beta(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n    ) -&gt; Column:\n        \"\"\"A function to extract the beta value from the effect size and confidence interval.\n\n        If the confidence interval contains the word \"increase\" or \"decrease\" it indicates, we are dealing with betas.\n        If it's \"increase\" and the effect size needs to be harmonized, then multiply the effect size by -1\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n\n        Returns:\n            Column: A column containing the beta value.\n        \"\"\"\n        return (\n            f.when(\n                GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(\n                    reference_allele, alternate_allele\n                ),\n                None,\n            )\n            .when(\n                (\n                    GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(\n                        risk_allele, reference_allele\n                    )\n                    &amp; confidence_interval.contains(\"increase\")\n                )\n                | (\n                    ~GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(\n                        risk_allele, reference_allele\n                    )\n                    &amp; confidence_interval.contains(\"decrease\")\n                ),\n                -effect_size,\n            )\n            .otherwise(effect_size)\n            .cast(DoubleType())\n        )\n\n    @staticmethod\n    def _harmonise_beta_ci(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n        p_value: Column,\n        direction: str,\n    ) -&gt; Column:\n        \"\"\"Calculating confidence intervals for beta values.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n            p_value (Column): GWAS Catalog p-value column\n            direction (str): This is the direction of the confidence interval. It can be either \"upper\" or \"lower\".\n\n        Returns:\n            Column: The upper and lower bounds of the confidence interval for the beta coefficient.\n        \"\"\"\n        zscore_95 = f.lit(1.96)\n        beta = GWASCatalogCuratedAssociationsParser._harmonise_beta(\n            risk_allele,\n            reference_allele,\n            alternate_allele,\n            effect_size,\n            confidence_interval,\n        )\n        zscore = pvalue_to_zscore(p_value)\n        return (\n            f.when(f.lit(direction) == \"upper\", beta + f.abs(zscore_95 * beta) / zscore)\n            .when(f.lit(direction) == \"lower\", beta - f.abs(zscore_95 * beta) / zscore)\n            .otherwise(None)\n        )\n\n    @staticmethod\n    def _harmonise_odds_ratio(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n    ) -&gt; Column:\n        \"\"\"Harmonizing odds ratio.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n\n        Returns:\n            Column: A column with the odds ratio, or 1/odds_ratio if harmonization required.\n        \"\"\"\n        return (\n            f.when(\n                GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(\n                    reference_allele, alternate_allele\n                ),\n                None,\n            )\n            .when(\n                (\n                    GWASCatalogCuratedAssociationsParser._effect_needs_harmonisation(\n                        risk_allele, reference_allele\n                    )\n                    &amp; ~confidence_interval.rlike(\"|\".join([\"decrease\", \"increase\"]))\n                ),\n                1 / effect_size,\n            )\n            .otherwise(effect_size)\n            .cast(DoubleType())\n        )\n\n    @staticmethod\n    def _harmonise_odds_ratio_ci(\n        risk_allele: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        effect_size: Column,\n        confidence_interval: Column,\n        p_value: Column,\n        direction: str,\n    ) -&gt; Column:\n        \"\"\"Calculating confidence intervals for beta values.\n\n        Args:\n            risk_allele (Column): Risk allele column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            effect_size (Column): GWAS Catalog effect size column\n            confidence_interval (Column): GWAS Catalog confidence interval column\n            p_value (Column): GWAS Catalog p-value column\n            direction (str): This is the direction of the confidence interval. It can be either \"upper\" or \"lower\".\n\n        Returns:\n            Column: The upper and lower bounds of the 95% confidence interval for the odds ratio.\n        \"\"\"\n        zscore_95 = f.lit(1.96)\n        odds_ratio = GWASCatalogCuratedAssociationsParser._harmonise_odds_ratio(\n            risk_allele,\n            reference_allele,\n            alternate_allele,\n            effect_size,\n            confidence_interval,\n        )\n        odds_ratio_estimate = f.log(odds_ratio)\n        zscore = pvalue_to_zscore(p_value)\n        odds_ratio_se = odds_ratio_estimate / zscore\n        return f.when(\n            f.lit(direction) == \"upper\",\n            f.exp(odds_ratio_estimate + f.abs(zscore_95 * odds_ratio_se)),\n        ).when(\n            f.lit(direction) == \"lower\",\n            f.exp(odds_ratio_estimate - f.abs(zscore_95 * odds_ratio_se)),\n        )\n\n    @staticmethod\n    def _concatenate_substudy_description(\n        association_trait: Column, pvalue_text: Column, mapped_trait_uri: Column\n    ) -&gt; Column:\n        \"\"\"Substudy description parsing. Complex string containing metadata about the substudy (e.g. QTL, specific EFO, etc.).\n\n        Args:\n            association_trait (Column): GWAS Catalog association trait column\n            pvalue_text (Column): GWAS Catalog p-value text column\n            mapped_trait_uri (Column): GWAS Catalog mapped trait URI column\n\n        Returns:\n            Column: A column with the substudy description in the shape trait|pvaluetext1_pvaluetext2|EFO1_EFO2.\n\n        Examples:\n        &gt;&gt;&gt; df = spark.createDataFrame([\n        ...    (\"Height\", \"http://www.ebi.ac.uk/efo/EFO_0000001,http://www.ebi.ac.uk/efo/EFO_0000002\", \"European Ancestry\"),\n        ...    (\"Schizophrenia\", \"http://www.ebi.ac.uk/efo/MONDO_0005090\", None)],\n        ...    [\"association_trait\", \"mapped_trait_uri\", \"pvalue_text\"]\n        ... )\n        &gt;&gt;&gt; df.withColumn('substudy_description', GWASCatalogCuratedAssociationsParser._concatenate_substudy_description(df.association_trait, df.pvalue_text, df.mapped_trait_uri)).show(truncate=False)\n        +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+\n        |association_trait|mapped_trait_uri                                                         |pvalue_text      |substudy_description                      |\n        +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+\n        |Height           |http://www.ebi.ac.uk/efo/EFO_0000001,http://www.ebi.ac.uk/efo/EFO_0000002|European Ancestry|Height|EA|EFO_0000001/EFO_0000002         |\n        |Schizophrenia    |http://www.ebi.ac.uk/efo/MONDO_0005090                                   |null             |Schizophrenia|no_pvalue_text|MONDO_0005090|\n        +-----------------+-------------------------------------------------------------------------+-----------------+------------------------------------------+\n        &lt;BLANKLINE&gt;\n        \"\"\"\n        p_value_text = f.coalesce(\n            GWASCatalogCuratedAssociationsParser._normalise_pvaluetext(pvalue_text),\n            f.array(f.lit(\"no_pvalue_text\")),\n        )\n        return f.concat_ws(\n            \"|\",\n            association_trait,\n            f.concat_ws(\n                \"/\",\n                p_value_text,\n            ),\n            f.concat_ws(\n                \"/\",\n                parse_efos(mapped_trait_uri),\n            ),\n        )\n\n    @staticmethod\n    def _qc_all(\n        qc: Column,\n        chromosome: Column,\n        position: Column,\n        reference_allele: Column,\n        alternate_allele: Column,\n        strongest_snp_risk_allele: Column,\n        p_value_mantissa: Column,\n        p_value_exponent: Column,\n        p_value_cutoff: float,\n    ) -&gt; Column:\n        \"\"\"Flag associations that fail any QC.\n\n        Args:\n            qc (Column): QC column\n            chromosome (Column): Chromosome column\n            position (Column): Position column\n            reference_allele (Column): Reference allele column\n            alternate_allele (Column): Alternate allele column\n            strongest_snp_risk_allele (Column): Strongest SNP risk allele column\n            p_value_mantissa (Column): P-value mantissa column\n            p_value_exponent (Column): P-value exponent column\n            p_value_cutoff (float): P-value cutoff\n\n        Returns:\n            Column: Updated QC column with flag.\n        \"\"\"\n        qc = GWASCatalogCuratedAssociationsParser._qc_variant_interactions(\n            qc, strongest_snp_risk_allele\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_subsignificant_associations(\n            qc, p_value_mantissa, p_value_exponent, p_value_cutoff\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_genomic_location(\n            qc, chromosome, position\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_variant_inconsistencies(\n            qc, chromosome, position, strongest_snp_risk_allele\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_unmapped_variants(\n            qc, alternate_allele\n        )\n        qc = GWASCatalogCuratedAssociationsParser._qc_palindromic_alleles(\n            qc, reference_allele, alternate_allele\n        )\n        return qc\n\n    @staticmethod\n    def _qc_variant_interactions(\n        qc: Column, strongest_snp_risk_allele: Column\n    ) -&gt; Column:\n        \"\"\"Flag associations based on variant x variant interactions.\n\n        Args:\n            qc (Column): QC column\n            strongest_snp_risk_allele (Column): Column with the strongest SNP risk allele\n\n        Returns:\n            Column: Updated QC column with flag.\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            strongest_snp_risk_allele.contains(\";\"),\n            StudyLocusQualityCheck.COMPOSITE_FLAG,\n        )\n\n    @staticmethod\n    def _qc_subsignificant_associations(\n        qc: Column,\n        p_value_mantissa: Column,\n        p_value_exponent: Column,\n        pvalue_cutoff: float,\n    ) -&gt; Column:\n        \"\"\"Flag associations below significant threshold.\n\n        Args:\n            qc (Column): QC column\n            p_value_mantissa (Column): P-value mantissa column\n            p_value_exponent (Column): P-value exponent column\n            pvalue_cutoff (float): association p-value cut-off\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Examples:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [{'qc': None, 'p_value_mantissa': 1, 'p_value_exponent': -7}, {'qc': None, 'p_value_mantissa': 1, 'p_value_exponent': -8}, {'qc': None, 'p_value_mantissa': 5, 'p_value_exponent': -8}, {'qc': None, 'p_value_mantissa': 1, 'p_value_exponent': -9}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, t.StructType([t.StructField('qc', t.ArrayType(t.StringType()), True), t.StructField('p_value_mantissa', t.IntegerType()), t.StructField('p_value_exponent', t.IntegerType())]))\n            &gt;&gt;&gt; df.withColumn('qc', GWASCatalogCuratedAssociationsParser._qc_subsignificant_associations(f.col(\"qc\"), f.col(\"p_value_mantissa\"), f.col(\"p_value_exponent\"), 5e-8)).show(truncate = False)\n            +------------------------+----------------+----------------+\n            |qc                      |p_value_mantissa|p_value_exponent|\n            +------------------------+----------------+----------------+\n            |[Subsignificant p-value]|1               |-7              |\n            |[]                      |1               |-8              |\n            |[]                      |5               |-8              |\n            |[]                      |1               |-9              |\n            +------------------------+----------------+----------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            calculate_neglog_pvalue(p_value_mantissa, p_value_exponent)\n            &lt; f.lit(-np.log10(pvalue_cutoff)),\n            StudyLocusQualityCheck.SUBSIGNIFICANT_FLAG,\n        )\n\n    @staticmethod\n    def _qc_genomic_location(\n        qc: Column, chromosome: Column, position: Column\n    ) -&gt; Column:\n        \"\"\"Flag associations without genomic location in GWAS Catalog.\n\n        Args:\n            qc (Column): QC column\n            chromosome (Column): Chromosome column in GWAS Catalog\n            position (Column): Position column in GWAS Catalog\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Examples:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [{'qc': None, 'chromosome': None, 'position': None}, {'qc': None, 'chromosome': '1', 'position': None}, {'qc': None, 'chromosome': None, 'position': 1}, {'qc': None, 'chromosome': '1', 'position': 1}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d, schema=t.StructType([t.StructField('qc', t.ArrayType(t.StringType()), True), t.StructField('chromosome', t.StringType()), t.StructField('position', t.IntegerType())]))\n            &gt;&gt;&gt; df.withColumn('qc', GWASCatalogCuratedAssociationsParser._qc_genomic_location(df.qc, df.chromosome, df.position)).show(truncate=False)\n            +----------------------------+----------+--------+\n            |qc                          |chromosome|position|\n            +----------------------------+----------+--------+\n            |[Incomplete genomic mapping]|null      |null    |\n            |[Incomplete genomic mapping]|1         |null    |\n            |[Incomplete genomic mapping]|null      |1       |\n            |[]                          |1         |1       |\n            +----------------------------+----------+--------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            position.isNull() | chromosome.isNull(),\n            StudyLocusQualityCheck.NO_GENOMIC_LOCATION_FLAG,\n        )\n\n    @staticmethod\n    def _qc_variant_inconsistencies(\n        qc: Column,\n        chromosome: Column,\n        position: Column,\n        strongest_snp_risk_allele: Column,\n    ) -&gt; Column:\n        \"\"\"Flag associations with inconsistencies in the variant annotation.\n\n        Args:\n            qc (Column): QC column\n            chromosome (Column): Chromosome column in GWAS Catalog\n            position (Column): Position column in GWAS Catalog\n            strongest_snp_risk_allele (Column): Strongest SNP risk allele column in GWAS Catalog\n\n        Returns:\n            Column: Updated QC column with flag.\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            # Number of chromosomes does not correspond to the number of positions:\n            (f.size(f.split(chromosome, \";\")) != f.size(f.split(position, \";\")))\n            # Number of chromosome values different from riskAllele values:\n            | (\n                f.size(f.split(chromosome, \";\"))\n                != f.size(f.split(strongest_snp_risk_allele, \";\"))\n            ),\n            StudyLocusQualityCheck.INCONSISTENCY_FLAG,\n        )\n\n    @staticmethod\n    def _qc_unmapped_variants(qc: Column, alternate_allele: Column) -&gt; Column:\n        \"\"\"Flag associations with variants not mapped to variantAnnotation.\n\n        Args:\n            qc (Column): QC column\n            alternate_allele (Column): alternate allele\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; d = [{'alternate_allele': 'A', 'qc': None}, {'alternate_allele': None, 'qc': None}]\n            &gt;&gt;&gt; schema = t.StructType([t.StructField('alternate_allele', t.StringType(), True), t.StructField('qc', t.ArrayType(t.StringType()), True)])\n            &gt;&gt;&gt; df = spark.createDataFrame(data=d, schema=schema)\n            &gt;&gt;&gt; df.withColumn(\"new_qc\", GWASCatalogCuratedAssociationsParser._qc_unmapped_variants(f.col(\"qc\"), f.col(\"alternate_allele\"))).show()\n            +----------------+----+--------------------+\n            |alternate_allele|  qc|              new_qc|\n            +----------------+----+--------------------+\n            |               A|null|                  []|\n            |            null|null|[No mapping in Gn...|\n            +----------------+----+--------------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            alternate_allele.isNull(),\n            StudyLocusQualityCheck.NON_MAPPED_VARIANT_FLAG,\n        )\n\n    @staticmethod\n    def _qc_palindromic_alleles(\n        qc: Column, reference_allele: Column, alternate_allele: Column\n    ) -&gt; Column:\n        \"\"\"Flag associations with palindromic variants which effects can not be harmonised.\n\n        Args:\n            qc (Column): QC column\n            reference_allele (Column): reference allele\n            alternate_allele (Column): alternate allele\n\n        Returns:\n            Column: Updated QC column with flag.\n\n        Example:\n            &gt;&gt;&gt; import pyspark.sql.types as t\n            &gt;&gt;&gt; schema = t.StructType([t.StructField('reference_allele', t.StringType(), True), t.StructField('alternate_allele', t.StringType(), True), t.StructField('qc', t.ArrayType(t.StringType()), True)])\n            &gt;&gt;&gt; d = [{'reference_allele': 'A', 'alternate_allele': 'T', 'qc': None}, {'reference_allele': 'AT', 'alternate_allele': 'TA', 'qc': None}, {'reference_allele': 'AT', 'alternate_allele': 'AT', 'qc': None}]\n            &gt;&gt;&gt; df = spark.createDataFrame(data=d, schema=schema)\n            &gt;&gt;&gt; df.withColumn(\"qc\", GWASCatalogCuratedAssociationsParser._qc_palindromic_alleles(f.col(\"qc\"), f.col(\"reference_allele\"), f.col(\"alternate_allele\"))).show(truncate=False)\n            +----------------+----------------+---------------------------------------+\n            |reference_allele|alternate_allele|qc                                     |\n            +----------------+----------------+---------------------------------------+\n            |A               |T               |[Palindrome alleles - cannot harmonize]|\n            |AT              |TA              |[]                                     |\n            |AT              |AT              |[Palindrome alleles - cannot harmonize]|\n            +----------------+----------------+---------------------------------------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return StudyLocus.update_quality_flag(\n            qc,\n            GWASCatalogCuratedAssociationsParser._are_alleles_palindromic(\n                reference_allele, alternate_allele\n            ),\n            StudyLocusQualityCheck.PALINDROMIC_ALLELE_FLAG,\n        )\n\n    @classmethod\n    def from_source(\n        cls: type[GWASCatalogCuratedAssociationsParser],\n        gwas_associations: DataFrame,\n        variant_annotation: VariantAnnotation,\n        pvalue_threshold: float = 5e-8,\n    ) -&gt; StudyLocusGWASCatalog:\n        \"\"\"Read GWASCatalog associations.\n\n        It reads the GWAS Catalog association dataset, selects and renames columns, casts columns, and\n        applies some pre-defined filters on the data:\n\n        Args:\n            gwas_associations (DataFrame): GWAS Catalog raw associations dataset\n            variant_annotation (VariantAnnotation): Variant annotation dataset\n            pvalue_threshold (float): P-value threshold for flagging associations\n\n        Returns:\n            StudyLocusGWASCatalog: GWASCatalogAssociations dataset\n        \"\"\"\n        return StudyLocusGWASCatalog(\n            _df=gwas_associations.withColumn(\n                \"studyLocusId\", f.monotonically_increasing_id().cast(LongType())\n            )\n            .transform(\n                # Map/harmonise variants to variant annotation dataset:\n                # This function adds columns: variantId, referenceAllele, alternateAllele, chromosome, position\n                lambda df: GWASCatalogCuratedAssociationsParser._map_to_variant_annotation_variants(\n                    df, variant_annotation\n                )\n            )\n            .withColumn(\n                # Perform all quality control checks:\n                \"qualityControls\",\n                GWASCatalogCuratedAssociationsParser._qc_all(\n                    f.array().alias(\"qualityControls\"),\n                    f.col(\"CHR_ID\"),\n                    f.col(\"CHR_POS\").cast(IntegerType()),\n                    f.col(\"referenceAllele\"),\n                    f.col(\"alternateAllele\"),\n                    f.col(\"STRONGEST SNP-RISK ALLELE\"),\n                    *GWASCatalogCuratedAssociationsParser._parse_pvalue(\n                        f.col(\"P-VALUE\")\n                    ),\n                    pvalue_threshold,\n                ),\n            )\n            .select(\n                # INSIDE STUDY-LOCUS SCHEMA:\n                \"studyLocusId\",\n                \"variantId\",\n                # Mapped genomic location of the variant (; separated list)\n                \"chromosome\",\n                \"position\",\n                f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n                # beta value of the association\n                GWASCatalogCuratedAssociationsParser._harmonise_beta(\n                    GWASCatalogCuratedAssociationsParser._normalise_risk_allele(\n                        f.col(\"STRONGEST SNP-RISK ALLELE\")\n                    ),\n                    f.col(\"referenceAllele\"),\n                    f.col(\"alternateAllele\"),\n                    f.col(\"OR or BETA\"),\n                    f.col(\"95% CI (TEXT)\"),\n                ).alias(\"beta\"),\n                # p-value of the association, string: split into exponent and mantissa.\n                *GWASCatalogCuratedAssociationsParser._parse_pvalue(f.col(\"P-VALUE\")),\n                # Capturing phenotype granularity at the association level\n                GWASCatalogCuratedAssociationsParser._concatenate_substudy_description(\n                    f.col(\"DISEASE/TRAIT\"),\n                    f.col(\"P-VALUE (TEXT)\"),\n                    f.col(\"MAPPED_TRAIT_URI\"),\n                ).alias(\"subStudyDescription\"),\n                # Quality controls (array of strings)\n                \"qualityControls\",\n            ),\n            _schema=StudyLocusGWASCatalog.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/associations/#gentropy.datasource.gwas_catalog.associations.GWASCatalogCuratedAssociationsParser.from_source","title":"<code>from_source(gwas_associations: DataFrame, variant_annotation: VariantAnnotation, pvalue_threshold: float = 5e-08) -&gt; StudyLocusGWASCatalog</code>  <code>classmethod</code>","text":"<p>Read GWASCatalog associations.</p> <p>It reads the GWAS Catalog association dataset, selects and renames columns, casts columns, and applies some pre-defined filters on the data:</p> <p>Parameters:</p> Name Type Description Default <code>gwas_associations</code> <code>DataFrame</code> <p>GWAS Catalog raw associations dataset</p> required <code>variant_annotation</code> <code>VariantAnnotation</code> <p>Variant annotation dataset</p> required <code>pvalue_threshold</code> <code>float</code> <p>P-value threshold for flagging associations</p> <code>5e-08</code> <p>Returns:</p> Name Type Description <code>StudyLocusGWASCatalog</code> <code>StudyLocusGWASCatalog</code> <p>GWASCatalogAssociations dataset</p> Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[GWASCatalogCuratedAssociationsParser],\n    gwas_associations: DataFrame,\n    variant_annotation: VariantAnnotation,\n    pvalue_threshold: float = 5e-8,\n) -&gt; StudyLocusGWASCatalog:\n    \"\"\"Read GWASCatalog associations.\n\n    It reads the GWAS Catalog association dataset, selects and renames columns, casts columns, and\n    applies some pre-defined filters on the data:\n\n    Args:\n        gwas_associations (DataFrame): GWAS Catalog raw associations dataset\n        variant_annotation (VariantAnnotation): Variant annotation dataset\n        pvalue_threshold (float): P-value threshold for flagging associations\n\n    Returns:\n        StudyLocusGWASCatalog: GWASCatalogAssociations dataset\n    \"\"\"\n    return StudyLocusGWASCatalog(\n        _df=gwas_associations.withColumn(\n            \"studyLocusId\", f.monotonically_increasing_id().cast(LongType())\n        )\n        .transform(\n            # Map/harmonise variants to variant annotation dataset:\n            # This function adds columns: variantId, referenceAllele, alternateAllele, chromosome, position\n            lambda df: GWASCatalogCuratedAssociationsParser._map_to_variant_annotation_variants(\n                df, variant_annotation\n            )\n        )\n        .withColumn(\n            # Perform all quality control checks:\n            \"qualityControls\",\n            GWASCatalogCuratedAssociationsParser._qc_all(\n                f.array().alias(\"qualityControls\"),\n                f.col(\"CHR_ID\"),\n                f.col(\"CHR_POS\").cast(IntegerType()),\n                f.col(\"referenceAllele\"),\n                f.col(\"alternateAllele\"),\n                f.col(\"STRONGEST SNP-RISK ALLELE\"),\n                *GWASCatalogCuratedAssociationsParser._parse_pvalue(\n                    f.col(\"P-VALUE\")\n                ),\n                pvalue_threshold,\n            ),\n        )\n        .select(\n            # INSIDE STUDY-LOCUS SCHEMA:\n            \"studyLocusId\",\n            \"variantId\",\n            # Mapped genomic location of the variant (; separated list)\n            \"chromosome\",\n            \"position\",\n            f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n            # beta value of the association\n            GWASCatalogCuratedAssociationsParser._harmonise_beta(\n                GWASCatalogCuratedAssociationsParser._normalise_risk_allele(\n                    f.col(\"STRONGEST SNP-RISK ALLELE\")\n                ),\n                f.col(\"referenceAllele\"),\n                f.col(\"alternateAllele\"),\n                f.col(\"OR or BETA\"),\n                f.col(\"95% CI (TEXT)\"),\n            ).alias(\"beta\"),\n            # p-value of the association, string: split into exponent and mantissa.\n            *GWASCatalogCuratedAssociationsParser._parse_pvalue(f.col(\"P-VALUE\")),\n            # Capturing phenotype granularity at the association level\n            GWASCatalogCuratedAssociationsParser._concatenate_substudy_description(\n                f.col(\"DISEASE/TRAIT\"),\n                f.col(\"P-VALUE (TEXT)\"),\n                f.col(\"MAPPED_TRAIT_URI\"),\n            ).alias(\"subStudyDescription\"),\n            # Quality controls (array of strings)\n            \"qualityControls\",\n        ),\n        _schema=StudyLocusGWASCatalog.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/associations/#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog","title":"<code>gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog</code>  <code>dataclass</code>","text":"<p>             Bases: <code>StudyLocus</code></p> <p>Study locus Dataset for GWAS Catalog curated associations.</p> <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code> <pre><code>@dataclass\nclass StudyLocusGWASCatalog(StudyLocus):\n    \"\"\"Study locus Dataset for GWAS Catalog curated associations.\n\n    A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.\n    \"\"\"\n\n    def update_study_id(\n        self: StudyLocusGWASCatalog, study_annotation: DataFrame\n    ) -&gt; StudyLocusGWASCatalog:\n        \"\"\"Update final studyId and studyLocusId with a dataframe containing study annotation.\n\n        Args:\n            study_annotation (DataFrame): Dataframe containing `updatedStudyId` and key columns `studyId` and `subStudyDescription`.\n\n        Returns:\n            StudyLocusGWASCatalog: Updated study locus with new `studyId` and `studyLocusId`.\n        \"\"\"\n        self.df = (\n            self._df.join(\n                study_annotation, on=[\"studyId\", \"subStudyDescription\"], how=\"left\"\n            )\n            .withColumn(\"studyId\", f.coalesce(\"updatedStudyId\", \"studyId\"))\n            .drop(\"subStudyDescription\", \"updatedStudyId\")\n        ).withColumn(\n            \"studyLocusId\",\n            StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n        )\n        return self\n\n    def qc_ambiguous_study(self: StudyLocusGWASCatalog) -&gt; StudyLocusGWASCatalog:\n        \"\"\"Flag associations with variants that can not be unambiguously associated with one study.\n\n        Returns:\n            StudyLocusGWASCatalog: Updated study locus.\n        \"\"\"\n        assoc_ambiguity_window = Window.partitionBy(\n            f.col(\"studyId\"), f.col(\"variantId\")\n        )\n\n        self._df.withColumn(\n            \"qualityControls\",\n            StudyLocus.update_quality_flag(\n                f.col(\"qualityControls\"),\n                f.count(f.col(\"variantId\")).over(assoc_ambiguity_window) &gt; 1,\n                StudyLocusQualityCheck.AMBIGUOUS_STUDY,\n            ),\n        )\n        return self\n\n    def apply_inclusion_list(\n        self: StudyLocusGWASCatalog, inclusion_list: DataFrame\n    ) -&gt; StudyLocusGWASCatalog:\n        \"\"\"Restricting GWAS Catalog studies based on a list of accpected study ids.\n\n        Args:\n            inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers\n\n        Returns:\n            StudyLocusGWASCatalog: Filtered dataset.\n        \"\"\"\n        return StudyLocusGWASCatalog(\n            _df=self.df.join(inclusion_list, on=\"studyId\", how=\"inner\"),\n            _schema=StudyLocusGWASCatalog.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/associations/#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.apply_inclusion_list","title":"<code>apply_inclusion_list(inclusion_list: DataFrame) -&gt; StudyLocusGWASCatalog</code>","text":"<p>Restricting GWAS Catalog studies based on a list of accpected study ids.</p> <p>Parameters:</p> Name Type Description Default <code>inclusion_list</code> <code>DataFrame</code> <p>List of accepted GWAS Catalog study identifiers</p> required <p>Returns:</p> Name Type Description <code>StudyLocusGWASCatalog</code> <code>StudyLocusGWASCatalog</code> <p>Filtered dataset.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code> <pre><code>def apply_inclusion_list(\n    self: StudyLocusGWASCatalog, inclusion_list: DataFrame\n) -&gt; StudyLocusGWASCatalog:\n    \"\"\"Restricting GWAS Catalog studies based on a list of accpected study ids.\n\n    Args:\n        inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers\n\n    Returns:\n        StudyLocusGWASCatalog: Filtered dataset.\n    \"\"\"\n    return StudyLocusGWASCatalog(\n        _df=self.df.join(inclusion_list, on=\"studyId\", how=\"inner\"),\n        _schema=StudyLocusGWASCatalog.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/associations/#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.qc_ambiguous_study","title":"<code>qc_ambiguous_study() -&gt; StudyLocusGWASCatalog</code>","text":"<p>Flag associations with variants that can not be unambiguously associated with one study.</p> <p>Returns:</p> Name Type Description <code>StudyLocusGWASCatalog</code> <code>StudyLocusGWASCatalog</code> <p>Updated study locus.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code> <pre><code>def qc_ambiguous_study(self: StudyLocusGWASCatalog) -&gt; StudyLocusGWASCatalog:\n    \"\"\"Flag associations with variants that can not be unambiguously associated with one study.\n\n    Returns:\n        StudyLocusGWASCatalog: Updated study locus.\n    \"\"\"\n    assoc_ambiguity_window = Window.partitionBy(\n        f.col(\"studyId\"), f.col(\"variantId\")\n    )\n\n    self._df.withColumn(\n        \"qualityControls\",\n        StudyLocus.update_quality_flag(\n            f.col(\"qualityControls\"),\n            f.count(f.col(\"variantId\")).over(assoc_ambiguity_window) &gt; 1,\n            StudyLocusQualityCheck.AMBIGUOUS_STUDY,\n        ),\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/associations/#gentropy.datasource.gwas_catalog.associations.StudyLocusGWASCatalog.update_study_id","title":"<code>update_study_id(study_annotation: DataFrame) -&gt; StudyLocusGWASCatalog</code>","text":"<p>Update final studyId and studyLocusId with a dataframe containing study annotation.</p> <p>Parameters:</p> Name Type Description Default <code>study_annotation</code> <code>DataFrame</code> <p>Dataframe containing <code>updatedStudyId</code> and key columns <code>studyId</code> and <code>subStudyDescription</code>.</p> required <p>Returns:</p> Name Type Description <code>StudyLocusGWASCatalog</code> <code>StudyLocusGWASCatalog</code> <p>Updated study locus with new <code>studyId</code> and <code>studyLocusId</code>.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/associations.py</code> <pre><code>def update_study_id(\n    self: StudyLocusGWASCatalog, study_annotation: DataFrame\n) -&gt; StudyLocusGWASCatalog:\n    \"\"\"Update final studyId and studyLocusId with a dataframe containing study annotation.\n\n    Args:\n        study_annotation (DataFrame): Dataframe containing `updatedStudyId` and key columns `studyId` and `subStudyDescription`.\n\n    Returns:\n        StudyLocusGWASCatalog: Updated study locus with new `studyId` and `studyLocusId`.\n    \"\"\"\n    self.df = (\n        self._df.join(\n            study_annotation, on=[\"studyId\", \"subStudyDescription\"], how=\"left\"\n        )\n        .withColumn(\"studyId\", f.coalesce(\"updatedStudyId\", \"studyId\"))\n        .drop(\"subStudyDescription\", \"updatedStudyId\")\n    ).withColumn(\n        \"studyLocusId\",\n        StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/","title":"Study Index","text":""},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser","title":"<code>gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser</code>  <code>dataclass</code>","text":"<p>GWAS Catalog study index parser.</p> <p>The following information is harmonised from the GWAS Catalog:</p> <ul> <li>All publication related information retained.</li> <li>Mapped measured and background traits parsed.</li> <li>Flagged if harmonized summary statistics datasets available.</li> <li>If available, the ftp path to these files presented.</li> <li>Ancestries from the discovery and replication stages are structured with sample counts.</li> <li>Case/control counts extracted.</li> <li>The number of samples with European ancestry extracted.</li> </ul> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>@dataclass\nclass StudyIndexGWASCatalogParser:\n    \"\"\"GWAS Catalog study index parser.\n\n    The following information is harmonised from the GWAS Catalog:\n\n    - All publication related information retained.\n    - Mapped measured and background traits parsed.\n    - Flagged if harmonized summary statistics datasets available.\n    - If available, the ftp path to these files presented.\n    - Ancestries from the discovery and replication stages are structured with sample counts.\n    - Case/control counts extracted.\n    - The number of samples with European ancestry extracted.\n\n    \"\"\"\n\n    @staticmethod\n    def _parse_discovery_samples(discovery_samples: Column) -&gt; Column:\n        \"\"\"Parse discovery sample sizes from GWAS Catalog.\n\n        This is a curated field. From publication sometimes it is not clear how the samples were split\n        across the reported ancestries. In such cases we are assuming the ancestries were evenly presented\n        and the total sample size is split:\n\n        [\"European, African\", 100] -&gt; [\"European, 50], [\"African\", 50]\n\n        Args:\n            discovery_samples (Column): Raw discovery sample sizes\n\n        Returns:\n            Column: Parsed and de-duplicated list of discovery ancestries with sample size.\n\n        Examples:\n            &gt;&gt;&gt; data = [('s1', \"European\", 10), ('s1', \"African\", 10), ('s2', \"European, African, Asian\", 100), ('s2', \"European\", 50)]\n            &gt;&gt;&gt; df = (\n            ...    spark.createDataFrame(data, ['studyId', 'ancestry', 'sampleSize'])\n            ...    .groupBy('studyId')\n            ...    .agg(\n            ...        f.collect_set(\n            ...            f.struct('ancestry', 'sampleSize')\n            ...        ).alias('discoverySampleSize')\n            ...    )\n            ...    .orderBy('studyId')\n            ...    .withColumn('discoverySampleSize', StudyIndexGWASCatalogParser._parse_discovery_samples(f.col('discoverySampleSize')))\n            ...    .select('discoverySampleSize')\n            ...    .show(truncate=False)\n            ... )\n            +--------------------------------------------+\n            |discoverySampleSize                         |\n            +--------------------------------------------+\n            |[{African, 10}, {European, 10}]             |\n            |[{European, 83}, {African, 33}, {Asian, 33}]|\n            +--------------------------------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        # To initialize return objects for aggregate functions, schema has to be defined:\n        schema = t.ArrayType(\n            t.StructType(\n                [\n                    t.StructField(\"ancestry\", t.StringType(), True),\n                    t.StructField(\"sampleSize\", t.IntegerType(), True),\n                ]\n            )\n        )\n\n        # Splitting comma separated ancestries:\n        exploded_ancestries = f.transform(\n            discovery_samples,\n            lambda sample: f.split(sample.ancestry, r\",\\s(?![^()]*\\))\"),\n        )\n\n        # Initialize discoverySample object from unique list of ancestries:\n        unique_ancestries = f.transform(\n            f.aggregate(\n                exploded_ancestries,\n                f.array().cast(t.ArrayType(t.StringType())),\n                lambda x, y: f.array_union(x, y),\n                f.array_distinct,\n            ),\n            lambda ancestry: f.struct(\n                ancestry.alias(\"ancestry\"),\n                f.lit(0).alias(\"sampleSize\"),\n            ),\n        )\n\n        # Computing sample sizes for ancestries when splitting is needed:\n        resolved_sample_count = f.transform(\n            f.arrays_zip(\n                f.transform(exploded_ancestries, lambda pop: f.size(pop)).alias(\n                    \"pop_size\"\n                ),\n                f.transform(discovery_samples, lambda pop: pop.sampleSize).alias(\n                    \"pop_count\"\n                ),\n            ),\n            lambda pop: (pop.pop_count / pop.pop_size).cast(t.IntegerType()),\n        )\n\n        # Flattening out ancestries with sample sizes:\n        parsed_sample_size = f.aggregate(\n            f.transform(\n                f.arrays_zip(\n                    exploded_ancestries.alias(\"ancestries\"),\n                    resolved_sample_count.alias(\"sample_count\"),\n                ),\n                StudyIndexGWASCatalogParser._merge_ancestries_and_counts,\n            ),\n            f.array().cast(schema),\n            lambda x, y: f.array_union(x, y),\n        )\n\n        # Normalize ancestries:\n        return f.aggregate(\n            parsed_sample_size,\n            unique_ancestries,\n            StudyIndexGWASCatalogParser._normalize_ancestries,\n        )\n\n    @staticmethod\n    def _normalize_ancestries(merged: Column, ancestry: Column) -&gt; Column:\n        \"\"\"Normalize ancestries from a list of structs.\n\n        As some ancestry label might be repeated with different sample counts,\n        these counts need to be collected.\n\n        Args:\n            merged (Column): Resulting list of struct with unique ancestries.\n            ancestry (Column): One ancestry object coming from raw.\n\n        Returns:\n            Column: Unique list of ancestries with the sample counts.\n        \"\"\"\n        # Iterating over the list of unique ancestries and adding the sample size if label matches:\n        return f.transform(\n            merged,\n            lambda a: f.when(\n                a.ancestry == ancestry.ancestry,\n                f.struct(\n                    a.ancestry.alias(\"ancestry\"),\n                    (a.sampleSize + ancestry.sampleSize)\n                    .cast(t.IntegerType())\n                    .alias(\"sampleSize\"),\n                ),\n            ).otherwise(a),\n        )\n\n    @staticmethod\n    def _merge_ancestries_and_counts(ancestry_group: Column) -&gt; Column:\n        \"\"\"Merge ancestries with sample sizes.\n\n        After splitting ancestry annotations, all resulting ancestries needs to be assigned\n        with the proper sample size.\n\n        Args:\n            ancestry_group (Column): Each element is a struct with `sample_count` (int) and `ancestries` (list)\n\n        Returns:\n            Column: a list of structs with `ancestry` and `sampleSize` fields.\n\n        Examples:\n            &gt;&gt;&gt; data = [(12, ['African', 'European']),(12, ['African'])]\n            &gt;&gt;&gt; (\n            ...     spark.createDataFrame(data, ['sample_count', 'ancestries'])\n            ...     .select(StudyIndexGWASCatalogParser._merge_ancestries_and_counts(f.struct('sample_count', 'ancestries')).alias('test'))\n            ...     .show(truncate=False)\n            ... )\n            +-------------------------------+\n            |test                           |\n            +-------------------------------+\n            |[{African, 12}, {European, 12}]|\n            |[{African, 12}]                |\n            +-------------------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        # Extract sample size for the ancestry group:\n        count = ancestry_group.sample_count\n\n        # We need to loop through the ancestries:\n        return f.transform(\n            ancestry_group.ancestries,\n            lambda ancestry: f.struct(\n                ancestry.alias(\"ancestry\"),\n                count.alias(\"sampleSize\"),\n            ),\n        )\n\n    @staticmethod\n    def parse_cohorts(raw_cohort: Column) -&gt; Column:\n        \"\"\"Return a list of unique cohort labels from pipe separated list if provided.\n\n        Args:\n            raw_cohort (Column): Cohort list column, where labels are separated by `|` sign.\n\n        Returns:\n            Column: an array colun with string elements.\n\n        Examples:\n        &gt;&gt;&gt; data = [('BioME|CaPS|Estonia|FHS|UKB|GERA|GERA|GERA',),(None,),]\n        &gt;&gt;&gt; spark.createDataFrame(data, ['cohorts']).select(StudyIndexGWASCatalogParser.parse_cohorts(f.col('cohorts')).alias('parsedCohorts')).show(truncate=False)\n        +--------------------------------------+\n        |parsedCohorts                         |\n        +--------------------------------------+\n        |[BioME, CaPS, Estonia, FHS, UKB, GERA]|\n        |[null]                                |\n        +--------------------------------------+\n        &lt;BLANKLINE&gt;\n        \"\"\"\n        return f.when(\n            (raw_cohort.isNull()) | (raw_cohort == \"\"),\n            f.array(f.lit(None).cast(t.StringType())),\n        ).otherwise(f.array_distinct(f.split(raw_cohort, r\"\\|\")))\n\n    @classmethod\n    def _parse_study_table(\n        cls: type[StudyIndexGWASCatalogParser], catalog_studies: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Harmonise GWASCatalog study table with `StudyIndex` schema.\n\n        Args:\n            catalog_studies (DataFrame): GWAS Catalog study table\n\n        Returns:\n            StudyIndexGWASCatalog: Parsed and annotated GWAS Catalog study table.\n        \"\"\"\n        return StudyIndexGWASCatalog(\n            _df=catalog_studies.select(\n                f.coalesce(\n                    f.col(\"STUDY ACCESSION\"), f.monotonically_increasing_id()\n                ).alias(\"studyId\"),\n                f.lit(\"GCST\").alias(\"projectId\"),\n                f.lit(\"gwas\").alias(\"studyType\"),\n                f.col(\"PUBMED ID\").alias(\"pubmedId\"),\n                f.col(\"FIRST AUTHOR\").alias(\"publicationFirstAuthor\"),\n                f.col(\"DATE\").alias(\"publicationDate\"),\n                f.col(\"JOURNAL\").alias(\"publicationJournal\"),\n                f.col(\"STUDY\").alias(\"publicationTitle\"),\n                f.coalesce(f.col(\"DISEASE/TRAIT\"), f.lit(\"Unreported\")).alias(\n                    \"traitFromSource\"\n                ),\n                f.col(\"INITIAL SAMPLE SIZE\").alias(\"initialSampleSize\"),\n                parse_efos(f.col(\"MAPPED_TRAIT_URI\")).alias(\"traitFromSourceMappedIds\"),\n                parse_efos(f.col(\"MAPPED BACKGROUND TRAIT URI\")).alias(\n                    \"backgroundTraitFromSourceMappedIds\"\n                ),\n            ),\n            _schema=StudyIndexGWASCatalog.get_schema(),\n        )\n\n    @classmethod\n    def from_source(\n        cls: type[StudyIndexGWASCatalogParser],\n        catalog_studies: DataFrame,\n        ancestry_file: DataFrame,\n        sumstats_lut: DataFrame,\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Ingests study level metadata from the GWAS Catalog.\n\n        Args:\n            catalog_studies (DataFrame): GWAS Catalog raw study table\n            ancestry_file (DataFrame): GWAS Catalog ancestry table.\n            sumstats_lut (DataFrame): GWAS Catalog summary statistics list.\n\n        Returns:\n            StudyIndexGWASCatalog: Parsed and annotated GWAS Catalog study table.\n        \"\"\"\n        # Read GWAS Catalogue raw data\n        return (\n            cls._parse_study_table(catalog_studies)\n            .annotate_ancestries(ancestry_file)\n            .annotate_sumstats_info(sumstats_lut)\n            .annotate_discovery_sample_sizes()\n        )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.from_source","title":"<code>from_source(catalog_studies: DataFrame, ancestry_file: DataFrame, sumstats_lut: DataFrame) -&gt; StudyIndexGWASCatalog</code>  <code>classmethod</code>","text":"<p>Ingests study level metadata from the GWAS Catalog.</p> <p>Parameters:</p> Name Type Description Default <code>catalog_studies</code> <code>DataFrame</code> <p>GWAS Catalog raw study table</p> required <code>ancestry_file</code> <code>DataFrame</code> <p>GWAS Catalog ancestry table.</p> required <code>sumstats_lut</code> <code>DataFrame</code> <p>GWAS Catalog summary statistics list.</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Parsed and annotated GWAS Catalog study table.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>@classmethod\ndef from_source(\n    cls: type[StudyIndexGWASCatalogParser],\n    catalog_studies: DataFrame,\n    ancestry_file: DataFrame,\n    sumstats_lut: DataFrame,\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Ingests study level metadata from the GWAS Catalog.\n\n    Args:\n        catalog_studies (DataFrame): GWAS Catalog raw study table\n        ancestry_file (DataFrame): GWAS Catalog ancestry table.\n        sumstats_lut (DataFrame): GWAS Catalog summary statistics list.\n\n    Returns:\n        StudyIndexGWASCatalog: Parsed and annotated GWAS Catalog study table.\n    \"\"\"\n    # Read GWAS Catalogue raw data\n    return (\n        cls._parse_study_table(catalog_studies)\n        .annotate_ancestries(ancestry_file)\n        .annotate_sumstats_info(sumstats_lut)\n        .annotate_discovery_sample_sizes()\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalogParser.parse_cohorts","title":"<code>parse_cohorts(raw_cohort: Column) -&gt; Column</code>  <code>staticmethod</code>","text":"<p>Return a list of unique cohort labels from pipe separated list if provided.</p> <p>Parameters:</p> Name Type Description Default <code>raw_cohort</code> <code>Column</code> <p>Cohort list column, where labels are separated by <code>|</code> sign.</p> required <p>Returns:</p> Name Type Description <code>Column</code> <code>Column</code> <p>an array colun with string elements.</p> <p>Examples:</p> <p>data = [('BioME|CaPS|Estonia|FHS|UKB|GERA|GERA|GERA',),(None,),] spark.createDataFrame(data, ['cohorts']).select(StudyIndexGWASCatalogParser.parse_cohorts(f.col('cohorts')).alias('parsedCohorts')).show(truncate=False) +--------------------------------------+ |parsedCohorts                         | +--------------------------------------+ |[BioME, CaPS, Estonia, FHS, UKB, GERA]| |[null]                                | +--------------------------------------+  Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>@staticmethod\ndef parse_cohorts(raw_cohort: Column) -&gt; Column:\n    \"\"\"Return a list of unique cohort labels from pipe separated list if provided.\n\n    Args:\n        raw_cohort (Column): Cohort list column, where labels are separated by `|` sign.\n\n    Returns:\n        Column: an array colun with string elements.\n\n    Examples:\n    &gt;&gt;&gt; data = [('BioME|CaPS|Estonia|FHS|UKB|GERA|GERA|GERA',),(None,),]\n    &gt;&gt;&gt; spark.createDataFrame(data, ['cohorts']).select(StudyIndexGWASCatalogParser.parse_cohorts(f.col('cohorts')).alias('parsedCohorts')).show(truncate=False)\n    +--------------------------------------+\n    |parsedCohorts                         |\n    +--------------------------------------+\n    |[BioME, CaPS, Estonia, FHS, UKB, GERA]|\n    |[null]                                |\n    +--------------------------------------+\n    &lt;BLANKLINE&gt;\n    \"\"\"\n    return f.when(\n        (raw_cohort.isNull()) | (raw_cohort == \"\"),\n        f.array(f.lit(None).cast(t.StringType())),\n    ).otherwise(f.array_distinct(f.split(raw_cohort, r\"\\|\")))\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog","title":"<code>gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog</code>  <code>dataclass</code>","text":"<p>             Bases: <code>StudyIndex</code></p> <p>Study index dataset from GWAS Catalog.</p> <p>A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>@dataclass\nclass StudyIndexGWASCatalog(StudyIndex):\n    \"\"\"Study index dataset from GWAS Catalog.\n\n    A study index dataset captures all the metadata for all studies including GWAS and Molecular QTL.\n    \"\"\"\n\n    def update_study_id(\n        self: StudyIndexGWASCatalog, study_annotation: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Update studyId with a dataframe containing study.\n\n        Args:\n            study_annotation (DataFrame): Dataframe containing `updatedStudyId`, `traitFromSource`, `traitFromSourceMappedIds` and key column `studyId`.\n\n        Returns:\n            StudyIndexGWASCatalog: Updated study table.\n        \"\"\"\n        self.df = (\n            self._df.join(\n                study_annotation.select(\n                    *[\n                        f.col(c).alias(f\"updated{c}\")\n                        if c not in [\"studyId\", \"updatedStudyId\"]\n                        else f.col(c)\n                        for c in study_annotation.columns\n                    ]\n                ),\n                on=\"studyId\",\n                how=\"left\",\n            )\n            .withColumn(\n                \"studyId\",\n                f.coalesce(f.col(\"updatedStudyId\"), f.col(\"studyId\")),\n            )\n            .withColumn(\n                \"traitFromSource\",\n                f.coalesce(f.col(\"updatedtraitFromSource\"), f.col(\"traitFromSource\")),\n            )\n            .withColumn(\n                \"traitFromSourceMappedIds\",\n                f.coalesce(\n                    f.col(\"updatedtraitFromSourceMappedIds\"),\n                    f.col(\"traitFromSourceMappedIds\"),\n                ),\n            )\n            .select(self._df.columns)\n        )\n\n        return self\n\n    def annotate_from_study_curation(\n        self: StudyIndexGWASCatalog, curation_table: DataFrame | None\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Annotating study index with curation.\n\n        Args:\n            curation_table (DataFrame | None): Curated GWAS Catalog studies with summary statistics\n\n        Returns:\n            StudyIndexGWASCatalog: Updated study index\n        \"\"\"\n        # Providing curation table is optional. However once this method is called, the quality and studyFlag columns are added.\n        if curation_table is None:\n            return self\n\n        columns = self.df.columns\n\n        # Adding prefix to columns in the curation table:\n        curation_table = curation_table.select(\n            *[\n                f.col(column).alias(f\"curation_{column}\")\n                if column != \"studyId\"\n                else f.col(column)\n                for column in curation_table.columns\n            ]\n        )\n\n        # Create expression how to update/create quality controls dataset:\n        qualityControls_expression = (\n            f.col(\"curation_qualityControls\")\n            if \"qualityControls\" not in columns\n            else f.when(\n                f.col(\"curation_qualityControls\").isNotNull(),\n                f.array_union(\n                    f.col(\"qualityControls\"), f.array(f.col(\"curation_qualityControls\"))\n                ),\n            ).otherwise(f.col(\"qualityControls\"))\n        )\n\n        # Create expression how to update/create analysis flag:\n        analysis_expression = (\n            f.col(\"curation_analysisFlags\")\n            if \"analysisFlags\" not in columns\n            else f.when(\n                f.col(\"curation_analysisFlags\").isNotNull(),\n                f.array_union(\n                    f.col(\"analysisFlags\"), f.array(f.col(\"curation_analysisFlags\"))\n                ),\n            ).otherwise(f.col(\"analysisFlags\"))\n        )\n\n        # Updating columns list. We might or might not list columns twice, but that doesn't matter, unique set will generated:\n        columns = list(set(columns + [\"qualityControls\", \"analysisFlags\"]))\n\n        # Based on the curation table, columns needs to be updated:\n        curated_df = (\n            self.df.join(curation_table, on=\"studyId\", how=\"left\")\n            # Updating study type:\n            .withColumn(\n                \"studyType\", f.coalesce(f.col(\"curation_studyType\"), f.col(\"studyType\"))\n            )\n            # Updating quality controls:\n            .withColumn(\"qualityControls\", qualityControls_expression)\n            # Updating study annotation flags:\n            .withColumn(\"analysisFlags\", analysis_expression)\n            # Dropping columns coming from the curation table:\n            .select(*columns)\n        )\n        return StudyIndexGWASCatalog(\n            _df=curated_df, _schema=StudyIndexGWASCatalog.get_schema()\n        )\n\n    def extract_studies_for_curation(\n        self: StudyIndexGWASCatalog, curation: DataFrame | None\n    ) -&gt; DataFrame:\n        \"\"\"Extract studies for curation.\n\n        Args:\n            curation (DataFrame | None): Dataframe with curation.\n\n        Returns:\n            DataFrame: Updated curation table. New studies are have the `isCurated` False.\n        \"\"\"\n        # If no curation table provided, assume all studies needs curation:\n        if curation is None:\n            return (\n                self.df\n                # Curation only applyed on studies with summary statistics:\n                .filter(f.col(\"hasSumstats\"))\n                # Adding columns expected in the curation table - array columns aready flattened:\n                .withColumn(\"studyType\", f.lit(None).cast(t.StringType()))\n                .withColumn(\"analysisFlag\", f.lit(None).cast(t.StringType()))\n                .withColumn(\"qualityControl\", f.lit(None).cast(t.StringType()))\n                .withColumn(\"isCurated\", f.lit(False).cast(t.StringType()))\n            )\n\n        # Adding prefix to columns in the curation table:\n        curation = curation.select(\n            *[\n                f.col(column).alias(f\"curation_{column}\")\n                if column != \"studyId\"\n                else f.col(column)\n                for column in curation.columns\n            ]\n        )\n\n        return (\n            self.df\n            # Curation only applyed on studies with summary statistics:\n            .filter(f.col(\"hasSumstats\"))\n            .join(curation, on=\"studyId\", how=\"left\")\n            .select(\n                \"studyId\",\n                # Propagate existing curation - array columns are being flattened:\n                f.col(\"curation_studyType\").alias(\"studyType\"),\n                f.array_join(f.col(\"curation_analysisFlags\"), \"|\").alias(\n                    \"analysisFlag\"\n                ),\n                f.array_join(f.col(\"curation_qualityControls\"), \"|\").alias(\n                    \"qualityControl\"\n                ),\n                # This boolean flag needs to be casted to string, because saving to tsv would fail otherwise:\n                f.coalesce(f.col(\"curation_isCurated\"), f.lit(False))\n                .cast(t.StringType())\n                .alias(\"isCurated\"),\n                # The following columns are propagated to make curation easier:\n                \"pubmedId\",\n                \"publicationTitle\",\n                \"traitFromSource\",\n            )\n        )\n\n    def annotate_ancestries(\n        self: StudyIndexGWASCatalog, ancestry_lut: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Extracting sample sizes and ancestry information.\n\n        This function parses the ancestry data. Also get counts for the europeans in the same\n        discovery stage.\n\n        Args:\n            ancestry_lut (DataFrame): Ancestry table as downloaded from the GWAS Catalog\n\n        Returns:\n            StudyIndexGWASCatalog: Slimmed and cleaned version of the ancestry annotation.\n        \"\"\"\n        from gentropy.datasource.gwas_catalog.study_index import (\n            StudyIndexGWASCatalogParser as GWASCatalogStudyIndexParser,\n        )\n\n        ancestry = (\n            ancestry_lut\n            # Convert column headers to camelcase:\n            .transform(\n                lambda df: df.select(\n                    *[f.expr(column2camel_case(x)) for x in df.columns]\n                )\n            ).withColumnRenamed(\n                \"studyAccession\", \"studyId\"\n            )  # studyId has not been split yet\n        )\n\n        # Parsing cohort information:\n        cohorts = ancestry_lut.select(\n            f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n            GWASCatalogStudyIndexParser.parse_cohorts(f.col(\"COHORT(S)\")).alias(\n                \"cohorts\"\n            ),\n        ).distinct()\n\n        # Get a high resolution dataset on experimental stage:\n        ancestry_stages = (\n            ancestry.groupBy(\"studyId\")\n            .pivot(\"stage\")\n            .agg(\n                f.collect_set(\n                    f.struct(\n                        f.col(\"broadAncestralCategory\").alias(\"ancestry\"),\n                        f.col(\"numberOfIndividuals\")\n                        .cast(t.IntegerType())\n                        .alias(\"sampleSize\"),\n                    )\n                )\n            )\n            .withColumn(\n                \"discoverySamples\",\n                GWASCatalogStudyIndexParser._parse_discovery_samples(f.col(\"initial\")),\n            )\n            .withColumnRenamed(\"replication\", \"replicationSamples\")\n            # Mapping discovery stage ancestries to LD reference:\n            .withColumn(\n                \"ldPopulationStructure\",\n                self.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n            )\n            .drop(\"initial\")\n            .persist()\n        )\n\n        # Generate information on the ancestry composition of the discovery stage, and calculate\n        # the proportion of the Europeans:\n        europeans_deconvoluted = (\n            ancestry\n            # Focus on discovery stage:\n            .filter(f.col(\"stage\") == \"initial\")\n            # Sorting ancestries if European:\n            .withColumn(\n                \"ancestryFlag\",\n                # Excluding finnish:\n                f.when(\n                    f.col(\"initialSampleDescription\").contains(\"Finnish\"),\n                    f.lit(\"other\"),\n                )\n                # Excluding Icelandic population:\n                .when(\n                    f.col(\"initialSampleDescription\").contains(\"Icelandic\"),\n                    f.lit(\"other\"),\n                )\n                # Including European ancestry:\n                .when(f.col(\"broadAncestralCategory\") == \"European\", f.lit(\"european\"))\n                # Exclude all other population:\n                .otherwise(\"other\"),\n            )\n            # Grouping by study accession and initial sample description:\n            .groupBy(\"studyId\")\n            .pivot(\"ancestryFlag\")\n            .agg(\n                # Summarizing sample sizes for all ancestries:\n                f.sum(f.col(\"numberOfIndividuals\"))\n            )\n            # Do arithmetics to make sure we have the right proportion of european in the set:\n            .withColumn(\n                \"initialSampleCountEuropean\",\n                f.when(f.col(\"european\").isNull(), f.lit(0)).otherwise(\n                    f.col(\"european\")\n                ),\n            )\n            .withColumn(\n                \"initialSampleCountOther\",\n                f.when(f.col(\"other\").isNull(), f.lit(0)).otherwise(f.col(\"other\")),\n            )\n            .withColumn(\n                \"initialSampleCount\",\n                f.col(\"initialSampleCountEuropean\") + f.col(\"other\"),\n            )\n            .drop(\n                \"european\",\n                \"other\",\n                \"initialSampleCount\",\n                \"initialSampleCountEuropean\",\n                \"initialSampleCountOther\",\n            )\n        )\n\n        parsed_ancestry_lut = ancestry_stages.join(\n            europeans_deconvoluted, on=\"studyId\", how=\"outer\"\n        ).select(\n            \"studyId\", \"discoverySamples\", \"ldPopulationStructure\", \"replicationSamples\"\n        )\n        self.df = self.df.join(parsed_ancestry_lut, on=\"studyId\", how=\"left\").join(\n            cohorts, on=\"studyId\", how=\"left\"\n        )\n        return self\n\n    def annotate_sumstats_info(\n        self: StudyIndexGWASCatalog, sumstats_lut: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Annotate summary stat locations.\n\n        Args:\n            sumstats_lut (DataFrame): listing GWAS Catalog summary stats paths\n\n        Returns:\n            StudyIndexGWASCatalog: including `summarystatsLocation` and `hasSumstats` columns\n\n        Raises:\n            ValueError: if the sumstats_lut table doesn't have the right columns\n        \"\"\"\n        gwas_sumstats_base_uri = (\n            \"ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/\"\n        )\n\n        if \"_c0\" not in sumstats_lut.columns:\n            raise ValueError(\n                f'Sumstats look-up table needs to have `_c0` column. However it has: {\",\".join(sumstats_lut.columns)}'\n            )\n\n        parsed_sumstats_lut = sumstats_lut.withColumn(\n            \"summarystatsLocation\",\n            f.concat(\n                f.lit(gwas_sumstats_base_uri),\n                f.regexp_replace(f.col(\"_c0\"), r\"^\\.\\/\", \"\"),\n            ),\n        ).select(\n            self._parse_gwas_catalog_study_id(\"summarystatsLocation\").alias(\"studyId\"),\n            \"summarystatsLocation\",\n            f.lit(True).alias(\"hasSumstats\"),\n        )\n        self.df = (\n            self.df.drop(\"hasSumstats\")\n            .join(parsed_sumstats_lut, on=\"studyId\", how=\"left\")\n            .withColumn(\"hasSumstats\", f.coalesce(f.col(\"hasSumstats\"), f.lit(False)))\n        )\n        return self\n\n    def annotate_discovery_sample_sizes(\n        self: StudyIndexGWASCatalog,\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Extract the sample size of the discovery stage of the study as annotated in the GWAS Catalog.\n\n        For some studies that measure quantitative traits, nCases and nControls can't be extracted. Therefore, we assume these are 0.\n\n        Returns:\n            StudyIndexGWASCatalog: object with columns `nCases`, `nControls`, and `nSamples` per `studyId` correctly extracted.\n        \"\"\"\n        sample_size_lut = (\n            self.df.select(\n                \"studyId\",\n                f.explode_outer(f.split(f.col(\"initialSampleSize\"), r\",\\s+\")).alias(\n                    \"samples\"\n                ),\n            )\n            # Extracting the sample size from the string:\n            .withColumn(\n                \"sampleSize\",\n                f.regexp_extract(\n                    f.regexp_replace(f.col(\"samples\"), \",\", \"\"), r\"[0-9,]+\", 0\n                ).cast(t.IntegerType()),\n            )\n            .select(\n                \"studyId\",\n                \"sampleSize\",\n                f.when(f.col(\"samples\").contains(\"cases\"), f.col(\"sampleSize\"))\n                .otherwise(f.lit(0))\n                .alias(\"nCases\"),\n                f.when(f.col(\"samples\").contains(\"controls\"), f.col(\"sampleSize\"))\n                .otherwise(f.lit(0))\n                .alias(\"nControls\"),\n            )\n            # Aggregating sample sizes for all ancestries:\n            .groupBy(\"studyId\")  # studyId has not been split yet\n            .agg(\n                f.sum(\"nCases\").cast(\"integer\").alias(\"nCases\"),\n                f.sum(\"nControls\").cast(\"integer\").alias(\"nControls\"),\n                f.sum(\"sampleSize\").cast(\"integer\").alias(\"nSamples\"),\n            )\n        )\n        self.df = self.df.join(sample_size_lut, on=\"studyId\", how=\"left\")\n        return self\n\n    def apply_inclusion_list(\n        self: StudyIndexGWASCatalog, inclusion_list: DataFrame\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Restricting GWAS Catalog studies based on a list of accepted study identifiers.\n\n        Args:\n            inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers\n\n        Returns:\n            StudyIndexGWASCatalog: Filtered dataset.\n        \"\"\"\n        return StudyIndexGWASCatalog(\n            _df=self.df.join(inclusion_list, on=\"studyId\", how=\"inner\"),\n            _schema=StudyIndexGWASCatalog.get_schema(),\n        )\n\n    @staticmethod\n    def _parse_gwas_catalog_study_id(sumstats_path_column: str) -&gt; Column:\n        \"\"\"Extract GWAS Catalog study accession from the summary statistics path.\n\n        Args:\n            sumstats_path_column (str): column *name* for the summary statistics path\n\n        Returns:\n            Column: GWAS Catalog study accession.\n\n        Examples:\n            &gt;&gt;&gt; data = [\n            ... ('./GCST90086001-GCST90087000/GCST90086758/harmonised/35078996-GCST90086758-EFO_0007937.h.tsv.gz',),\n            ...    ('gs://open-targets-gwas-summary-stats/harmonised/GCST000568.parquet/',),\n            ...    (None,)\n            ... ]\n            &gt;&gt;&gt; spark.createDataFrame(data, ['testColumn']).select(StudyIndexGWASCatalog._parse_gwas_catalog_study_id('testColumn').alias('accessions')).collect()\n            [Row(accessions='GCST90086758'), Row(accessions='GCST000568'), Row(accessions=None)]\n        \"\"\"\n        accesions = f.expr(rf\"regexp_extract_all({sumstats_path_column}, '(GCST\\\\d+)')\")\n        return accesions[f.size(accesions) - 1]\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_ancestries","title":"<code>annotate_ancestries(ancestry_lut: DataFrame) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Extracting sample sizes and ancestry information.</p> <p>This function parses the ancestry data. Also get counts for the europeans in the same discovery stage.</p> <p>Parameters:</p> Name Type Description Default <code>ancestry_lut</code> <code>DataFrame</code> <p>Ancestry table as downloaded from the GWAS Catalog</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Slimmed and cleaned version of the ancestry annotation.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>def annotate_ancestries(\n    self: StudyIndexGWASCatalog, ancestry_lut: DataFrame\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Extracting sample sizes and ancestry information.\n\n    This function parses the ancestry data. Also get counts for the europeans in the same\n    discovery stage.\n\n    Args:\n        ancestry_lut (DataFrame): Ancestry table as downloaded from the GWAS Catalog\n\n    Returns:\n        StudyIndexGWASCatalog: Slimmed and cleaned version of the ancestry annotation.\n    \"\"\"\n    from gentropy.datasource.gwas_catalog.study_index import (\n        StudyIndexGWASCatalogParser as GWASCatalogStudyIndexParser,\n    )\n\n    ancestry = (\n        ancestry_lut\n        # Convert column headers to camelcase:\n        .transform(\n            lambda df: df.select(\n                *[f.expr(column2camel_case(x)) for x in df.columns]\n            )\n        ).withColumnRenamed(\n            \"studyAccession\", \"studyId\"\n        )  # studyId has not been split yet\n    )\n\n    # Parsing cohort information:\n    cohorts = ancestry_lut.select(\n        f.col(\"STUDY ACCESSION\").alias(\"studyId\"),\n        GWASCatalogStudyIndexParser.parse_cohorts(f.col(\"COHORT(S)\")).alias(\n            \"cohorts\"\n        ),\n    ).distinct()\n\n    # Get a high resolution dataset on experimental stage:\n    ancestry_stages = (\n        ancestry.groupBy(\"studyId\")\n        .pivot(\"stage\")\n        .agg(\n            f.collect_set(\n                f.struct(\n                    f.col(\"broadAncestralCategory\").alias(\"ancestry\"),\n                    f.col(\"numberOfIndividuals\")\n                    .cast(t.IntegerType())\n                    .alias(\"sampleSize\"),\n                )\n            )\n        )\n        .withColumn(\n            \"discoverySamples\",\n            GWASCatalogStudyIndexParser._parse_discovery_samples(f.col(\"initial\")),\n        )\n        .withColumnRenamed(\"replication\", \"replicationSamples\")\n        # Mapping discovery stage ancestries to LD reference:\n        .withColumn(\n            \"ldPopulationStructure\",\n            self.aggregate_and_map_ancestries(f.col(\"discoverySamples\")),\n        )\n        .drop(\"initial\")\n        .persist()\n    )\n\n    # Generate information on the ancestry composition of the discovery stage, and calculate\n    # the proportion of the Europeans:\n    europeans_deconvoluted = (\n        ancestry\n        # Focus on discovery stage:\n        .filter(f.col(\"stage\") == \"initial\")\n        # Sorting ancestries if European:\n        .withColumn(\n            \"ancestryFlag\",\n            # Excluding finnish:\n            f.when(\n                f.col(\"initialSampleDescription\").contains(\"Finnish\"),\n                f.lit(\"other\"),\n            )\n            # Excluding Icelandic population:\n            .when(\n                f.col(\"initialSampleDescription\").contains(\"Icelandic\"),\n                f.lit(\"other\"),\n            )\n            # Including European ancestry:\n            .when(f.col(\"broadAncestralCategory\") == \"European\", f.lit(\"european\"))\n            # Exclude all other population:\n            .otherwise(\"other\"),\n        )\n        # Grouping by study accession and initial sample description:\n        .groupBy(\"studyId\")\n        .pivot(\"ancestryFlag\")\n        .agg(\n            # Summarizing sample sizes for all ancestries:\n            f.sum(f.col(\"numberOfIndividuals\"))\n        )\n        # Do arithmetics to make sure we have the right proportion of european in the set:\n        .withColumn(\n            \"initialSampleCountEuropean\",\n            f.when(f.col(\"european\").isNull(), f.lit(0)).otherwise(\n                f.col(\"european\")\n            ),\n        )\n        .withColumn(\n            \"initialSampleCountOther\",\n            f.when(f.col(\"other\").isNull(), f.lit(0)).otherwise(f.col(\"other\")),\n        )\n        .withColumn(\n            \"initialSampleCount\",\n            f.col(\"initialSampleCountEuropean\") + f.col(\"other\"),\n        )\n        .drop(\n            \"european\",\n            \"other\",\n            \"initialSampleCount\",\n            \"initialSampleCountEuropean\",\n            \"initialSampleCountOther\",\n        )\n    )\n\n    parsed_ancestry_lut = ancestry_stages.join(\n        europeans_deconvoluted, on=\"studyId\", how=\"outer\"\n    ).select(\n        \"studyId\", \"discoverySamples\", \"ldPopulationStructure\", \"replicationSamples\"\n    )\n    self.df = self.df.join(parsed_ancestry_lut, on=\"studyId\", how=\"left\").join(\n        cohorts, on=\"studyId\", how=\"left\"\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_discovery_sample_sizes","title":"<code>annotate_discovery_sample_sizes() -&gt; StudyIndexGWASCatalog</code>","text":"<p>Extract the sample size of the discovery stage of the study as annotated in the GWAS Catalog.</p> <p>For some studies that measure quantitative traits, nCases and nControls can't be extracted. Therefore, we assume these are 0.</p> <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>object with columns <code>nCases</code>, <code>nControls</code>, and <code>nSamples</code> per <code>studyId</code> correctly extracted.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>def annotate_discovery_sample_sizes(\n    self: StudyIndexGWASCatalog,\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Extract the sample size of the discovery stage of the study as annotated in the GWAS Catalog.\n\n    For some studies that measure quantitative traits, nCases and nControls can't be extracted. Therefore, we assume these are 0.\n\n    Returns:\n        StudyIndexGWASCatalog: object with columns `nCases`, `nControls`, and `nSamples` per `studyId` correctly extracted.\n    \"\"\"\n    sample_size_lut = (\n        self.df.select(\n            \"studyId\",\n            f.explode_outer(f.split(f.col(\"initialSampleSize\"), r\",\\s+\")).alias(\n                \"samples\"\n            ),\n        )\n        # Extracting the sample size from the string:\n        .withColumn(\n            \"sampleSize\",\n            f.regexp_extract(\n                f.regexp_replace(f.col(\"samples\"), \",\", \"\"), r\"[0-9,]+\", 0\n            ).cast(t.IntegerType()),\n        )\n        .select(\n            \"studyId\",\n            \"sampleSize\",\n            f.when(f.col(\"samples\").contains(\"cases\"), f.col(\"sampleSize\"))\n            .otherwise(f.lit(0))\n            .alias(\"nCases\"),\n            f.when(f.col(\"samples\").contains(\"controls\"), f.col(\"sampleSize\"))\n            .otherwise(f.lit(0))\n            .alias(\"nControls\"),\n        )\n        # Aggregating sample sizes for all ancestries:\n        .groupBy(\"studyId\")  # studyId has not been split yet\n        .agg(\n            f.sum(\"nCases\").cast(\"integer\").alias(\"nCases\"),\n            f.sum(\"nControls\").cast(\"integer\").alias(\"nControls\"),\n            f.sum(\"sampleSize\").cast(\"integer\").alias(\"nSamples\"),\n        )\n    )\n    self.df = self.df.join(sample_size_lut, on=\"studyId\", how=\"left\")\n    return self\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_from_study_curation","title":"<code>annotate_from_study_curation(curation_table: DataFrame | None) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Annotating study index with curation.</p> <p>Parameters:</p> Name Type Description Default <code>curation_table</code> <code>DataFrame | None</code> <p>Curated GWAS Catalog studies with summary statistics</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Updated study index</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>def annotate_from_study_curation(\n    self: StudyIndexGWASCatalog, curation_table: DataFrame | None\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Annotating study index with curation.\n\n    Args:\n        curation_table (DataFrame | None): Curated GWAS Catalog studies with summary statistics\n\n    Returns:\n        StudyIndexGWASCatalog: Updated study index\n    \"\"\"\n    # Providing curation table is optional. However once this method is called, the quality and studyFlag columns are added.\n    if curation_table is None:\n        return self\n\n    columns = self.df.columns\n\n    # Adding prefix to columns in the curation table:\n    curation_table = curation_table.select(\n        *[\n            f.col(column).alias(f\"curation_{column}\")\n            if column != \"studyId\"\n            else f.col(column)\n            for column in curation_table.columns\n        ]\n    )\n\n    # Create expression how to update/create quality controls dataset:\n    qualityControls_expression = (\n        f.col(\"curation_qualityControls\")\n        if \"qualityControls\" not in columns\n        else f.when(\n            f.col(\"curation_qualityControls\").isNotNull(),\n            f.array_union(\n                f.col(\"qualityControls\"), f.array(f.col(\"curation_qualityControls\"))\n            ),\n        ).otherwise(f.col(\"qualityControls\"))\n    )\n\n    # Create expression how to update/create analysis flag:\n    analysis_expression = (\n        f.col(\"curation_analysisFlags\")\n        if \"analysisFlags\" not in columns\n        else f.when(\n            f.col(\"curation_analysisFlags\").isNotNull(),\n            f.array_union(\n                f.col(\"analysisFlags\"), f.array(f.col(\"curation_analysisFlags\"))\n            ),\n        ).otherwise(f.col(\"analysisFlags\"))\n    )\n\n    # Updating columns list. We might or might not list columns twice, but that doesn't matter, unique set will generated:\n    columns = list(set(columns + [\"qualityControls\", \"analysisFlags\"]))\n\n    # Based on the curation table, columns needs to be updated:\n    curated_df = (\n        self.df.join(curation_table, on=\"studyId\", how=\"left\")\n        # Updating study type:\n        .withColumn(\n            \"studyType\", f.coalesce(f.col(\"curation_studyType\"), f.col(\"studyType\"))\n        )\n        # Updating quality controls:\n        .withColumn(\"qualityControls\", qualityControls_expression)\n        # Updating study annotation flags:\n        .withColumn(\"analysisFlags\", analysis_expression)\n        # Dropping columns coming from the curation table:\n        .select(*columns)\n    )\n    return StudyIndexGWASCatalog(\n        _df=curated_df, _schema=StudyIndexGWASCatalog.get_schema()\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.annotate_sumstats_info","title":"<code>annotate_sumstats_info(sumstats_lut: DataFrame) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Annotate summary stat locations.</p> <p>Parameters:</p> Name Type Description Default <code>sumstats_lut</code> <code>DataFrame</code> <p>listing GWAS Catalog summary stats paths</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>including <code>summarystatsLocation</code> and <code>hasSumstats</code> columns</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>if the sumstats_lut table doesn't have the right columns</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>def annotate_sumstats_info(\n    self: StudyIndexGWASCatalog, sumstats_lut: DataFrame\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Annotate summary stat locations.\n\n    Args:\n        sumstats_lut (DataFrame): listing GWAS Catalog summary stats paths\n\n    Returns:\n        StudyIndexGWASCatalog: including `summarystatsLocation` and `hasSumstats` columns\n\n    Raises:\n        ValueError: if the sumstats_lut table doesn't have the right columns\n    \"\"\"\n    gwas_sumstats_base_uri = (\n        \"ftp://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/\"\n    )\n\n    if \"_c0\" not in sumstats_lut.columns:\n        raise ValueError(\n            f'Sumstats look-up table needs to have `_c0` column. However it has: {\",\".join(sumstats_lut.columns)}'\n        )\n\n    parsed_sumstats_lut = sumstats_lut.withColumn(\n        \"summarystatsLocation\",\n        f.concat(\n            f.lit(gwas_sumstats_base_uri),\n            f.regexp_replace(f.col(\"_c0\"), r\"^\\.\\/\", \"\"),\n        ),\n    ).select(\n        self._parse_gwas_catalog_study_id(\"summarystatsLocation\").alias(\"studyId\"),\n        \"summarystatsLocation\",\n        f.lit(True).alias(\"hasSumstats\"),\n    )\n    self.df = (\n        self.df.drop(\"hasSumstats\")\n        .join(parsed_sumstats_lut, on=\"studyId\", how=\"left\")\n        .withColumn(\"hasSumstats\", f.coalesce(f.col(\"hasSumstats\"), f.lit(False)))\n    )\n    return self\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.apply_inclusion_list","title":"<code>apply_inclusion_list(inclusion_list: DataFrame) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Restricting GWAS Catalog studies based on a list of accepted study identifiers.</p> <p>Parameters:</p> Name Type Description Default <code>inclusion_list</code> <code>DataFrame</code> <p>List of accepted GWAS Catalog study identifiers</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Filtered dataset.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>def apply_inclusion_list(\n    self: StudyIndexGWASCatalog, inclusion_list: DataFrame\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Restricting GWAS Catalog studies based on a list of accepted study identifiers.\n\n    Args:\n        inclusion_list (DataFrame): List of accepted GWAS Catalog study identifiers\n\n    Returns:\n        StudyIndexGWASCatalog: Filtered dataset.\n    \"\"\"\n    return StudyIndexGWASCatalog(\n        _df=self.df.join(inclusion_list, on=\"studyId\", how=\"inner\"),\n        _schema=StudyIndexGWASCatalog.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.extract_studies_for_curation","title":"<code>extract_studies_for_curation(curation: DataFrame | None) -&gt; DataFrame</code>","text":"<p>Extract studies for curation.</p> <p>Parameters:</p> Name Type Description Default <code>curation</code> <code>DataFrame | None</code> <p>Dataframe with curation.</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Updated curation table. New studies are have the <code>isCurated</code> False.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>def extract_studies_for_curation(\n    self: StudyIndexGWASCatalog, curation: DataFrame | None\n) -&gt; DataFrame:\n    \"\"\"Extract studies for curation.\n\n    Args:\n        curation (DataFrame | None): Dataframe with curation.\n\n    Returns:\n        DataFrame: Updated curation table. New studies are have the `isCurated` False.\n    \"\"\"\n    # If no curation table provided, assume all studies needs curation:\n    if curation is None:\n        return (\n            self.df\n            # Curation only applyed on studies with summary statistics:\n            .filter(f.col(\"hasSumstats\"))\n            # Adding columns expected in the curation table - array columns aready flattened:\n            .withColumn(\"studyType\", f.lit(None).cast(t.StringType()))\n            .withColumn(\"analysisFlag\", f.lit(None).cast(t.StringType()))\n            .withColumn(\"qualityControl\", f.lit(None).cast(t.StringType()))\n            .withColumn(\"isCurated\", f.lit(False).cast(t.StringType()))\n        )\n\n    # Adding prefix to columns in the curation table:\n    curation = curation.select(\n        *[\n            f.col(column).alias(f\"curation_{column}\")\n            if column != \"studyId\"\n            else f.col(column)\n            for column in curation.columns\n        ]\n    )\n\n    return (\n        self.df\n        # Curation only applyed on studies with summary statistics:\n        .filter(f.col(\"hasSumstats\"))\n        .join(curation, on=\"studyId\", how=\"left\")\n        .select(\n            \"studyId\",\n            # Propagate existing curation - array columns are being flattened:\n            f.col(\"curation_studyType\").alias(\"studyType\"),\n            f.array_join(f.col(\"curation_analysisFlags\"), \"|\").alias(\n                \"analysisFlag\"\n            ),\n            f.array_join(f.col(\"curation_qualityControls\"), \"|\").alias(\n                \"qualityControl\"\n            ),\n            # This boolean flag needs to be casted to string, because saving to tsv would fail otherwise:\n            f.coalesce(f.col(\"curation_isCurated\"), f.lit(False))\n            .cast(t.StringType())\n            .alias(\"isCurated\"),\n            # The following columns are propagated to make curation easier:\n            \"pubmedId\",\n            \"publicationTitle\",\n            \"traitFromSource\",\n        )\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_index/#gentropy.datasource.gwas_catalog.study_index.StudyIndexGWASCatalog.update_study_id","title":"<code>update_study_id(study_annotation: DataFrame) -&gt; StudyIndexGWASCatalog</code>","text":"<p>Update studyId with a dataframe containing study.</p> <p>Parameters:</p> Name Type Description Default <code>study_annotation</code> <code>DataFrame</code> <p>Dataframe containing <code>updatedStudyId</code>, <code>traitFromSource</code>, <code>traitFromSourceMappedIds</code> and key column <code>studyId</code>.</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Updated study table.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_index.py</code> <pre><code>def update_study_id(\n    self: StudyIndexGWASCatalog, study_annotation: DataFrame\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Update studyId with a dataframe containing study.\n\n    Args:\n        study_annotation (DataFrame): Dataframe containing `updatedStudyId`, `traitFromSource`, `traitFromSourceMappedIds` and key column `studyId`.\n\n    Returns:\n        StudyIndexGWASCatalog: Updated study table.\n    \"\"\"\n    self.df = (\n        self._df.join(\n            study_annotation.select(\n                *[\n                    f.col(c).alias(f\"updated{c}\")\n                    if c not in [\"studyId\", \"updatedStudyId\"]\n                    else f.col(c)\n                    for c in study_annotation.columns\n                ]\n            ),\n            on=\"studyId\",\n            how=\"left\",\n        )\n        .withColumn(\n            \"studyId\",\n            f.coalesce(f.col(\"updatedStudyId\"), f.col(\"studyId\")),\n        )\n        .withColumn(\n            \"traitFromSource\",\n            f.coalesce(f.col(\"updatedtraitFromSource\"), f.col(\"traitFromSource\")),\n        )\n        .withColumn(\n            \"traitFromSourceMappedIds\",\n            f.coalesce(\n                f.col(\"updatedtraitFromSourceMappedIds\"),\n                f.col(\"traitFromSourceMappedIds\"),\n            ),\n        )\n        .select(self._df.columns)\n    )\n\n    return self\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_splitter/","title":"Study Splitter","text":""},{"location":"python_api/datasources/gwas_catalog/study_splitter/#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter","title":"<code>gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter</code>","text":"<p>Splitting multi-trait GWAS Catalog studies.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_splitter.py</code> <pre><code>class GWASCatalogStudySplitter:\n    \"\"\"Splitting multi-trait GWAS Catalog studies.\"\"\"\n\n    @staticmethod\n    def _resolve_trait(\n        study_trait: Column, association_trait: Column, p_value_text: Column\n    ) -&gt; Column:\n        \"\"\"Resolve trait names by consolidating association-level and study-level trait names.\n\n        Args:\n            study_trait (Column): Study-level trait name.\n            association_trait (Column): Association-level trait name.\n            p_value_text (Column): P-value text.\n\n        Returns:\n            Column: Resolved trait name.\n        \"\"\"\n        return (\n            f.when(\n                (p_value_text.isNotNull()) &amp; (p_value_text != (\"no_pvalue_text\")),\n                f.concat(\n                    association_trait,\n                    f.lit(\" [\"),\n                    p_value_text,\n                    f.lit(\"]\"),\n                ),\n            )\n            .when(\n                association_trait.isNotNull(),\n                association_trait,\n            )\n            .otherwise(study_trait)\n        )\n\n    @staticmethod\n    def _resolve_efo(association_efo: Column, study_efo: Column) -&gt; Column:\n        \"\"\"Resolve EFOs by consolidating association-level and study-level EFOs.\n\n        Args:\n            association_efo (Column): EFO column from the association table.\n            study_efo (Column): EFO column from the study table.\n\n        Returns:\n            Column: Consolidated EFO column.\n        \"\"\"\n        return f.coalesce(f.split(association_efo, r\"\\/\"), study_efo)\n\n    @staticmethod\n    def _resolve_study_id(study_id: Column, sub_study_description: Column) -&gt; Column:\n        \"\"\"Resolve study IDs by exploding association-level information (e.g. pvalue_text, EFO).\n\n        Args:\n            study_id (Column): Study ID column.\n            sub_study_description (Column): Sub-study description column from the association table.\n\n        Returns:\n            Column: Resolved study ID column.\n        \"\"\"\n        split_w = Window.partitionBy(study_id).orderBy(sub_study_description)\n        row_number = f.dense_rank().over(split_w)\n        substudy_count = f.approx_count_distinct(row_number).over(split_w)\n        return f.when(substudy_count == 1, study_id).otherwise(\n            f.concat_ws(\"_\", study_id, row_number)\n        )\n\n    @classmethod\n    def split(\n        cls: type[GWASCatalogStudySplitter],\n        studies: StudyIndexGWASCatalog,\n        associations: StudyLocusGWASCatalog,\n    ) -&gt; Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]:\n        \"\"\"Splitting multi-trait GWAS Catalog studies.\n\n        If assigned disease of the study and the association don't agree, we assume the study needs to be split.\n        Then disease EFOs, trait names and study ID are consolidated\n\n        Args:\n            studies (StudyIndexGWASCatalog): GWAS Catalog studies.\n            associations (StudyLocusGWASCatalog): GWAS Catalog associations.\n\n        Returns:\n            Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations.\n        \"\"\"\n        # Composite of studies and associations to resolve scattered information\n        st_ass = (\n            associations.df.join(f.broadcast(studies.df), on=\"studyId\", how=\"inner\")\n            .select(\n                \"studyId\",\n                \"subStudyDescription\",\n                cls._resolve_study_id(\n                    f.col(\"studyId\"), f.col(\"subStudyDescription\")\n                ).alias(\"updatedStudyId\"),\n                cls._resolve_trait(\n                    f.col(\"traitFromSource\"),\n                    f.split(\"subStudyDescription\", r\"\\|\").getItem(0),\n                    f.split(\"subStudyDescription\", r\"\\|\").getItem(1),\n                ).alias(\"traitFromSource\"),\n                cls._resolve_efo(\n                    f.split(\"subStudyDescription\", r\"\\|\").getItem(2),\n                    f.col(\"traitFromSourceMappedIds\"),\n                ).alias(\"traitFromSourceMappedIds\"),\n            )\n            .persist()\n        )\n\n        return (\n            studies.update_study_id(\n                st_ass.select(\n                    \"studyId\",\n                    \"updatedStudyId\",\n                    \"traitFromSource\",\n                    \"traitFromSourceMappedIds\",\n                ).distinct()\n            ),\n            associations.update_study_id(\n                st_ass.select(\n                    \"updatedStudyId\", \"studyId\", \"subStudyDescription\"\n                ).distinct()\n            ).qc_ambiguous_study(),\n        )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/study_splitter/#gentropy.datasource.gwas_catalog.study_splitter.GWASCatalogStudySplitter.split","title":"<code>split(studies: StudyIndexGWASCatalog, associations: StudyLocusGWASCatalog) -&gt; Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]</code>  <code>classmethod</code>","text":"<p>Splitting multi-trait GWAS Catalog studies.</p> <p>If assigned disease of the study and the association don't agree, we assume the study needs to be split. Then disease EFOs, trait names and study ID are consolidated</p> <p>Parameters:</p> Name Type Description Default <code>studies</code> <code>StudyIndexGWASCatalog</code> <p>GWAS Catalog studies.</p> required <code>associations</code> <code>StudyLocusGWASCatalog</code> <p>GWAS Catalog associations.</p> required <p>Returns:</p> Type Description <code>Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]</code> <p>Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/study_splitter.py</code> <pre><code>@classmethod\ndef split(\n    cls: type[GWASCatalogStudySplitter],\n    studies: StudyIndexGWASCatalog,\n    associations: StudyLocusGWASCatalog,\n) -&gt; Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]:\n    \"\"\"Splitting multi-trait GWAS Catalog studies.\n\n    If assigned disease of the study and the association don't agree, we assume the study needs to be split.\n    Then disease EFOs, trait names and study ID are consolidated\n\n    Args:\n        studies (StudyIndexGWASCatalog): GWAS Catalog studies.\n        associations (StudyLocusGWASCatalog): GWAS Catalog associations.\n\n    Returns:\n        Tuple[StudyIndexGWASCatalog, StudyLocusGWASCatalog]: Split studies and associations.\n    \"\"\"\n    # Composite of studies and associations to resolve scattered information\n    st_ass = (\n        associations.df.join(f.broadcast(studies.df), on=\"studyId\", how=\"inner\")\n        .select(\n            \"studyId\",\n            \"subStudyDescription\",\n            cls._resolve_study_id(\n                f.col(\"studyId\"), f.col(\"subStudyDescription\")\n            ).alias(\"updatedStudyId\"),\n            cls._resolve_trait(\n                f.col(\"traitFromSource\"),\n                f.split(\"subStudyDescription\", r\"\\|\").getItem(0),\n                f.split(\"subStudyDescription\", r\"\\|\").getItem(1),\n            ).alias(\"traitFromSource\"),\n            cls._resolve_efo(\n                f.split(\"subStudyDescription\", r\"\\|\").getItem(2),\n                f.col(\"traitFromSourceMappedIds\"),\n            ).alias(\"traitFromSourceMappedIds\"),\n        )\n        .persist()\n    )\n\n    return (\n        studies.update_study_id(\n            st_ass.select(\n                \"studyId\",\n                \"updatedStudyId\",\n                \"traitFromSource\",\n                \"traitFromSourceMappedIds\",\n            ).distinct()\n        ),\n        associations.update_study_id(\n            st_ass.select(\n                \"updatedStudyId\", \"studyId\", \"subStudyDescription\"\n            ).distinct()\n        ).qc_ambiguous_study(),\n    )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/summary_statistics/","title":"Summary statistics","text":""},{"location":"python_api/datasources/gwas_catalog/summary_statistics/#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics","title":"<code>gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics</code>  <code>dataclass</code>","text":"<p>             Bases: <code>SummaryStatistics</code></p> <p>GWAS Catalog Summary Statistics reader.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/summary_statistics.py</code> <pre><code>@dataclass\nclass GWASCatalogSummaryStatistics(SummaryStatistics):\n    \"\"\"GWAS Catalog Summary Statistics reader.\"\"\"\n\n    @classmethod\n    def from_gwas_harmonized_summary_stats(\n        cls: type[GWASCatalogSummaryStatistics],\n        spark: SparkSession,\n        sumstats_file: str,\n    ) -&gt; GWASCatalogSummaryStatistics:\n        \"\"\"Create summary statistics object from summary statistics flatfile, harmonized by the GWAS Catalog.\n\n        Things got slightly complicated given the GWAS Catalog harmonization pipelines changed recently so we had to accomodate to\n        both formats.\n\n        Args:\n            spark (SparkSession): spark session\n            sumstats_file (str): list of GWAS Catalog summary stat files, with study ids in them.\n\n        Returns:\n            GWASCatalogSummaryStatistics: Summary statistics object.\n        \"\"\"\n        sumstats_df = spark.read.csv(sumstats_file, sep=\"\\t\", header=True).withColumn(\n            # Parsing GWAS Catalog study identifier from filename:\n            \"studyId\",\n            f.lit(filename_to_study_identifier(sumstats_file)),\n        )\n\n        # Parsing variant id fields:\n        chromosome = (\n            f.col(\"hm_chrom\")\n            if \"hm_chrom\" in sumstats_df.columns\n            else f.col(\"chromosome\")\n        ).cast(t.StringType())\n        position = (\n            f.col(\"hm_pos\")\n            if \"hm_pos\" in sumstats_df.columns\n            else f.col(\"base_pair_location\")\n        ).cast(t.IntegerType())\n        ref_allele = (\n            f.col(\"hm_other_allele\")\n            if \"hm_other_allele\" in sumstats_df.columns\n            else f.col(\"other_allele\")\n        )\n        alt_allele = (\n            f.col(\"hm_effect_allele\")\n            if \"hm_effect_allele\" in sumstats_df.columns\n            else f.col(\"effect_allele\")\n        )\n\n        # Parsing p-value (get a tuple with mantissa and exponent):\n        p_value_expression = (\n            parse_pvalue(f.col(\"p_value\"))\n            if \"p_value\" in sumstats_df.columns\n            else neglog_pvalue_to_mantissa_and_exponent(f.col(\"neg_log_10_p_value\"))\n        )\n\n        # The effect allele frequency is an optional column, we have to test if it is there:\n        allele_frequency = (\n            f.col(\"effect_allele_frequency\")\n            if \"effect_allele_frequency\" in sumstats_df.columns\n            else f.lit(None)\n        ).cast(t.FloatType())\n\n        # Do we have sample size? This expression captures 99.7% of sample size columns.\n        sample_size = (f.col(\"n\") if \"n\" in sumstats_df.columns else f.lit(None)).cast(\n            t.IntegerType()\n        )\n\n        # Depending on the input, we might have beta, but the column might not be there at all also old format calls differently:\n        beta_expression = (\n            f.col(\"hm_beta\")\n            if \"hm_beta\" in sumstats_df.columns\n            else f.col(\"beta\")\n            if \"beta\" in sumstats_df.columns\n            # If no column, create one:\n            else f.lit(None)\n        ).cast(t.DoubleType())\n\n        # We might have odds ratio or hazard ratio, wich are basically the same:\n        odds_ratio_expression = (\n            f.col(\"hm_odds_ratio\")\n            if \"hm_odds_ratio\" in sumstats_df.columns\n            else f.col(\"odds_ratio\")\n            if \"odds_ratio\" in sumstats_df.columns\n            else f.col(\"hazard_ratio\")\n            if \"hazard_ratio\" in sumstats_df.columns\n            # If no column, create one:\n            else f.lit(None)\n        ).cast(t.DoubleType())\n\n        # Does the file have standard error column?\n        standard_error = (\n            f.col(\"standard_error\")\n            if \"standard_error\" in sumstats_df.columns\n            else f.lit(None)\n        ).cast(t.DoubleType())\n\n        # Processing columns of interest:\n        processed_sumstats_df = (\n            sumstats_df\n            # Dropping rows which doesn't have proper position:\n            .select(\n                \"studyId\",\n                # Adding variant identifier:\n                f.concat_ws(\n                    \"_\",\n                    chromosome,\n                    position,\n                    ref_allele,\n                    alt_allele,\n                ).alias(\"variantId\"),\n                chromosome.alias(\"chromosome\"),\n                position.alias(\"position\"),\n                # Parsing p-value mantissa and exponent:\n                *p_value_expression,\n                # Converting/calculating effect and confidence interval:\n                *convert_odds_ratio_to_beta(\n                    beta_expression,\n                    odds_ratio_expression,\n                    standard_error,\n                ),\n                allele_frequency.alias(\"effectAlleleFrequencyFromSource\"),\n                sample_size.alias(\"sampleSize\"),\n            )\n            .filter(\n                # Dropping associations where no harmonized position is available:\n                f.col(\"position\").isNotNull()\n                &amp;\n                # We are not interested in associations with zero effect:\n                (f.col(\"beta\") != 0)\n            )\n            .orderBy(f.col(\"chromosome\"), f.col(\"position\"))\n            # median study size is 200Mb, max is 2.6Gb\n            .repartition(20)\n        )\n\n        # Initializing summary statistics object:\n        return cls(\n            _df=processed_sumstats_df,\n            _schema=cls.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/gwas_catalog/summary_statistics/#gentropy.datasource.gwas_catalog.summary_statistics.GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats","title":"<code>from_gwas_harmonized_summary_stats(spark: SparkSession, sumstats_file: str) -&gt; GWASCatalogSummaryStatistics</code>  <code>classmethod</code>","text":"<p>Create summary statistics object from summary statistics flatfile, harmonized by the GWAS Catalog.</p> <p>Things got slightly complicated given the GWAS Catalog harmonization pipelines changed recently so we had to accomodate to both formats.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>spark session</p> required <code>sumstats_file</code> <code>str</code> <p>list of GWAS Catalog summary stat files, with study ids in them.</p> required <p>Returns:</p> Name Type Description <code>GWASCatalogSummaryStatistics</code> <code>GWASCatalogSummaryStatistics</code> <p>Summary statistics object.</p> Source code in <code>src/gentropy/datasource/gwas_catalog/summary_statistics.py</code> <pre><code>@classmethod\ndef from_gwas_harmonized_summary_stats(\n    cls: type[GWASCatalogSummaryStatistics],\n    spark: SparkSession,\n    sumstats_file: str,\n) -&gt; GWASCatalogSummaryStatistics:\n    \"\"\"Create summary statistics object from summary statistics flatfile, harmonized by the GWAS Catalog.\n\n    Things got slightly complicated given the GWAS Catalog harmonization pipelines changed recently so we had to accomodate to\n    both formats.\n\n    Args:\n        spark (SparkSession): spark session\n        sumstats_file (str): list of GWAS Catalog summary stat files, with study ids in them.\n\n    Returns:\n        GWASCatalogSummaryStatistics: Summary statistics object.\n    \"\"\"\n    sumstats_df = spark.read.csv(sumstats_file, sep=\"\\t\", header=True).withColumn(\n        # Parsing GWAS Catalog study identifier from filename:\n        \"studyId\",\n        f.lit(filename_to_study_identifier(sumstats_file)),\n    )\n\n    # Parsing variant id fields:\n    chromosome = (\n        f.col(\"hm_chrom\")\n        if \"hm_chrom\" in sumstats_df.columns\n        else f.col(\"chromosome\")\n    ).cast(t.StringType())\n    position = (\n        f.col(\"hm_pos\")\n        if \"hm_pos\" in sumstats_df.columns\n        else f.col(\"base_pair_location\")\n    ).cast(t.IntegerType())\n    ref_allele = (\n        f.col(\"hm_other_allele\")\n        if \"hm_other_allele\" in sumstats_df.columns\n        else f.col(\"other_allele\")\n    )\n    alt_allele = (\n        f.col(\"hm_effect_allele\")\n        if \"hm_effect_allele\" in sumstats_df.columns\n        else f.col(\"effect_allele\")\n    )\n\n    # Parsing p-value (get a tuple with mantissa and exponent):\n    p_value_expression = (\n        parse_pvalue(f.col(\"p_value\"))\n        if \"p_value\" in sumstats_df.columns\n        else neglog_pvalue_to_mantissa_and_exponent(f.col(\"neg_log_10_p_value\"))\n    )\n\n    # The effect allele frequency is an optional column, we have to test if it is there:\n    allele_frequency = (\n        f.col(\"effect_allele_frequency\")\n        if \"effect_allele_frequency\" in sumstats_df.columns\n        else f.lit(None)\n    ).cast(t.FloatType())\n\n    # Do we have sample size? This expression captures 99.7% of sample size columns.\n    sample_size = (f.col(\"n\") if \"n\" in sumstats_df.columns else f.lit(None)).cast(\n        t.IntegerType()\n    )\n\n    # Depending on the input, we might have beta, but the column might not be there at all also old format calls differently:\n    beta_expression = (\n        f.col(\"hm_beta\")\n        if \"hm_beta\" in sumstats_df.columns\n        else f.col(\"beta\")\n        if \"beta\" in sumstats_df.columns\n        # If no column, create one:\n        else f.lit(None)\n    ).cast(t.DoubleType())\n\n    # We might have odds ratio or hazard ratio, wich are basically the same:\n    odds_ratio_expression = (\n        f.col(\"hm_odds_ratio\")\n        if \"hm_odds_ratio\" in sumstats_df.columns\n        else f.col(\"odds_ratio\")\n        if \"odds_ratio\" in sumstats_df.columns\n        else f.col(\"hazard_ratio\")\n        if \"hazard_ratio\" in sumstats_df.columns\n        # If no column, create one:\n        else f.lit(None)\n    ).cast(t.DoubleType())\n\n    # Does the file have standard error column?\n    standard_error = (\n        f.col(\"standard_error\")\n        if \"standard_error\" in sumstats_df.columns\n        else f.lit(None)\n    ).cast(t.DoubleType())\n\n    # Processing columns of interest:\n    processed_sumstats_df = (\n        sumstats_df\n        # Dropping rows which doesn't have proper position:\n        .select(\n            \"studyId\",\n            # Adding variant identifier:\n            f.concat_ws(\n                \"_\",\n                chromosome,\n                position,\n                ref_allele,\n                alt_allele,\n            ).alias(\"variantId\"),\n            chromosome.alias(\"chromosome\"),\n            position.alias(\"position\"),\n            # Parsing p-value mantissa and exponent:\n            *p_value_expression,\n            # Converting/calculating effect and confidence interval:\n            *convert_odds_ratio_to_beta(\n                beta_expression,\n                odds_ratio_expression,\n                standard_error,\n            ),\n            allele_frequency.alias(\"effectAlleleFrequencyFromSource\"),\n            sample_size.alias(\"sampleSize\"),\n        )\n        .filter(\n            # Dropping associations where no harmonized position is available:\n            f.col(\"position\").isNotNull()\n            &amp;\n            # We are not interested in associations with zero effect:\n            (f.col(\"beta\") != 0)\n        )\n        .orderBy(f.col(\"chromosome\"), f.col(\"position\"))\n        # median study size is 200Mb, max is 2.6Gb\n        .repartition(20)\n    )\n\n    # Initializing summary statistics object:\n    return cls(\n        _df=processed_sumstats_df,\n        _schema=cls.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/intervals/_intervals/","title":"List of Interaction and Interval-based Studies","text":"<p>In this section, we provide a list of studies that focus on interaction and interval-based investigations, shedding light on the intricate relationships between genetic elements and their functional implications.</p> <ol> <li> <p>Promoter Capture Hi-C (Javierre et al., 2016): Title: \"Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters\".    This study presents evidence linking genetic variation to genes through the application of Promoter Capture Hi-C across each of the 17 human primary hematopoietic cell types. The method captures interactions between promoters and distal regulatory elements, providing valuable insights into the three-dimensional chromatin architecture. DOI: 10.1016/j.cell.2016.09.037</p> </li> <li> <p>Enhancer-TSS Correlation (Andersson et al., 2014): Title: \"An Atlas of Active Enhancers across Human Cell Types and Tissues\".    This study explores genetic variation's impact on genes by examining the correlation between the transcriptional activity of enhancers and transcription start sites. The findings are documented in the FANTOM5 CAGE expression atlas, offering a comprehensive view of the regulatory landscape. DOI: 10.1038/nature12787</p> </li> <li> <p>DHS-Promoter Correlation (Thurman et al., 2012): Title: \"The accessible chromatin landscape of the human genome\".    Investigating genetic variation's connection to genes, this study employs the correlation of DNase I hypersensitive sites (DHS) and gene promoters. The analysis spans 125 cell and tissue types from the ENCODE project, providing a broad understanding of the regulatory interactions across diverse biological contexts. DOI: 10.1038/nature11232</p> </li> <li> <p>Promoter Capture Hi-C (Jung et al., 2019): Title: \"A compendium of promoter-centered long-range chromatin interactions in the human genome\".    This study compiles a compendium of promoter-centered long-range chromatin interactions in the human genome. By focusing on the three-dimensional organization of chromatin, the research contributes to our understanding of the spatial arrangement of genetic elements and their implications in gene regulation. DOI: 10.1038/s41588-019-0494-8</p> </li> </ol> <p>For in-depth details on each study, you may refer to the respective publications.</p>"},{"location":"python_api/datasources/intervals/andersson/","title":"Andersson et al.","text":""},{"location":"python_api/datasources/intervals/andersson/#gentropy.datasource.intervals.andersson.IntervalsAndersson","title":"<code>gentropy.datasource.intervals.andersson.IntervalsAndersson</code>","text":"<p>Interval dataset from Andersson et al. 2014.</p> Source code in <code>src/gentropy/datasource/intervals/andersson.py</code> <pre><code>class IntervalsAndersson:\n    \"\"\"Interval dataset from Andersson et al. 2014.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read andersson2014 dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to the dataset\n\n        Returns:\n            DataFrame: Raw Andersson et al. dataframe\n        \"\"\"\n        input_schema = t.StructType.fromJson(\n            json.loads(\n                pkg_resources.read_text(schemas, \"andersson2014.json\", encoding=\"utf-8\")\n            )\n        )\n        return (\n            spark.read.option(\"delimiter\", \"\\t\")\n            .option(\"mode\", \"DROPMALFORMED\")\n            .option(\"header\", \"true\")\n            .schema(input_schema)\n            .csv(path)\n        )\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsAndersson],\n        raw_anderson_df: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse Andersson et al. 2014 dataset.\n\n        Args:\n            raw_anderson_df (DataFrame): Raw Andersson et al. dataset\n            gene_index (GeneIndex): Gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Intervals dataset\n        \"\"\"\n        # Constant values:\n        dataset_name = \"andersson2014\"\n        experiment_type = \"fantom5\"\n        pmid = \"24670763\"\n        bio_feature = \"aggregate\"\n        twosided_threshold = 2.45e6  # &lt;-  this needs to phased out. Filter by percentile instead of absolute value.\n\n        # Read the anderson file:\n        parsed_anderson_df = (\n            raw_anderson_df\n            # Parsing score column and casting as float:\n            .withColumn(\"score\", f.col(\"score\").cast(\"float\") / f.lit(1000))\n            # Parsing the 'name' column:\n            .withColumn(\"parsedName\", f.split(f.col(\"name\"), \";\"))\n            .withColumn(\"gene_symbol\", f.col(\"parsedName\")[2])\n            .withColumn(\"location\", f.col(\"parsedName\")[0])\n            .withColumn(\n                \"chrom\",\n                f.regexp_replace(f.split(f.col(\"location\"), \":|-\")[0], \"chr\", \"\"),\n            )\n            .withColumn(\n                \"start\", f.split(f.col(\"location\"), \":|-\")[1].cast(t.IntegerType())\n            )\n            .withColumn(\n                \"end\", f.split(f.col(\"location\"), \":|-\")[2].cast(t.IntegerType())\n            )\n            # Select relevant columns:\n            .select(\"chrom\", \"start\", \"end\", \"gene_symbol\", \"score\")\n            # Drop rows with non-canonical chromosomes:\n            .filter(\n                f.col(\"chrom\").isin([str(x) for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"])\n            )\n            # For each region/gene, keep only one row with the highest score:\n            .groupBy(\"chrom\", \"start\", \"end\", \"gene_symbol\")\n            .agg(f.max(\"score\").alias(\"resourceScore\"))\n            .orderBy(\"chrom\", \"start\")\n        )\n\n        return Intervals(\n            _df=(\n                # Lift over the intervals:\n                lift.convert_intervals(parsed_anderson_df, \"chrom\", \"start\", \"end\")\n                .drop(\"start\", \"end\")\n                .withColumnRenamed(\"mapped_start\", \"start\")\n                .withColumnRenamed(\"mapped_end\", \"end\")\n                .distinct()\n                # Joining with the gene index\n                .alias(\"intervals\")\n                .join(\n                    gene_index.symbols_lut().alias(\"genes\"),\n                    on=[\n                        f.col(\"intervals.gene_symbol\") == f.col(\"genes.geneSymbol\"),\n                        # Drop rows where the TSS is far from the start of the region\n                        f.abs(\n                            (f.col(\"intervals.start\") + f.col(\"intervals.end\")) / 2\n                            - f.col(\"tss\")\n                        )\n                        &lt;= twosided_threshold,\n                    ],\n                    how=\"left\",\n                )\n                # Select relevant columns:\n                .select(\n                    f.col(\"chrom\").alias(\"chromosome\"),\n                    f.col(\"intervals.start\").alias(\"start\"),\n                    f.col(\"intervals.end\").alias(\"end\"),\n                    \"geneId\",\n                    \"resourceScore\",\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                    f.lit(bio_feature).alias(\"biofeature\"),\n                )\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/intervals/andersson/#gentropy.datasource.intervals.andersson.IntervalsAndersson.parse","title":"<code>parse(raw_anderson_df: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse Andersson et al. 2014 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>raw_anderson_df</code> <code>DataFrame</code> <p>Raw Andersson et al. dataset</p> required <code>gene_index</code> <code>GeneIndex</code> <p>Gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Intervals dataset</p> Source code in <code>src/gentropy/datasource/intervals/andersson.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsAndersson],\n    raw_anderson_df: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse Andersson et al. 2014 dataset.\n\n    Args:\n        raw_anderson_df (DataFrame): Raw Andersson et al. dataset\n        gene_index (GeneIndex): Gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Intervals dataset\n    \"\"\"\n    # Constant values:\n    dataset_name = \"andersson2014\"\n    experiment_type = \"fantom5\"\n    pmid = \"24670763\"\n    bio_feature = \"aggregate\"\n    twosided_threshold = 2.45e6  # &lt;-  this needs to phased out. Filter by percentile instead of absolute value.\n\n    # Read the anderson file:\n    parsed_anderson_df = (\n        raw_anderson_df\n        # Parsing score column and casting as float:\n        .withColumn(\"score\", f.col(\"score\").cast(\"float\") / f.lit(1000))\n        # Parsing the 'name' column:\n        .withColumn(\"parsedName\", f.split(f.col(\"name\"), \";\"))\n        .withColumn(\"gene_symbol\", f.col(\"parsedName\")[2])\n        .withColumn(\"location\", f.col(\"parsedName\")[0])\n        .withColumn(\n            \"chrom\",\n            f.regexp_replace(f.split(f.col(\"location\"), \":|-\")[0], \"chr\", \"\"),\n        )\n        .withColumn(\n            \"start\", f.split(f.col(\"location\"), \":|-\")[1].cast(t.IntegerType())\n        )\n        .withColumn(\n            \"end\", f.split(f.col(\"location\"), \":|-\")[2].cast(t.IntegerType())\n        )\n        # Select relevant columns:\n        .select(\"chrom\", \"start\", \"end\", \"gene_symbol\", \"score\")\n        # Drop rows with non-canonical chromosomes:\n        .filter(\n            f.col(\"chrom\").isin([str(x) for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"])\n        )\n        # For each region/gene, keep only one row with the highest score:\n        .groupBy(\"chrom\", \"start\", \"end\", \"gene_symbol\")\n        .agg(f.max(\"score\").alias(\"resourceScore\"))\n        .orderBy(\"chrom\", \"start\")\n    )\n\n    return Intervals(\n        _df=(\n            # Lift over the intervals:\n            lift.convert_intervals(parsed_anderson_df, \"chrom\", \"start\", \"end\")\n            .drop(\"start\", \"end\")\n            .withColumnRenamed(\"mapped_start\", \"start\")\n            .withColumnRenamed(\"mapped_end\", \"end\")\n            .distinct()\n            # Joining with the gene index\n            .alias(\"intervals\")\n            .join(\n                gene_index.symbols_lut().alias(\"genes\"),\n                on=[\n                    f.col(\"intervals.gene_symbol\") == f.col(\"genes.geneSymbol\"),\n                    # Drop rows where the TSS is far from the start of the region\n                    f.abs(\n                        (f.col(\"intervals.start\") + f.col(\"intervals.end\")) / 2\n                        - f.col(\"tss\")\n                    )\n                    &lt;= twosided_threshold,\n                ],\n                how=\"left\",\n            )\n            # Select relevant columns:\n            .select(\n                f.col(\"chrom\").alias(\"chromosome\"),\n                f.col(\"intervals.start\").alias(\"start\"),\n                f.col(\"intervals.end\").alias(\"end\"),\n                \"geneId\",\n                \"resourceScore\",\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n                f.lit(bio_feature).alias(\"biofeature\"),\n            )\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/intervals/andersson/#gentropy.datasource.intervals.andersson.IntervalsAndersson.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read andersson2014 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to the dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Raw Andersson et al. dataframe</p> Source code in <code>src/gentropy/datasource/intervals/andersson.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read andersson2014 dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to the dataset\n\n    Returns:\n        DataFrame: Raw Andersson et al. dataframe\n    \"\"\"\n    input_schema = t.StructType.fromJson(\n        json.loads(\n            pkg_resources.read_text(schemas, \"andersson2014.json\", encoding=\"utf-8\")\n        )\n    )\n    return (\n        spark.read.option(\"delimiter\", \"\\t\")\n        .option(\"mode\", \"DROPMALFORMED\")\n        .option(\"header\", \"true\")\n        .schema(input_schema)\n        .csv(path)\n    )\n</code></pre>"},{"location":"python_api/datasources/intervals/javierre/","title":"Javierre et al.","text":""},{"location":"python_api/datasources/intervals/javierre/#gentropy.datasource.intervals.javierre.IntervalsJavierre","title":"<code>gentropy.datasource.intervals.javierre.IntervalsJavierre</code>","text":"<p>Interval dataset from Javierre et al. 2016.</p> Source code in <code>src/gentropy/datasource/intervals/javierre.py</code> <pre><code>class IntervalsJavierre:\n    \"\"\"Interval dataset from Javierre et al. 2016.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read Javierre dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to dataset\n\n        Returns:\n            DataFrame: Raw Javierre dataset\n        \"\"\"\n        return spark.read.parquet(path)\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsJavierre],\n        javierre_raw: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse Javierre et al. 2016 dataset.\n\n        Args:\n            javierre_raw (DataFrame): Raw Javierre data\n            gene_index (GeneIndex): Gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Javierre et al. 2016 interval data\n        \"\"\"\n        # Constant values:\n        dataset_name = \"javierre2016\"\n        experiment_type = \"pchic\"\n        pmid = \"27863249\"\n        twosided_threshold = 2.45e6\n\n        # Read Javierre data:\n        javierre_parsed = (\n            javierre_raw\n            # Splitting name column into chromosome, start, end, and score:\n            .withColumn(\"name_split\", f.split(f.col(\"name\"), r\":|-|,\"))\n            .withColumn(\n                \"name_chr\",\n                f.regexp_replace(f.col(\"name_split\")[0], \"chr\", \"\").cast(\n                    t.StringType()\n                ),\n            )\n            .withColumn(\"name_start\", f.col(\"name_split\")[1].cast(t.IntegerType()))\n            .withColumn(\"name_end\", f.col(\"name_split\")[2].cast(t.IntegerType()))\n            .withColumn(\"name_score\", f.col(\"name_split\")[3].cast(t.FloatType()))\n            # Cleaning up chromosome:\n            .withColumn(\n                \"chrom\",\n                f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").cast(t.StringType()),\n            )\n            .drop(\"name_split\", \"name\", \"annotation\")\n            # Keep canonical chromosomes and consistent chromosomes with scores:\n            .filter(\n                (f.col(\"name_score\").isNotNull())\n                &amp; (f.col(\"chrom\") == f.col(\"name_chr\"))\n                &amp; f.col(\"name_chr\").isin(\n                    [f\"{x}\" for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"]\n                )\n            )\n        )\n\n        # Lifting over intervals:\n        javierre_remapped = (\n            javierre_parsed\n            # Lifting over to GRCh38 interval 1:\n            .transform(lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\"))\n            .drop(\"start\", \"end\")\n            .withColumnRenamed(\"mapped_chrom\", \"chrom\")\n            .withColumnRenamed(\"mapped_start\", \"start\")\n            .withColumnRenamed(\"mapped_end\", \"end\")\n            # Lifting over interval 2 to GRCh38:\n            .transform(\n                lambda df: lift.convert_intervals(\n                    df, \"name_chr\", \"name_start\", \"name_end\"\n                )\n            )\n            .drop(\"name_start\", \"name_end\")\n            .withColumnRenamed(\"mapped_name_chr\", \"name_chr\")\n            .withColumnRenamed(\"mapped_name_start\", \"name_start\")\n            .withColumnRenamed(\"mapped_name_end\", \"name_end\")\n        )\n\n        # Once the intervals are lifted, extracting the unique intervals:\n        unique_intervals_with_genes = (\n            javierre_remapped.select(\n                f.col(\"chrom\"),\n                f.col(\"start\").cast(t.IntegerType()),\n                f.col(\"end\").cast(t.IntegerType()),\n            )\n            .distinct()\n            .alias(\"intervals\")\n            .join(\n                gene_index.locations_lut().alias(\"genes\"),\n                on=[\n                    f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                    (\n                        (f.col(\"intervals.start\") &gt;= f.col(\"genes.start\"))\n                        &amp; (f.col(\"intervals.start\") &lt;= f.col(\"genes.end\"))\n                    )\n                    | (\n                        (f.col(\"intervals.end\") &gt;= f.col(\"genes.start\"))\n                        &amp; (f.col(\"intervals.end\") &lt;= f.col(\"genes.end\"))\n                    ),\n                ],\n                how=\"left\",\n            )\n            .select(\n                f.col(\"intervals.chrom\").alias(\"chrom\"),\n                f.col(\"intervals.start\").alias(\"start\"),\n                f.col(\"intervals.end\").alias(\"end\"),\n                f.col(\"genes.geneId\").alias(\"geneId\"),\n                f.col(\"genes.tss\").alias(\"tss\"),\n            )\n        )\n\n        # Joining back the data:\n        return Intervals(\n            _df=(\n                javierre_remapped.join(\n                    unique_intervals_with_genes,\n                    on=[\"chrom\", \"start\", \"end\"],\n                    how=\"left\",\n                )\n                .filter(\n                    # Drop rows where the TSS is far from the start of the region\n                    f.abs((f.col(\"start\") + f.col(\"end\")) / 2 - f.col(\"tss\"))\n                    &lt;= twosided_threshold\n                )\n                # For each gene, keep only the highest scoring interval:\n                .groupBy(\"name_chr\", \"name_start\", \"name_end\", \"geneId\", \"bio_feature\")\n                .agg(f.max(f.col(\"name_score\")).alias(\"resourceScore\"))\n                # Create the output:\n                .select(\n                    f.col(\"name_chr\").alias(\"chromosome\"),\n                    f.col(\"name_start\").alias(\"start\"),\n                    f.col(\"name_end\").alias(\"end\"),\n                    f.col(\"resourceScore\").cast(t.DoubleType()),\n                    f.col(\"geneId\"),\n                    f.col(\"bio_feature\").alias(\"biofeature\"),\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                )\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/intervals/javierre/#gentropy.datasource.intervals.javierre.IntervalsJavierre.parse","title":"<code>parse(javierre_raw: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse Javierre et al. 2016 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>javierre_raw</code> <code>DataFrame</code> <p>Raw Javierre data</p> required <code>gene_index</code> <code>GeneIndex</code> <p>Gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Javierre et al. 2016 interval data</p> Source code in <code>src/gentropy/datasource/intervals/javierre.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsJavierre],\n    javierre_raw: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse Javierre et al. 2016 dataset.\n\n    Args:\n        javierre_raw (DataFrame): Raw Javierre data\n        gene_index (GeneIndex): Gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Javierre et al. 2016 interval data\n    \"\"\"\n    # Constant values:\n    dataset_name = \"javierre2016\"\n    experiment_type = \"pchic\"\n    pmid = \"27863249\"\n    twosided_threshold = 2.45e6\n\n    # Read Javierre data:\n    javierre_parsed = (\n        javierre_raw\n        # Splitting name column into chromosome, start, end, and score:\n        .withColumn(\"name_split\", f.split(f.col(\"name\"), r\":|-|,\"))\n        .withColumn(\n            \"name_chr\",\n            f.regexp_replace(f.col(\"name_split\")[0], \"chr\", \"\").cast(\n                t.StringType()\n            ),\n        )\n        .withColumn(\"name_start\", f.col(\"name_split\")[1].cast(t.IntegerType()))\n        .withColumn(\"name_end\", f.col(\"name_split\")[2].cast(t.IntegerType()))\n        .withColumn(\"name_score\", f.col(\"name_split\")[3].cast(t.FloatType()))\n        # Cleaning up chromosome:\n        .withColumn(\n            \"chrom\",\n            f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").cast(t.StringType()),\n        )\n        .drop(\"name_split\", \"name\", \"annotation\")\n        # Keep canonical chromosomes and consistent chromosomes with scores:\n        .filter(\n            (f.col(\"name_score\").isNotNull())\n            &amp; (f.col(\"chrom\") == f.col(\"name_chr\"))\n            &amp; f.col(\"name_chr\").isin(\n                [f\"{x}\" for x in range(1, 23)] + [\"X\", \"Y\", \"MT\"]\n            )\n        )\n    )\n\n    # Lifting over intervals:\n    javierre_remapped = (\n        javierre_parsed\n        # Lifting over to GRCh38 interval 1:\n        .transform(lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\"))\n        .drop(\"start\", \"end\")\n        .withColumnRenamed(\"mapped_chrom\", \"chrom\")\n        .withColumnRenamed(\"mapped_start\", \"start\")\n        .withColumnRenamed(\"mapped_end\", \"end\")\n        # Lifting over interval 2 to GRCh38:\n        .transform(\n            lambda df: lift.convert_intervals(\n                df, \"name_chr\", \"name_start\", \"name_end\"\n            )\n        )\n        .drop(\"name_start\", \"name_end\")\n        .withColumnRenamed(\"mapped_name_chr\", \"name_chr\")\n        .withColumnRenamed(\"mapped_name_start\", \"name_start\")\n        .withColumnRenamed(\"mapped_name_end\", \"name_end\")\n    )\n\n    # Once the intervals are lifted, extracting the unique intervals:\n    unique_intervals_with_genes = (\n        javierre_remapped.select(\n            f.col(\"chrom\"),\n            f.col(\"start\").cast(t.IntegerType()),\n            f.col(\"end\").cast(t.IntegerType()),\n        )\n        .distinct()\n        .alias(\"intervals\")\n        .join(\n            gene_index.locations_lut().alias(\"genes\"),\n            on=[\n                f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                (\n                    (f.col(\"intervals.start\") &gt;= f.col(\"genes.start\"))\n                    &amp; (f.col(\"intervals.start\") &lt;= f.col(\"genes.end\"))\n                )\n                | (\n                    (f.col(\"intervals.end\") &gt;= f.col(\"genes.start\"))\n                    &amp; (f.col(\"intervals.end\") &lt;= f.col(\"genes.end\"))\n                ),\n            ],\n            how=\"left\",\n        )\n        .select(\n            f.col(\"intervals.chrom\").alias(\"chrom\"),\n            f.col(\"intervals.start\").alias(\"start\"),\n            f.col(\"intervals.end\").alias(\"end\"),\n            f.col(\"genes.geneId\").alias(\"geneId\"),\n            f.col(\"genes.tss\").alias(\"tss\"),\n        )\n    )\n\n    # Joining back the data:\n    return Intervals(\n        _df=(\n            javierre_remapped.join(\n                unique_intervals_with_genes,\n                on=[\"chrom\", \"start\", \"end\"],\n                how=\"left\",\n            )\n            .filter(\n                # Drop rows where the TSS is far from the start of the region\n                f.abs((f.col(\"start\") + f.col(\"end\")) / 2 - f.col(\"tss\"))\n                &lt;= twosided_threshold\n            )\n            # For each gene, keep only the highest scoring interval:\n            .groupBy(\"name_chr\", \"name_start\", \"name_end\", \"geneId\", \"bio_feature\")\n            .agg(f.max(f.col(\"name_score\")).alias(\"resourceScore\"))\n            # Create the output:\n            .select(\n                f.col(\"name_chr\").alias(\"chromosome\"),\n                f.col(\"name_start\").alias(\"start\"),\n                f.col(\"name_end\").alias(\"end\"),\n                f.col(\"resourceScore\").cast(t.DoubleType()),\n                f.col(\"geneId\"),\n                f.col(\"bio_feature\").alias(\"biofeature\"),\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n            )\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/intervals/javierre/#gentropy.datasource.intervals.javierre.IntervalsJavierre.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read Javierre dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Raw Javierre dataset</p> Source code in <code>src/gentropy/datasource/intervals/javierre.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read Javierre dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to dataset\n\n    Returns:\n        DataFrame: Raw Javierre dataset\n    \"\"\"\n    return spark.read.parquet(path)\n</code></pre>"},{"location":"python_api/datasources/intervals/jung/","title":"Jung et al.","text":""},{"location":"python_api/datasources/intervals/jung/#gentropy.datasource.intervals.jung.IntervalsJung","title":"<code>gentropy.datasource.intervals.jung.IntervalsJung</code>","text":"<p>Interval dataset from Jung et al. 2019.</p> Source code in <code>src/gentropy/datasource/intervals/jung.py</code> <pre><code>class IntervalsJung:\n    \"\"\"Interval dataset from Jung et al. 2019.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read jung dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to dataset\n\n        Returns:\n            DataFrame: DataFrame with raw jung data\n        \"\"\"\n        return spark.read.csv(path, sep=\",\", header=True)\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsJung],\n        jung_raw: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse the Jung et al. 2019 dataset.\n\n        Args:\n            jung_raw (DataFrame): raw Jung et al. 2019 dataset\n            gene_index (GeneIndex): gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Interval dataset containing Jung et al. 2019 data\n        \"\"\"\n        dataset_name = \"jung2019\"\n        experiment_type = \"pchic\"\n        pmid = \"31501517\"\n\n        # Lifting over the coordinates:\n        return Intervals(\n            _df=(\n                jung_raw.withColumn(\n                    \"interval\", f.split(f.col(\"Interacting_fragment\"), r\"\\.\")\n                )\n                .select(\n                    # Parsing intervals:\n                    f.regexp_replace(f.col(\"interval\")[0], \"chr\", \"\").alias(\"chrom\"),\n                    f.col(\"interval\")[1].cast(t.IntegerType()).alias(\"start\"),\n                    f.col(\"interval\")[2].cast(t.IntegerType()).alias(\"end\"),\n                    # Extract other columns:\n                    f.col(\"Promoter\").alias(\"gene_name\"),\n                    f.col(\"Tissue_type\").alias(\"tissue\"),\n                )\n                # Lifting over to GRCh38 interval 1:\n                .transform(\n                    lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n                )\n                .select(\n                    \"chrom\",\n                    f.col(\"mapped_start\").alias(\"start\"),\n                    f.col(\"mapped_end\").alias(\"end\"),\n                    f.explode(f.split(f.col(\"gene_name\"), \";\")).alias(\"gene_name\"),\n                    \"tissue\",\n                )\n                .alias(\"intervals\")\n                # Joining with genes:\n                .join(\n                    gene_index.symbols_lut().alias(\"genes\"),\n                    on=[f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\")],\n                    how=\"inner\",\n                )\n                # Finalize dataset:\n                .select(\n                    \"chromosome\",\n                    f.col(\"intervals.start\").alias(\"start\"),\n                    f.col(\"intervals.end\").alias(\"end\"),\n                    \"geneId\",\n                    f.col(\"tissue\").alias(\"biofeature\"),\n                    f.lit(1.0).alias(\"score\"),\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                )\n                .drop_duplicates()\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/intervals/jung/#gentropy.datasource.intervals.jung.IntervalsJung.parse","title":"<code>parse(jung_raw: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse the Jung et al. 2019 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>jung_raw</code> <code>DataFrame</code> <p>raw Jung et al. 2019 dataset</p> required <code>gene_index</code> <code>GeneIndex</code> <p>gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Interval dataset containing Jung et al. 2019 data</p> Source code in <code>src/gentropy/datasource/intervals/jung.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsJung],\n    jung_raw: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse the Jung et al. 2019 dataset.\n\n    Args:\n        jung_raw (DataFrame): raw Jung et al. 2019 dataset\n        gene_index (GeneIndex): gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Interval dataset containing Jung et al. 2019 data\n    \"\"\"\n    dataset_name = \"jung2019\"\n    experiment_type = \"pchic\"\n    pmid = \"31501517\"\n\n    # Lifting over the coordinates:\n    return Intervals(\n        _df=(\n            jung_raw.withColumn(\n                \"interval\", f.split(f.col(\"Interacting_fragment\"), r\"\\.\")\n            )\n            .select(\n                # Parsing intervals:\n                f.regexp_replace(f.col(\"interval\")[0], \"chr\", \"\").alias(\"chrom\"),\n                f.col(\"interval\")[1].cast(t.IntegerType()).alias(\"start\"),\n                f.col(\"interval\")[2].cast(t.IntegerType()).alias(\"end\"),\n                # Extract other columns:\n                f.col(\"Promoter\").alias(\"gene_name\"),\n                f.col(\"Tissue_type\").alias(\"tissue\"),\n            )\n            # Lifting over to GRCh38 interval 1:\n            .transform(\n                lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n            )\n            .select(\n                \"chrom\",\n                f.col(\"mapped_start\").alias(\"start\"),\n                f.col(\"mapped_end\").alias(\"end\"),\n                f.explode(f.split(f.col(\"gene_name\"), \";\")).alias(\"gene_name\"),\n                \"tissue\",\n            )\n            .alias(\"intervals\")\n            # Joining with genes:\n            .join(\n                gene_index.symbols_lut().alias(\"genes\"),\n                on=[f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\")],\n                how=\"inner\",\n            )\n            # Finalize dataset:\n            .select(\n                \"chromosome\",\n                f.col(\"intervals.start\").alias(\"start\"),\n                f.col(\"intervals.end\").alias(\"end\"),\n                \"geneId\",\n                f.col(\"tissue\").alias(\"biofeature\"),\n                f.lit(1.0).alias(\"score\"),\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n            )\n            .drop_duplicates()\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/intervals/jung/#gentropy.datasource.intervals.jung.IntervalsJung.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read jung dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>DataFrame with raw jung data</p> Source code in <code>src/gentropy/datasource/intervals/jung.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read jung dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to dataset\n\n    Returns:\n        DataFrame: DataFrame with raw jung data\n    \"\"\"\n    return spark.read.csv(path, sep=\",\", header=True)\n</code></pre>"},{"location":"python_api/datasources/intervals/thurman/","title":"Thurman et al.","text":""},{"location":"python_api/datasources/intervals/thurman/#gentropy.datasource.intervals.thurman.IntervalsThurman","title":"<code>gentropy.datasource.intervals.thurman.IntervalsThurman</code>","text":"<p>Interval dataset from Thurman et al. 2012.</p> Source code in <code>src/gentropy/datasource/intervals/thurman.py</code> <pre><code>class IntervalsThurman:\n    \"\"\"Interval dataset from Thurman et al. 2012.\"\"\"\n\n    @staticmethod\n    def read(spark: SparkSession, path: str) -&gt; DataFrame:\n        \"\"\"Read thurman dataset.\n\n        Args:\n            spark (SparkSession): Spark session\n            path (str): Path to dataset\n\n        Returns:\n            DataFrame: DataFrame with raw thurman data\n        \"\"\"\n        thurman_schema = t.StructType(\n            [\n                t.StructField(\"gene_chr\", t.StringType(), False),\n                t.StructField(\"gene_start\", t.IntegerType(), False),\n                t.StructField(\"gene_end\", t.IntegerType(), False),\n                t.StructField(\"gene_name\", t.StringType(), False),\n                t.StructField(\"chrom\", t.StringType(), False),\n                t.StructField(\"start\", t.IntegerType(), False),\n                t.StructField(\"end\", t.IntegerType(), False),\n                t.StructField(\"score\", t.FloatType(), False),\n            ]\n        )\n        return spark.read.csv(path, sep=\"\\t\", header=True, schema=thurman_schema)\n\n    @classmethod\n    def parse(\n        cls: type[IntervalsThurman],\n        thurman_raw: DataFrame,\n        gene_index: GeneIndex,\n        lift: LiftOverSpark,\n    ) -&gt; Intervals:\n        \"\"\"Parse the Thurman et al. 2012 dataset.\n\n        Args:\n            thurman_raw (DataFrame): raw Thurman et al. 2019 dataset\n            gene_index (GeneIndex): gene index\n            lift (LiftOverSpark): LiftOverSpark instance\n\n        Returns:\n            Intervals: Interval dataset containing Thurman et al. 2012 data\n        \"\"\"\n        dataset_name = \"thurman2012\"\n        experiment_type = \"dhscor\"\n        pmid = \"22955617\"\n\n        return Intervals(\n            _df=(\n                thurman_raw.select(\n                    f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").alias(\"chrom\"),\n                    \"start\",\n                    \"end\",\n                    \"gene_name\",\n                    \"score\",\n                )\n                # Lift over to the GRCh38 build:\n                .transform(\n                    lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n                )\n                .alias(\"intervals\")\n                # Map gene names to gene IDs:\n                .join(\n                    gene_index.symbols_lut().alias(\"genes\"),\n                    on=[\n                        f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\"),\n                        f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                    ],\n                    how=\"inner\",\n                )\n                # Select relevant columns and add constant columns:\n                .select(\n                    f.col(\"chrom\").alias(\"chromosome\"),\n                    f.col(\"mapped_start\").alias(\"start\"),\n                    f.col(\"mapped_end\").alias(\"end\"),\n                    \"geneId\",\n                    f.col(\"score\").cast(t.DoubleType()).alias(\"resourceScore\"),\n                    f.lit(dataset_name).alias(\"datasourceId\"),\n                    f.lit(experiment_type).alias(\"datatypeId\"),\n                    f.lit(pmid).alias(\"pmid\"),\n                )\n                .distinct()\n            ),\n            _schema=Intervals.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/intervals/thurman/#gentropy.datasource.intervals.thurman.IntervalsThurman.parse","title":"<code>parse(thurman_raw: DataFrame, gene_index: GeneIndex, lift: LiftOverSpark) -&gt; Intervals</code>  <code>classmethod</code>","text":"<p>Parse the Thurman et al. 2012 dataset.</p> <p>Parameters:</p> Name Type Description Default <code>thurman_raw</code> <code>DataFrame</code> <p>raw Thurman et al. 2019 dataset</p> required <code>gene_index</code> <code>GeneIndex</code> <p>gene index</p> required <code>lift</code> <code>LiftOverSpark</code> <p>LiftOverSpark instance</p> required <p>Returns:</p> Name Type Description <code>Intervals</code> <code>Intervals</code> <p>Interval dataset containing Thurman et al. 2012 data</p> Source code in <code>src/gentropy/datasource/intervals/thurman.py</code> <pre><code>@classmethod\ndef parse(\n    cls: type[IntervalsThurman],\n    thurman_raw: DataFrame,\n    gene_index: GeneIndex,\n    lift: LiftOverSpark,\n) -&gt; Intervals:\n    \"\"\"Parse the Thurman et al. 2012 dataset.\n\n    Args:\n        thurman_raw (DataFrame): raw Thurman et al. 2019 dataset\n        gene_index (GeneIndex): gene index\n        lift (LiftOverSpark): LiftOverSpark instance\n\n    Returns:\n        Intervals: Interval dataset containing Thurman et al. 2012 data\n    \"\"\"\n    dataset_name = \"thurman2012\"\n    experiment_type = \"dhscor\"\n    pmid = \"22955617\"\n\n    return Intervals(\n        _df=(\n            thurman_raw.select(\n                f.regexp_replace(f.col(\"chrom\"), \"chr\", \"\").alias(\"chrom\"),\n                \"start\",\n                \"end\",\n                \"gene_name\",\n                \"score\",\n            )\n            # Lift over to the GRCh38 build:\n            .transform(\n                lambda df: lift.convert_intervals(df, \"chrom\", \"start\", \"end\")\n            )\n            .alias(\"intervals\")\n            # Map gene names to gene IDs:\n            .join(\n                gene_index.symbols_lut().alias(\"genes\"),\n                on=[\n                    f.col(\"intervals.gene_name\") == f.col(\"genes.geneSymbol\"),\n                    f.col(\"intervals.chrom\") == f.col(\"genes.chromosome\"),\n                ],\n                how=\"inner\",\n            )\n            # Select relevant columns and add constant columns:\n            .select(\n                f.col(\"chrom\").alias(\"chromosome\"),\n                f.col(\"mapped_start\").alias(\"start\"),\n                f.col(\"mapped_end\").alias(\"end\"),\n                \"geneId\",\n                f.col(\"score\").cast(t.DoubleType()).alias(\"resourceScore\"),\n                f.lit(dataset_name).alias(\"datasourceId\"),\n                f.lit(experiment_type).alias(\"datatypeId\"),\n                f.lit(pmid).alias(\"pmid\"),\n            )\n            .distinct()\n        ),\n        _schema=Intervals.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/intervals/thurman/#gentropy.datasource.intervals.thurman.IntervalsThurman.read","title":"<code>read(spark: SparkSession, path: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Read thurman dataset.</p> <p>Parameters:</p> Name Type Description Default <code>spark</code> <code>SparkSession</code> <p>Spark session</p> required <code>path</code> <code>str</code> <p>Path to dataset</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>DataFrame with raw thurman data</p> Source code in <code>src/gentropy/datasource/intervals/thurman.py</code> <pre><code>@staticmethod\ndef read(spark: SparkSession, path: str) -&gt; DataFrame:\n    \"\"\"Read thurman dataset.\n\n    Args:\n        spark (SparkSession): Spark session\n        path (str): Path to dataset\n\n    Returns:\n        DataFrame: DataFrame with raw thurman data\n    \"\"\"\n    thurman_schema = t.StructType(\n        [\n            t.StructField(\"gene_chr\", t.StringType(), False),\n            t.StructField(\"gene_start\", t.IntegerType(), False),\n            t.StructField(\"gene_end\", t.IntegerType(), False),\n            t.StructField(\"gene_name\", t.StringType(), False),\n            t.StructField(\"chrom\", t.StringType(), False),\n            t.StructField(\"start\", t.IntegerType(), False),\n            t.StructField(\"end\", t.IntegerType(), False),\n            t.StructField(\"score\", t.FloatType(), False),\n        ]\n    )\n    return spark.read.csv(path, sep=\"\\t\", header=True, schema=thurman_schema)\n</code></pre>"},{"location":"python_api/datasources/open_targets/_open_targets/","title":"Open Targets","text":"<p>The Open Targets Platform is a comprehensive resource that aims to aggregate and harmonize various types of data to facilitate the identification, prioritization, and validation of drug targets. By integrating publicly available datasets, including data generated by the Open Targets consortium, the Platform builds and scores target-disease associations to assist in drug target identification and prioritization. It also integrates relevant annotation information about targets, diseases, phenotypes, and drugs, as well as their most relevant relationships.</p> <p>Within our analyses, we utilize Open Targets to infer two datasets:</p> <ol> <li> <p>The list of targets:    This dataset provides a compilation of targets. In the Open Targets Platform, a target is understood as any naturally-occurring molecule that can be targeted by a medicinal product. The EMBL-EBI Ensembl database serves as the source for human targets in the Platform, with the Ensembl gene ID as the primary identifier. For more details, refer to this link.</p> </li> <li> <p>The list of Gold Standard Positives:    We use this dataset for training the Locus-to-Gene model. The current list contains 496 Gold Standard Positives.</p> </li> </ol>"},{"location":"python_api/datasources/open_targets/l2g_gold_standard/","title":"L2G Gold Standard","text":""},{"location":"python_api/datasources/open_targets/l2g_gold_standard/#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard","title":"<code>gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard</code>","text":"<p>Parser for OTGenetics locus to gene gold standards curation.</p> The curation is processed to generate a dataset with 2 labels <ul> <li>Gold Standard Positive (GSP): When the lead variant is part of a curated list of GWAS loci with known gene-trait associations.</li> <li>Gold Standard Negative (GSN): When the lead variant is not part of a curated list of GWAS loci with known gene-trait associations but is in the vicinity of a gene's TSS.</li> </ul> Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>class OpenTargetsL2GGoldStandard:\n    \"\"\"Parser for OTGenetics locus to gene gold standards curation.\n\n    The curation is processed to generate a dataset with 2 labels:\n        - Gold Standard Positive (GSP): When the lead variant is part of a curated list of GWAS loci with known gene-trait associations.\n        - Gold Standard Negative (GSN): When the lead variant is not part of a curated list of GWAS loci with known gene-trait associations but is in the vicinity of a gene's TSS.\n    \"\"\"\n\n    LOCUS_TO_GENE_WINDOW = 500_000\n\n    @classmethod\n    def parse_positive_curation(\n        cls: Type[OpenTargetsL2GGoldStandard], gold_standard_curation: DataFrame\n    ) -&gt; DataFrame:\n        \"\"\"Parse positive set from gold standard curation.\n\n        Args:\n            gold_standard_curation (DataFrame): Gold standard curation dataframe\n\n        Returns:\n            DataFrame: Positive set\n        \"\"\"\n        return (\n            gold_standard_curation.filter(\n                f.col(\"gold_standard_info.highest_confidence\").isin([\"High\", \"Medium\"])\n            )\n            .select(\n                f.col(\"association_info.otg_id\").alias(\"studyId\"),\n                f.col(\"gold_standard_info.gene_id\").alias(\"geneId\"),\n                f.concat_ws(\n                    \"_\",\n                    f.col(\"sentinel_variant.locus_GRCh38.chromosome\"),\n                    f.col(\"sentinel_variant.locus_GRCh38.position\"),\n                    f.col(\"sentinel_variant.alleles.reference\"),\n                    f.col(\"sentinel_variant.alleles.alternative\"),\n                ).alias(\"variantId\"),\n                f.col(\"metadata.set_label\").alias(\"source\"),\n            )\n            .withColumn(\n                \"studyLocusId\",\n                StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n            )\n            .groupBy(\"studyLocusId\", \"studyId\", \"variantId\", \"geneId\")\n            .agg(f.collect_set(\"source\").alias(\"sources\"))\n        )\n\n    @classmethod\n    def expand_gold_standard_with_negatives(\n        cls: Type[OpenTargetsL2GGoldStandard], positive_set: DataFrame, v2g: V2G\n    ) -&gt; DataFrame:\n        \"\"\"Create full set of positive and negative evidence of locus to gene associations.\n\n        Negative evidence consists of all genes within a window of 500kb of the lead variant that are not in the positive set.\n\n        Args:\n            positive_set (DataFrame): Positive set from curation\n            v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n        Returns:\n            DataFrame: Full set of positive and negative evidence of locus to gene associations\n        \"\"\"\n        return (\n            positive_set.withColumnRenamed(\"geneId\", \"curated_geneId\")\n            .join(\n                v2g.df.selectExpr(\n                    \"variantId\", \"geneId as non_curated_geneId\", \"distance\"\n                ).filter(f.col(\"distance\") &lt;= cls.LOCUS_TO_GENE_WINDOW),\n                on=\"variantId\",\n                how=\"left\",\n            )\n            .withColumn(\n                \"goldStandardSet\",\n                f.when(\n                    (f.col(\"curated_geneId\") == f.col(\"non_curated_geneId\"))\n                    # to keep the positives that are outside the v2g dataset\n                    | (f.col(\"non_curated_geneId\").isNull()),\n                    f.lit(L2GGoldStandard.GS_POSITIVE_LABEL),\n                ).otherwise(L2GGoldStandard.GS_NEGATIVE_LABEL),\n            )\n            .withColumn(\n                \"geneId\",\n                f.when(\n                    f.col(\"goldStandardSet\") == L2GGoldStandard.GS_POSITIVE_LABEL,\n                    f.col(\"curated_geneId\"),\n                ).otherwise(f.col(\"non_curated_geneId\")),\n            )\n            .drop(\"distance\", \"curated_geneId\", \"non_curated_geneId\")\n        )\n\n    @classmethod\n    def as_l2g_gold_standard(\n        cls: type[OpenTargetsL2GGoldStandard],\n        gold_standard_curation: DataFrame,\n        v2g: V2G,\n    ) -&gt; L2GGoldStandard:\n        \"\"\"Initialise L2GGoldStandard from source dataset.\n\n        Args:\n            gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from https://github.com/opentargets/genetics-gold-standards\n            v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n        Returns:\n            L2GGoldStandard: L2G Gold Standard dataset. False negatives have not yet been removed.\n        \"\"\"\n        return L2GGoldStandard(\n            _df=cls.parse_positive_curation(gold_standard_curation).transform(\n                cls.expand_gold_standard_with_negatives, v2g\n            ),\n            _schema=L2GGoldStandard.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/open_targets/l2g_gold_standard/#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.as_l2g_gold_standard","title":"<code>as_l2g_gold_standard(gold_standard_curation: DataFrame, v2g: V2G) -&gt; L2GGoldStandard</code>  <code>classmethod</code>","text":"<p>Initialise L2GGoldStandard from source dataset.</p> <p>Parameters:</p> Name Type Description Default <code>gold_standard_curation</code> <code>DataFrame</code> <p>Gold standard curation dataframe, extracted from https://github.com/opentargets/genetics-gold-standards</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset to bring distance between a variant and a gene's TSS</p> required <p>Returns:</p> Name Type Description <code>L2GGoldStandard</code> <code>L2GGoldStandard</code> <p>L2G Gold Standard dataset. False negatives have not yet been removed.</p> Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef as_l2g_gold_standard(\n    cls: type[OpenTargetsL2GGoldStandard],\n    gold_standard_curation: DataFrame,\n    v2g: V2G,\n) -&gt; L2GGoldStandard:\n    \"\"\"Initialise L2GGoldStandard from source dataset.\n\n    Args:\n        gold_standard_curation (DataFrame): Gold standard curation dataframe, extracted from https://github.com/opentargets/genetics-gold-standards\n        v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n    Returns:\n        L2GGoldStandard: L2G Gold Standard dataset. False negatives have not yet been removed.\n    \"\"\"\n    return L2GGoldStandard(\n        _df=cls.parse_positive_curation(gold_standard_curation).transform(\n            cls.expand_gold_standard_with_negatives, v2g\n        ),\n        _schema=L2GGoldStandard.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/datasources/open_targets/l2g_gold_standard/#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.expand_gold_standard_with_negatives","title":"<code>expand_gold_standard_with_negatives(positive_set: DataFrame, v2g: V2G) -&gt; DataFrame</code>  <code>classmethod</code>","text":"<p>Create full set of positive and negative evidence of locus to gene associations.</p> <p>Negative evidence consists of all genes within a window of 500kb of the lead variant that are not in the positive set.</p> <p>Parameters:</p> Name Type Description Default <code>positive_set</code> <code>DataFrame</code> <p>Positive set from curation</p> required <code>v2g</code> <code>V2G</code> <p>Variant to gene dataset to bring distance between a variant and a gene's TSS</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Full set of positive and negative evidence of locus to gene associations</p> Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef expand_gold_standard_with_negatives(\n    cls: Type[OpenTargetsL2GGoldStandard], positive_set: DataFrame, v2g: V2G\n) -&gt; DataFrame:\n    \"\"\"Create full set of positive and negative evidence of locus to gene associations.\n\n    Negative evidence consists of all genes within a window of 500kb of the lead variant that are not in the positive set.\n\n    Args:\n        positive_set (DataFrame): Positive set from curation\n        v2g (V2G): Variant to gene dataset to bring distance between a variant and a gene's TSS\n\n    Returns:\n        DataFrame: Full set of positive and negative evidence of locus to gene associations\n    \"\"\"\n    return (\n        positive_set.withColumnRenamed(\"geneId\", \"curated_geneId\")\n        .join(\n            v2g.df.selectExpr(\n                \"variantId\", \"geneId as non_curated_geneId\", \"distance\"\n            ).filter(f.col(\"distance\") &lt;= cls.LOCUS_TO_GENE_WINDOW),\n            on=\"variantId\",\n            how=\"left\",\n        )\n        .withColumn(\n            \"goldStandardSet\",\n            f.when(\n                (f.col(\"curated_geneId\") == f.col(\"non_curated_geneId\"))\n                # to keep the positives that are outside the v2g dataset\n                | (f.col(\"non_curated_geneId\").isNull()),\n                f.lit(L2GGoldStandard.GS_POSITIVE_LABEL),\n            ).otherwise(L2GGoldStandard.GS_NEGATIVE_LABEL),\n        )\n        .withColumn(\n            \"geneId\",\n            f.when(\n                f.col(\"goldStandardSet\") == L2GGoldStandard.GS_POSITIVE_LABEL,\n                f.col(\"curated_geneId\"),\n            ).otherwise(f.col(\"non_curated_geneId\")),\n        )\n        .drop(\"distance\", \"curated_geneId\", \"non_curated_geneId\")\n    )\n</code></pre>"},{"location":"python_api/datasources/open_targets/l2g_gold_standard/#gentropy.datasource.open_targets.l2g_gold_standard.OpenTargetsL2GGoldStandard.parse_positive_curation","title":"<code>parse_positive_curation(gold_standard_curation: DataFrame) -&gt; DataFrame</code>  <code>classmethod</code>","text":"<p>Parse positive set from gold standard curation.</p> <p>Parameters:</p> Name Type Description Default <code>gold_standard_curation</code> <code>DataFrame</code> <p>Gold standard curation dataframe</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Positive set</p> Source code in <code>src/gentropy/datasource/open_targets/l2g_gold_standard.py</code> <pre><code>@classmethod\ndef parse_positive_curation(\n    cls: Type[OpenTargetsL2GGoldStandard], gold_standard_curation: DataFrame\n) -&gt; DataFrame:\n    \"\"\"Parse positive set from gold standard curation.\n\n    Args:\n        gold_standard_curation (DataFrame): Gold standard curation dataframe\n\n    Returns:\n        DataFrame: Positive set\n    \"\"\"\n    return (\n        gold_standard_curation.filter(\n            f.col(\"gold_standard_info.highest_confidence\").isin([\"High\", \"Medium\"])\n        )\n        .select(\n            f.col(\"association_info.otg_id\").alias(\"studyId\"),\n            f.col(\"gold_standard_info.gene_id\").alias(\"geneId\"),\n            f.concat_ws(\n                \"_\",\n                f.col(\"sentinel_variant.locus_GRCh38.chromosome\"),\n                f.col(\"sentinel_variant.locus_GRCh38.position\"),\n                f.col(\"sentinel_variant.alleles.reference\"),\n                f.col(\"sentinel_variant.alleles.alternative\"),\n            ).alias(\"variantId\"),\n            f.col(\"metadata.set_label\").alias(\"source\"),\n        )\n        .withColumn(\n            \"studyLocusId\",\n            StudyLocus.assign_study_locus_id(f.col(\"studyId\"), f.col(\"variantId\")),\n        )\n        .groupBy(\"studyLocusId\", \"studyId\", \"variantId\", \"geneId\")\n        .agg(f.collect_set(\"source\").alias(\"sources\"))\n    )\n</code></pre>"},{"location":"python_api/datasources/open_targets/target/","title":"Target","text":""},{"location":"python_api/datasources/open_targets/target/#gentropy.datasource.open_targets.target.OpenTargetsTarget","title":"<code>gentropy.datasource.open_targets.target.OpenTargetsTarget</code>","text":"<p>Parser for OTPlatform target dataset.</p> <p>Genomic data from Open Targets provides gene identification and genomic coordinates that are integrated into the gene index of our ETL pipeline.</p> <p>The EMBL-EBI Ensembl database is used as a source for human targets in the Platform, with the Ensembl gene ID as the primary identifier. The criteria for target inclusion is: - Genes from all biotypes encoded in canonical chromosomes - Genes in alternative assemblies encoding for a reviewed protein product.</p> Source code in <code>src/gentropy/datasource/open_targets/target.py</code> <pre><code>class OpenTargetsTarget:\n    \"\"\"Parser for OTPlatform target dataset.\n\n    Genomic data from Open Targets provides gene identification and genomic coordinates that are integrated into the gene index of our ETL pipeline.\n\n    The EMBL-EBI Ensembl database is used as a source for human targets in the Platform, with the Ensembl gene ID as the primary identifier. The criteria for target inclusion is:\n    - Genes from all biotypes encoded in canonical chromosomes\n    - Genes in alternative assemblies encoding for a reviewed protein product.\n    \"\"\"\n\n    @staticmethod\n    def _get_gene_tss(strand_col: Column, start_col: Column, end_col: Column) -&gt; Column:\n        \"\"\"Returns the TSS of a gene based on its orientation.\n\n        Args:\n            strand_col (Column): Column containing 1 if the coding strand of the gene is forward, and -1 if it is reverse.\n            start_col (Column): Column containing the start position of the gene.\n            end_col (Column): Column containing the end position of the gene.\n\n        Returns:\n            Column: Column containing the TSS of the gene.\n\n        Examples:\n            &gt;&gt;&gt; df = spark.createDataFrame([{\"strand\": 1, \"start\": 100, \"end\": 200}, {\"strand\": -1, \"start\": 100, \"end\": 200}])\n            &gt;&gt;&gt; df.withColumn(\"tss\", OpenTargetsTarget._get_gene_tss(f.col(\"strand\"), f.col(\"start\"), f.col(\"end\"))).show()\n            +---+-----+------+---+\n            |end|start|strand|tss|\n            +---+-----+------+---+\n            |200|  100|     1|100|\n            |200|  100|    -1|200|\n            +---+-----+------+---+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return f.when(strand_col == 1, start_col).when(strand_col == -1, end_col)\n\n    @classmethod\n    def as_gene_index(\n        cls: type[OpenTargetsTarget], target_index: DataFrame\n    ) -&gt; GeneIndex:\n        \"\"\"Initialise GeneIndex from source dataset.\n\n        Args:\n            target_index (DataFrame): Target index dataframe\n\n        Returns:\n            GeneIndex: Gene index dataset\n        \"\"\"\n        return GeneIndex(\n            _df=target_index.select(\n                f.coalesce(f.col(\"id\"), f.lit(\"unknown\")).alias(\"geneId\"),\n                \"approvedSymbol\",\n                \"approvedName\",\n                \"biotype\",\n                f.col(\"obsoleteSymbols.label\").alias(\"obsoleteSymbols\"),\n                f.coalesce(f.col(\"genomicLocation.chromosome\"), f.lit(\"unknown\")).alias(\n                    \"chromosome\"\n                ),\n                OpenTargetsTarget._get_gene_tss(\n                    f.col(\"genomicLocation.strand\"),\n                    f.col(\"genomicLocation.start\"),\n                    f.col(\"genomicLocation.end\"),\n                ).alias(\"tss\"),\n                f.col(\"genomicLocation.start\").alias(\"start\"),\n                f.col(\"genomicLocation.end\").alias(\"end\"),\n                f.col(\"genomicLocation.strand\").alias(\"strand\"),\n            ),\n            _schema=GeneIndex.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/datasources/open_targets/target/#gentropy.datasource.open_targets.target.OpenTargetsTarget.as_gene_index","title":"<code>as_gene_index(target_index: DataFrame) -&gt; GeneIndex</code>  <code>classmethod</code>","text":"<p>Initialise GeneIndex from source dataset.</p> <p>Parameters:</p> Name Type Description Default <code>target_index</code> <code>DataFrame</code> <p>Target index dataframe</p> required <p>Returns:</p> Name Type Description <code>GeneIndex</code> <code>GeneIndex</code> <p>Gene index dataset</p> Source code in <code>src/gentropy/datasource/open_targets/target.py</code> <pre><code>@classmethod\ndef as_gene_index(\n    cls: type[OpenTargetsTarget], target_index: DataFrame\n) -&gt; GeneIndex:\n    \"\"\"Initialise GeneIndex from source dataset.\n\n    Args:\n        target_index (DataFrame): Target index dataframe\n\n    Returns:\n        GeneIndex: Gene index dataset\n    \"\"\"\n    return GeneIndex(\n        _df=target_index.select(\n            f.coalesce(f.col(\"id\"), f.lit(\"unknown\")).alias(\"geneId\"),\n            \"approvedSymbol\",\n            \"approvedName\",\n            \"biotype\",\n            f.col(\"obsoleteSymbols.label\").alias(\"obsoleteSymbols\"),\n            f.coalesce(f.col(\"genomicLocation.chromosome\"), f.lit(\"unknown\")).alias(\n                \"chromosome\"\n            ),\n            OpenTargetsTarget._get_gene_tss(\n                f.col(\"genomicLocation.strand\"),\n                f.col(\"genomicLocation.start\"),\n                f.col(\"genomicLocation.end\"),\n            ).alias(\"tss\"),\n            f.col(\"genomicLocation.start\").alias(\"start\"),\n            f.col(\"genomicLocation.end\").alias(\"end\"),\n            f.col(\"genomicLocation.strand\").alias(\"strand\"),\n        ),\n        _schema=GeneIndex.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/methods/_methods/","title":"Methods","text":"<p>This section consists of all the methods available in the package. It provides detailed explanations and usage examples for each method. Developers can refer to this section to understand how to use the methods effectively in their code. The list of methods is constantly updated.</p>"},{"location":"python_api/methods/carma/","title":"CARMA","text":"<p>CARMA is the method of the fine-mapping and outlier detection, originally implemented in R (CARMA on GitHub).</p> <p>The full repository for the reimplementation of CARMA in Python can be found here.</p> <p>This is a simplified version of CARMA with the following features:</p> <ol> <li>It uses only Spike-slab effect size priors and Poisson model priors.</li> <li>C++ is re-implemented in Python.</li> <li>The way of storing the configuration list is changed. It uses a string with the list of indexes for causal SNPs instead of a sparse matrix.</li> <li>Fixed bugs in PIP calculation.</li> <li>No credible models.</li> <li>No credible sets, only PIPs.</li> <li>No functional annotations.</li> <li>Removed unnecessary parameters.</li> </ol>"},{"location":"python_api/methods/carma/#gentropy.method.carma.CARMA","title":"<code>gentropy.method.carma.CARMA</code>","text":"<p>Implementation of CARMA outlier detection method.</p> Source code in <code>src/gentropy/method/carma.py</code> <pre><code>class CARMA:\n    \"\"\"Implementation of CARMA outlier detection method.\"\"\"\n\n    @staticmethod\n    def CARMA_spike_slab_noEM(\n        z: np.ndarray,\n        ld: np.ndarray,\n        lambda_val: float = 1,\n        Max_Model_Dim: int = 200_000,\n        all_iter: int = 1,\n        all_inner_iter: int = 10,\n        epsilon_threshold: float = 1e-5,\n        num_causal: int = 10,\n        tau: float = 0.04,\n        outlier_switch: bool = True,\n        outlier_BF_index: float = 1 / 3.2,\n    ) -&gt; dict[str, Any]:\n        \"\"\"Perform CARMA analysis using a Spike-and-Slab prior without Expectation-Maximization (EM).\n\n        Args:\n            z (np.ndarray): Numeric vector representing z-scores.\n            ld (np.ndarray): Numeric matrix representing the linkage disequilibrium (LD) matrix.\n            lambda_val (float): Regularization parameter controlling the strength of the L1 penalty.\n            Max_Model_Dim (int): Maximum allowed dimension for the causal models.\n            all_iter (int): The total number of iterations to run the CARMA analysis.\n            all_inner_iter (int): The number of inner iterations in each CARMA iteration.\n            epsilon_threshold (float): Threshold for convergence in CARMA iterations.\n            num_causal (int): Maximal number of causal variants to be selected in the final model.\n            tau (float): Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.\n            outlier_switch (bool): Whether to consider outlier detection in the analysis.\n            outlier_BF_index (float): Bayes Factor threshold for identifying outliers.\n\n        Returns:\n            dict[str, Any]: A dictionary containing the following results:\n                - PIPs: A numeric vector of posterior inclusion probabilities (PIPs) for all SNPs.\n                - B_list: A dataframe containing the marginal likelihoods and the corresponding model space.\n                - Outliers: A list of outlier SNPs.\n        \"\"\"\n        p_snp = len(z)\n        epsilon_list = epsilon_threshold * p_snp\n        all_epsilon_threshold = epsilon_threshold * p_snp\n\n        # Zero step\n        all_C_list = CARMA._MCS_modified(\n            z=z,\n            ld_matrix=ld,\n            epsilon=epsilon_list,\n            Max_Model_Dim=Max_Model_Dim,\n            lambda_val=lambda_val,\n            outlier_switch=outlier_switch,\n            tau=tau,\n            num_causal=num_causal,\n            inner_all_iter=all_inner_iter,\n            outlier_BF_index=outlier_BF_index,\n        )\n\n        # Main steps\n        for _ in range(0, all_iter):\n            ac1 = all_C_list[\"B_list\"][\"set_gamma_margin\"]\n            previous_result = np.mean(ac1[0 : round(len(ac1) / 4)])\n\n            all_C_list = CARMA._MCS_modified(\n                z=z,\n                ld_matrix=ld,\n                input_conditional_S_list=all_C_list[\"conditional_S_list\"],\n                Max_Model_Dim=Max_Model_Dim,\n                num_causal=num_causal,\n                epsilon=epsilon_list,\n                outlier_switch=outlier_switch,\n                tau=tau,\n                lambda_val=lambda_val,\n                inner_all_iter=all_inner_iter,\n                outlier_BF_index=outlier_BF_index,\n            )\n\n            ac1 = all_C_list[\"B_list\"][\"set_gamma_margin\"]\n            difference = np.abs(previous_result - np.mean(ac1[0 : round(len(ac1) / 4)]))\n            if difference &lt; all_epsilon_threshold:\n                break\n\n        # Calculate PIPs and Credible Set\n        pip = CARMA._PIP_func(\n            likeli=all_C_list[\"B_list\"][\"set_gamma_margin\"],\n            model_space=all_C_list[\"B_list\"][\"matrix_gamma\"],\n            p=p_snp,\n            num_causal=num_causal,\n        )\n\n        results_list = {\n            \"PIPs\": pip,\n            \"B_list\": all_C_list[\"B_list\"],\n            \"Outliers\": all_C_list[\"conditional_S_list\"],\n        }\n\n\n        return results_list\n\n    @staticmethod\n    def _ind_normal_sigma_fixed_marginal_fun_indi(\n        zSigmaz_S: np.ndarray, tau: float, p_S: int, det_S: float\n    ) -&gt; float:\n        \"\"\"Internal function for calculating the marginal likelihood of configuration model.\n\n        Args:\n            zSigmaz_S (np.ndarray): The zSigmaz_S value.\n            tau (float): The tau value.\n            p_S (int): The number of SNPs.\n            det_S (float): The det_S value.\n\n        Returns:\n            float: The marginal likelihood of a model.\n\n        Examples:\n            &gt;&gt;&gt; zSigmaz_S = 0.1\n            &gt;&gt;&gt; tau = 1 / 0.05**2\n            &gt;&gt;&gt; p_S = 3\n            &gt;&gt;&gt; det_S = 0.1\n            &gt;&gt;&gt; np.round(CARMA._ind_normal_sigma_fixed_marginal_fun_indi(zSigmaz_S, tau, p_S, det_S),decimals=5)\n            10.18849\n        \"\"\"\n        return p_S / 2.0 * np.log(tau) - 0.5 * np.log(det_S) + zSigmaz_S / 2.0\n\n    @staticmethod\n    def _ind_Normal_fixed_sigma_marginal_external(\n        index_vec_input: np.ndarray,\n        Sigma: np.ndarray,\n        z: np.ndarray,\n        tau: float,\n        p_S: int,\n    ) -&gt; float:\n        \"\"\"Marginal likelihood of configuration model.\n\n        Args:\n            index_vec_input (np.ndarray): The index vector.\n            Sigma (np.ndarray): The Sigma matrix.\n            z (np.ndarray): The z vector.\n            tau (float): The tau value.\n            p_S (int): The number of SNPs.\n\n        Returns:\n            float: The marginal likelihood of a model.\n\n        Examples:\n            &gt;&gt;&gt; index_vec_input = np.array([1, 2])\n            &gt;&gt;&gt; Sigma = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])\n            &gt;&gt;&gt; z = np.array([10, 11, 10])\n            &gt;&gt;&gt; tau = 1\n            &gt;&gt;&gt; p_S = 2\n            &gt;&gt;&gt; np.round(CARMA._ind_Normal_fixed_sigma_marginal_external(index_vec_input, Sigma, z, tau, p_S),decimals=5)\n            43.60579\n        \"\"\"\n        index_vec = index_vec_input - 1\n        Sigma_S = Sigma[np.ix_(index_vec, index_vec)]\n        A = tau * np.eye(p_S)\n\n        det_S = det(Sigma_S + A)\n        Sigma_S_inv = inv(Sigma_S + A)\n\n        sub_z = z[index_vec]\n        zSigmaz_S = np.dot(sub_z.T, np.dot(Sigma_S_inv, sub_z))\n\n        b = CARMA._ind_normal_sigma_fixed_marginal_fun_indi(zSigmaz_S, tau, p_S, det_S)\n\n        results = b\n\n        return results\n\n    @staticmethod\n    def _outlier_ind_Normal_marginal_external(\n        index_vec_input: np.ndarray,\n        Sigma: np.ndarray,\n        z: np.ndarray,\n        tau: float,\n        p_S: int,\n    ) -&gt; float:\n        \"\"\"Likehood of outlier model.\n\n        Args:\n            index_vec_input (np.ndarray): The index vector.\n            Sigma (np.ndarray): The Sigma matrix.\n            z (np.ndarray): The z vector.\n            tau (float): The tau value.\n            p_S (int): The number of SNPs.\n\n        Returns:\n            float: The likelihood of a model.\n\n        Examples:\n            &gt;&gt;&gt; index_vec_input = np.array([1, 2, 3])\n            &gt;&gt;&gt; Sigma = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])\n            &gt;&gt;&gt; z = np.array([0.1, 0.2, 0.3])\n            &gt;&gt;&gt; tau = 1 / 0.05**2\n            &gt;&gt;&gt; p_S = 3\n            &gt;&gt;&gt; np.round(CARMA._outlier_ind_Normal_marginal_external(index_vec_input, Sigma, z, tau, p_S),decimals=5)\n            -8.8497\n        \"\"\"\n        index_vec = index_vec_input - 1\n\n        Sigma_S = Sigma[np.ix_(index_vec, index_vec)]\n        A = tau * np.eye(p_S)\n\n        Sigma_S_I_inv = pinv(Sigma_S + A, rtol=0.00001)\n        Sigma_S_inv = pinv(Sigma_S, rtol=0.00001)\n\n        det_S = np.abs(det(Sigma_S_inv))\n        det_I_S = np.abs(det(Sigma_S_I_inv))\n\n        sub_z = z[index_vec]\n        zSigmaz_S = np.dot(sub_z, np.dot(Sigma_S_inv, sub_z))\n        zSigmaz_I_S = np.dot(sub_z, np.dot(Sigma_S_I_inv, sub_z))\n\n        b = 0.5 * (np.log(det_S) + np.log(det_I_S)) - 0.5 * (zSigmaz_S - zSigmaz_I_S)\n        results = b\n\n        return results\n\n    @staticmethod\n    def _add_function(S_sub: np.ndarray, y: Any) -&gt; np.ndarray:\n        \"\"\"Concatenate two arrays and sort the result.\n\n        Args:\n            S_sub (np.ndarray): The first array.\n            y (Any): The second array.\n\n        Returns:\n            np.ndarray: The concatenated and sorted array.\n\n        Examples:\n            &gt;&gt;&gt; S_sub = np.array([3, 4])\n            &gt;&gt;&gt; y = np.array([1, 2])\n            &gt;&gt;&gt; CARMA._add_function(S_sub, y)\n            array([[1, 2, 3],\n                   [1, 2, 4]])\n        \"\"\"\n        return np.array([np.sort(np.concatenate(([x], y))) for x in S_sub])\n\n    @staticmethod\n    def _set_gamma_func_base(S: Any, p: int) -&gt; dict[int, np.ndarray]:\n        \"\"\"Creates a dictionary of sets of configurations assuming no conditional set.\n\n        Args:\n            S (Any): The input set.\n            p (int): The number of SNPs.\n\n        Returns:\n            dict[int, np.ndarray]: A dictionary of sets of configurations.\n\n        Examples:\n        &gt;&gt;&gt; S = [0,1]\n        &gt;&gt;&gt; p = 4\n        &gt;&gt;&gt; CARMA._set_gamma_func_base(S, p)\n        {0: array([[0],\n               [1]]), 1: array([[0, 1, 2],\n               [0, 1, 3]]), 2: array([[0, 2],\n               [0, 3],\n               [1, 2],\n               [1, 3]])}\n\n        &gt;&gt;&gt; S = [0]\n        &gt;&gt;&gt; p = 2\n        &gt;&gt;&gt; CARMA._set_gamma_func_base(S, p)\n        {0: None, 1: array([[0, 1]]), 2: array([[1]])}\n\n        &gt;&gt;&gt; S = []\n        &gt;&gt;&gt; p = 2\n        &gt;&gt;&gt; CARMA._set_gamma_func_base(S, p)\n        {0: None, 1: array([[0],\n               [1]]), 2: None}\n        \"\"\"\n        set_gamma: dict[int, Any] = {}\n\n        if len(S) == 0:\n            set_gamma[0] = None\n            set_gamma[1] = np.arange(0, p).reshape(-1, 1)\n            set_gamma[2] = None\n\n        if len(S) == 1:\n            S_sub = np.setdiff1d(np.arange(0, p), S)\n            set_gamma[0] = None\n            set_gamma[1] = CARMA._add_function(S_sub, S)\n            set_gamma[2] = S_sub.reshape(-1, 1)\n\n        if len(S) &gt; 1:\n            S_sub = np.setdiff1d(np.arange(0, p), S)\n            S = np.sort(S)\n            set_gamma[0] = np.array(list(combinations(S, len(S) - 1)))\n            set_gamma[1] = CARMA._add_function(S_sub, S)\n            xs = np.vstack([CARMA._add_function(S_sub, row) for row in set_gamma[0]])\n            set_gamma[2] = xs\n\n        return set_gamma\n\n    @staticmethod\n    def _set_gamma_func_conditional(\n        input_S: Any, condition_index: list[int], p: int\n    ) -&gt; dict[int, np.ndarray]:\n        \"\"\"Creates a dictionary of sets of configurations assuming conditional set.\n\n        Args:\n            input_S (Any): The input set.\n            condition_index (list[int]): The conditional set.\n            p (int): The number of SNPs.\n\n        Returns:\n            dict[int, np.ndarray]: A dictionary of sets of configurations.\n\n        Examples:\n        &gt;&gt;&gt; input_S = [0,1,2]\n        &gt;&gt;&gt; condition_index = [2]\n        &gt;&gt;&gt; p = 4\n        &gt;&gt;&gt; CARMA._set_gamma_func_conditional(input_S, condition_index, p)\n        {0: array([[0],\n               [1]]), 1: array([[0, 1, 3]]), 2: array([[0, 3],\n               [1, 3]])}\n        \"\"\"\n        set_gamma: dict[int, Any] = {}\n        S = np.setdiff1d(input_S, condition_index)\n\n        # set of gamma-\n        if len(S) == 0:\n            S_sub = np.setdiff1d(np.arange(0, p), condition_index)\n            set_gamma[0] = None\n            set_gamma[1] = S_sub.reshape(-1, 1)\n            set_gamma[2] = None\n\n        if len(S) == 1:\n            S_sub = np.setdiff1d(np.arange(0, p), input_S)\n            set_gamma[0] = None\n            set_gamma[1] = CARMA._add_function(S_sub, S)\n            set_gamma[2] = S_sub.reshape(-1, 1)\n\n        if len(S) &gt; 1:\n            S_sub = np.setdiff1d(np.arange(0, p), input_S)\n            S = np.sort(S)\n            set_gamma[0] = np.array(list(combinations(S, len(S) - 1)))\n            set_gamma[1] = CARMA._add_function(S_sub, S)\n            xs = np.vstack([CARMA._add_function(S_sub, row) for row in set_gamma[0]])\n            set_gamma[2] = xs\n\n        return set_gamma\n\n    @staticmethod\n    def _set_gamma_func(\n        input_S: Any, p: int, condition_index: list[int] | None = None\n    ) -&gt; dict[int, np.ndarray]:\n        \"\"\"Creates a dictionary of sets of configurations.\n\n        Args:\n            input_S (Any): The input set.\n            p (int): The number of SNPs.\n            condition_index (list[int] | None): The conditional set. Defaults to None.\n\n        Returns:\n            dict[int, np.ndarray]: A dictionary of sets of configurations.\n\n        Examples:\n        &gt;&gt;&gt; input_S = [0,1,2]\n        &gt;&gt;&gt; condition_index=[2]\n        &gt;&gt;&gt; p = 4\n        &gt;&gt;&gt; CARMA._set_gamma_func(input_S, p, condition_index)\n        {0: array([[0],\n               [1]]), 1: array([[0, 1, 3]]), 2: array([[0, 3],\n               [1, 3]])}\n        \"\"\"\n        if condition_index is None:\n            results = CARMA._set_gamma_func_base(input_S, p)\n        else:\n            results = CARMA._set_gamma_func_conditional(input_S, condition_index, p)\n        return results\n\n    @staticmethod\n    def _index_fun_internal(x: np.ndarray) -&gt; str:\n        \"\"\"Convert an array of causal SNP indexes to comma-separated string.\n\n        Args:\n            x (np.ndarray): The input array.\n\n        Returns:\n            str: The comma-separated string.\n\n        Examples:\n        &gt;&gt;&gt; x = np.array([1,2,3])\n        &gt;&gt;&gt; CARMA._index_fun_internal(x)\n        '1,2,3'\n        \"\"\"\n        y = np.sort(x)\n        y = y.astype(str)\n        return \",\".join(y)\n\n    @staticmethod\n    def _index_fun(y: np.ndarray) -&gt; np.ndarray:\n        \"\"\"Convert an array of causal SNP indexes to comma-separated string.\n\n        Args:\n            y (np.ndarray): The input array.\n\n        Returns:\n            np.ndarray: The comma-separated string.\n\n        Examples:\n        &gt;&gt;&gt; y = np.array([[1,2,3],[4,5,6]])\n        &gt;&gt;&gt; CARMA._index_fun(y)\n        array(['1,2,3', '4,5,6'], dtype='&lt;U5')\n        \"\"\"\n        return np.array([CARMA._index_fun_internal(x) for x in y])\n\n    @staticmethod\n    def _ridge_fun(\n        x: float,\n        Sigma: np.ndarray,\n        modi_ld_S: np.ndarray,\n        test_S: np.ndarray,\n        z: np.ndarray,\n        outlier_tau: float,\n        outlier_likelihood: Any,\n    ) -&gt; float:\n        \"\"\"Estimate the matrix shrinkage parameter for outlier detection.\n\n        Args:\n            x (float): The input parameter.\n            Sigma (np.ndarray): The Sigma matrix.\n            modi_ld_S (np.ndarray): The modi_ld_S matrix.\n            test_S (np.ndarray): The test_S matrix.\n            z (np.ndarray): The z vector.\n            outlier_tau (float): The outlier_tau value.\n            outlier_likelihood (Any): The outlier_likelihood function.\n\n        Returns:\n            float: The estimated matrix shrinkage parameter.\n\n        Examples:\n        &gt;&gt;&gt; x = 0.5\n        &gt;&gt;&gt; Sigma = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])\n        &gt;&gt;&gt; modi_ld_S = np.array([[1, 0.5], [0.5, 1]])\n        &gt;&gt;&gt; test_S = np.array([1, 2])\n        &gt;&gt;&gt; z = np.array([0.1, 0.2, 0.3])\n        &gt;&gt;&gt; outlier_tau = 1 / 0.05**2\n        &gt;&gt;&gt; outlier_likelihood = CARMA._outlier_ind_Normal_marginal_external\n        &gt;&gt;&gt; np.round(CARMA._ridge_fun(x, Sigma, modi_ld_S, test_S, z, outlier_tau, outlier_likelihood),decimals=5)\n        6.01486\n        \"\"\"\n        temp_Sigma = Sigma.copy()\n        temp_ld_S = x * modi_ld_S + (1 - x) * np.eye(len(modi_ld_S))\n        temp_Sigma[np.ix_(test_S, test_S)] = temp_ld_S\n        return -outlier_likelihood(\n            index_vec_input=test_S + 1,\n            Sigma=temp_Sigma,\n            z=z,\n            tau=outlier_tau,\n            p_S=len(test_S),\n        )\n\n    @staticmethod\n    def _prior_dist(t: str, lambda_val: float, p: int) -&gt; float:\n        \"\"\"Estimate the priors for the given configurations.\n\n        Args:\n            t (str): The input string for the given configuration.\n            lambda_val (float): The lambda value.\n            p (int): The number of SNPs.\n\n        Returns:\n            float: The estimated prior.\n\n        Examples:\n        &gt;&gt;&gt; t = \"1,2,3\"\n        &gt;&gt;&gt; lambda_val = 1\n        &gt;&gt;&gt; p = 4\n        &gt;&gt;&gt; np.round(CARMA._prior_dist(t, lambda_val, p),decimals=5)\n        -3.17805\n        \"\"\"\n        index_array = t.split(\",\")\n        dim_model = len(index_array)\n        if t == \"\":\n            dim_model = 0\n        return (\n            dim_model * np.log(lambda_val) + lgamma(p - dim_model + 1) - lgamma(p + 1)\n        )\n\n    @staticmethod\n    def _PIP_func(\n        likeli: pd.DataFrame, model_space: pd.DataFrame, p: int, num_causal: int\n    ) -&gt; np.ndarray:\n        \"\"\"Estimates the posterior inclusion probabilities (PIPs) for all SNPs.\n\n        Args:\n            likeli (pd.DataFrame): The marginal likelihoods.\n            model_space (pd.DataFrame): The corresponding model space.\n            p (int): The number of SNPs.\n            num_causal (int): The maximal number of causal SNPs.\n\n        Returns:\n            np.ndarray: The posterior inclusion probabilities (PIPs) for all SNPs.\n\n        Examples:\n        &gt;&gt;&gt; likeli = pd.DataFrame([10, 10, 5,11,0], columns=['likeli']).squeeze()\n        &gt;&gt;&gt; model_space = pd.DataFrame(['0', '1', '2','0,1',''], columns=['config']).squeeze()\n        &gt;&gt;&gt; p = 3\n        &gt;&gt;&gt; num_causal = 2\n        &gt;&gt;&gt; CARMA._PIP_func(likeli, model_space, p, num_causal)\n        array([0.7869271, 0.7869271, 0.001426 ])\n        \"\"\"\n        likeli = likeli.reset_index(drop=True)\n        model_space = model_space.reset_index(drop=True)\n\n        model_space_matrix = np.zeros((len(model_space), p), dtype=int)\n\n        for i in range(len(model_space)):\n            if model_space.iloc[i] != \"\":\n                ind = list(map(int, model_space.iloc[i].split(\",\")))\n                if len(ind) &gt; 0:\n                    model_space_matrix[i, ind] = 1\n\n        infi_index = np.where(np.isinf(likeli))[0]\n        if len(infi_index) != 0:\n            likeli = likeli.drop(infi_index).reset_index(drop=True)\n            model_space_matrix = np.delete(model_space_matrix, infi_index, axis=0)\n\n        na_index = np.where(np.isnan(likeli))[0]\n        if len(na_index) != 0:\n            likeli = likeli.drop(na_index).reset_index(drop=True)\n            model_space_matrix = np.delete(model_space_matrix, na_index, axis=0)\n\n        row_sums = np.sum(model_space_matrix, axis=1)\n        model_space_matrix = model_space_matrix[row_sums &lt;= num_causal]\n        likeli = likeli[row_sums &lt;= num_causal]\n\n        aa = likeli - max(likeli)\n        prob_sum = np.sum(np.exp(aa))\n\n        result_prob = np.zeros(p)\n        for i in range(p):\n            result_prob[i] = (\n                np.sum(np.exp(aa[model_space_matrix[:, i] == 1])) / prob_sum\n            )\n\n        return result_prob\n\n    @staticmethod\n    def _MCS_modified(  # noqa: C901\n        z: np.ndarray,\n        ld_matrix: np.ndarray,\n        Max_Model_Dim: int = 10_000,\n        lambda_val: float = 1,\n        num_causal: int = 10,\n        outlier_switch: bool = True,\n        input_conditional_S_list: list[int] | None = None,\n        tau: float = 1 / 0.05**2,\n        epsilon: float = 1e-3,\n        inner_all_iter: int = 10,\n        outlier_BF_index: float | None = None,\n    ) -&gt; dict[str, Any]:\n        \"\"\"Modified Monte Carlo shotgun sampling (MCS) algorithm.\n\n        Args:\n            z (np.ndarray): Numeric vector representing z-scores.\n            ld_matrix (np.ndarray): Numeric matrix representing the linkage disequilibrium (LD) matrix.\n            Max_Model_Dim (int): Maximum allowed dimension for the causal models.\n            lambda_val (float): Regularization parameter controlling the strength of the L1 penalty.\n            num_causal (int): Maximal number of causal variants to be selected in the final model.\n            outlier_switch (bool): Whether to consider outlier detection in the analysis.\n            input_conditional_S_list (list[int] | None): The conditional set. Defaults to None.\n            tau (float): Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.\n            epsilon (float): Threshold for convergence in CARMA iterations.\n            inner_all_iter (int): The number of inner iterations in each CARMA iteration.\n            outlier_BF_index (float | None): Bayes Factor threshold for identifying outliers. Defaults to None.\n\n        Returns:\n            dict[str, Any]: A dictionary containing the following results:\n                - B_list: A dataframe containing the marginal likelihoods and the corresponding model space.\n                - conditional_S_list: A list of outliers.\n\n        Examples:\n        &gt;&gt;&gt; z = np.array([0.1, 0.2, 0.3])\n        &gt;&gt;&gt; ld_matrix = np.array([[1, 0.5, 0.2], [0.5, 1, 0.3], [0.2, 0.3, 1]])\n        &gt;&gt;&gt; Max_Model_Dim = 10_000\n        &gt;&gt;&gt; lambda_val = 1\n\n        &gt;&gt;&gt; num_causal = 10\n        &gt;&gt;&gt; outlier_switch = True\n        \"\"\"\n        p = len(z)\n        marginal_likelihood = CARMA._ind_Normal_fixed_sigma_marginal_external\n        tau_sample = tau\n        if outlier_switch:\n            outlier_likelihood = CARMA._outlier_ind_Normal_marginal_external\n            outlier_tau = tau\n\n        B = Max_Model_Dim\n        stored_bf = 0\n        Sigma = ld_matrix\n\n        S = []\n\n        null_model = \"\"\n        null_margin = CARMA._prior_dist(null_model, lambda_val=lambda_val, p=p)\n\n        B_list = pd.DataFrame({\"set_gamma_margin\": [null_margin], \"matrix_gamma\": [\"\"]})\n\n        if input_conditional_S_list is None:\n            conditional_S = []\n        else:\n            conditional_S = input_conditional_S_list\n            S = conditional_S\n\n        for _i in range(0, inner_all_iter):\n            for _j in range(0, 10):\n                set_gamma = CARMA._set_gamma_func(\n                    input_S=S, p=p, condition_index=conditional_S\n                )\n\n                if conditional_S is None:\n                    working_S = S\n                else:\n                    working_S = np.sort(np.setdiff1d(S, conditional_S)).astype(int)\n\n                set_gamma_margin: list[Any] = [None, None, None]\n                set_gamma_prior: list[Any] = [None, None, None]\n                matrix_gamma: list[Any] = [None, None, None]\n\n                for i in range(0, len(set_gamma)):\n                    if set_gamma[i] is not None:\n                        matrix_gamma[i] = CARMA._index_fun(set_gamma[i])\n                        p_S = set_gamma[i].shape[1]\n                        set_gamma_margin[i] = np.apply_along_axis(\n                            marginal_likelihood,\n                            1,\n                            set_gamma[i] + 1,\n                            Sigma=Sigma,\n                            z=z,\n                            tau=tau_sample,\n                            p_S=p_S,\n                        )\n                        set_gamma_prior[i] = np.array(\n                            [\n                                CARMA._prior_dist(model, lambda_val=lambda_val, p=p)\n                                for model in matrix_gamma[i]\n                            ]\n                        )\n                        set_gamma_margin[i] = set_gamma_prior[i] + set_gamma_margin[i]\n                    else:\n                        set_gamma_margin[i] = np.array(null_margin)\n                        set_gamma_prior[i] = 0\n                        matrix_gamma[i] = np.array(null_model)\n\n                columns = [\"set_gamma_margin\", \"matrix_gamma\"]\n                add_B = pd.DataFrame(columns=columns)\n\n                for i in range(len(set_gamma)):\n                    if isinstance(set_gamma_margin[i].tolist(), list):\n                        new_row = pd.DataFrame(\n                            {\n                                \"set_gamma_margin\": set_gamma_margin[i].tolist(),\n                                \"matrix_gamma\": matrix_gamma[i].tolist(),\n                            }\n                        )\n                        add_B = pd.concat([add_B, new_row], ignore_index=True)\n                    else:\n                        new_row = pd.DataFrame(\n                            {\n                                \"set_gamma_margin\": [set_gamma_margin[i].tolist()],\n                                \"matrix_gamma\": [matrix_gamma[i].tolist()],\n                            }\n                        )\n                        add_B = pd.concat([add_B, new_row], ignore_index=True)\n\n                # Add visited models into the storage space of models\n                B_list = pd.concat([B_list, add_B], ignore_index=True)\n                B_list = B_list.drop_duplicates(\n                    subset=\"matrix_gamma\", ignore_index=True\n                )\n                B_list = B_list.sort_values(\n                    by=\"set_gamma_margin\", ignore_index=True, ascending=False\n                )\n\n                if len(working_S) == 0:\n                    # Create a DataFrame set.star\n                    set_star = pd.DataFrame(\n                        {\n                            \"set_index\": [0, 1, 2],\n                            \"gamma_set_index\": [np.nan, np.nan, np.nan],\n                            \"margin\": [np.nan, np.nan, np.nan],\n                        }\n                    )\n\n                    # Assuming set.gamma.margin and current.log.margin are defined\n                    aa = set_gamma_margin[1]\n                    aa = aa - aa[np.argmax(aa)]\n\n                    min_half_len = min(len(aa), floor(p / 2))\n                    decr_ind = np.argsort(np.exp(aa))[::-1]\n                    decr_half_ind = decr_ind[:min_half_len]\n\n                    probs = np.exp(aa)[decr_half_ind]\n\n                    chosen_index = np.random.choice(\n                        decr_half_ind, 1, p=probs / np.sum(probs)\n                    )\n                    set_star.at[1, \"gamma_set_index\"] = chosen_index[0]\n                    set_star.at[1, \"margin\"] = set_gamma_margin[1][chosen_index[0]]\n\n                    S = set_gamma[1][chosen_index[0]].tolist()\n\n                else:\n                    set_star = pd.DataFrame(\n                        {\n                            \"set_index\": [0, 1, 2],\n                            \"gamma_set_index\": [np.nan, np.nan, np.nan],\n                            \"margin\": [np.nan, np.nan, np.nan],\n                        }\n                    )\n                    for i in range(0, 3):\n                        aa = set_gamma_margin[i]\n                        if np.size(aa) &gt; 1:\n                            aa = aa - aa[np.argmax(aa)]\n                            chosen_index = np.random.choice(\n                                range(0, np.size(set_gamma_margin[i])),\n                                1,\n                                p=np.exp(aa) / np.sum(np.exp(aa)),\n                            )\n                            set_star.at[i, \"gamma_set_index\"] = chosen_index\n                            set_star.at[i, \"margin\"] = set_gamma_margin[i][chosen_index]\n                        else:\n                            set_star.at[i, \"gamma_set_index\"] = 0\n                            set_star.at[i, \"margin\"] = set_gamma_margin[i]\n\n                    if outlier_switch:\n                        for i in range(1, len(set_gamma)):\n                            test_log_BF: float = 100\n                            while True:\n                                aa = set_gamma_margin[i]\n                                aa = aa - aa[np.argmax(aa)]\n                                chosen_index = np.random.choice(\n                                    range(0, np.size(set_gamma_margin[i])),\n                                    1,\n                                    p=np.exp(aa) / np.sum(np.exp(aa)),\n                                )\n                                set_star.at[i, \"gamma_set_index\"] = chosen_index\n                                set_star.at[i, \"margin\"] = set_gamma_margin[i][\n                                    chosen_index\n                                ]\n\n                                test_S = set_gamma[i][int(chosen_index), :]\n\n                                modi_Sigma = Sigma.copy()\n                                if np.size(test_S) &gt; 1:\n                                    modi_ld_S = modi_Sigma[test_S][:, test_S]\n\n                                    result = minimize_scalar(\n                                        CARMA._ridge_fun,\n                                        bounds=(0, 1),\n                                        args=(\n                                            Sigma,\n                                            modi_ld_S,\n                                            test_S,\n                                            z,\n                                            outlier_tau,\n                                            outlier_likelihood,\n                                        ),\n                                        method=\"bounded\",\n                                    )\n                                    modi_ld_S = result.x * modi_ld_S + (\n                                        1 - result.x\n                                    ) * np.eye(len(modi_ld_S))\n\n                                    modi_Sigma[np.ix_(test_S, test_S)] = modi_ld_S\n\n                                    test_log_BF = outlier_likelihood(\n                                        test_S + 1, Sigma, z, outlier_tau, len(test_S)\n                                    ) - outlier_likelihood(\n                                        test_S + 1,\n                                        modi_Sigma,\n                                        z,\n                                        outlier_tau,\n                                        len(test_S),\n                                    )\n                                    test_log_BF = -np.abs(test_log_BF)\n\n                                if np.exp(test_log_BF) &lt; outlier_BF_index:\n                                    set_gamma[i] = np.delete(\n                                        set_gamma[i],\n                                        int(set_star[\"gamma_set_index\"][i]),\n                                        axis=0,\n                                    )\n                                    set_gamma_margin[i] = np.delete(\n                                        set_gamma_margin[i],\n                                        int(set_star[\"gamma_set_index\"][i]),\n                                        axis=0,\n                                    )\n                                    conditional_S = np.concatenate(\n                                        [conditional_S, np.setdiff1d(test_S, working_S)]\n                                    )\n                                    conditional_S = (\n                                        np.unique(conditional_S).astype(int).tolist()\n                                    )\n                                else:\n                                    break\n\n                    if len(working_S) == num_causal:\n                        set_star = set_star.drop(1)\n                        aa = set_star[\"margin\"] - max(set_star[\"margin\"])\n                        sec_sample = np.random.choice(\n                            [0, 2], 1, p=np.exp(aa) / np.sum(np.exp(aa))\n                        )\n                        ind_sec = int(\n                            set_star[\"gamma_set_index\"][\n                                set_star[\"set_index\"] == int(sec_sample)\n                            ]\n                        )\n                        S = set_gamma[sec_sample[0]][ind_sec].tolist()\n                    else:\n                        aa = set_star[\"margin\"] - max(set_star[\"margin\"])\n                        sec_sample = np.random.choice(\n                            range(0, 3), 1, p=np.exp(aa) / np.sum(np.exp(aa))\n                        )\n                        S = set_gamma[sec_sample[0]][\n                            int(set_star[\"gamma_set_index\"][sec_sample[0]])\n                        ].tolist()\n\n                for item in conditional_S:\n                    if item not in S:\n                        S.append(item)\n            # END h_ind loop\n            #\n            if conditional_S is not None:\n                all_c_index = []\n                index_array = [s.split(\",\") for s in B_list[\"matrix_gamma\"]]\n                for tt in conditional_S:\n                    tt_str = str(tt)\n                    ind = [\n                        i for i, sublist in enumerate(index_array) if tt_str in sublist\n                    ]\n                    all_c_index.extend(ind)\n\n                all_c_index = list(set(all_c_index))\n\n                if len(all_c_index) &gt; 0:\n                    temp_B_list = B_list.copy()\n                    temp_B_list = B_list.drop(all_c_index)\n                else:\n                    temp_B_list = B_list.copy()\n            else:\n                temp_B_list = B_list.copy()\n\n            result_B_list = temp_B_list[: min(int(B), len(temp_B_list))]\n\n            rb1 = result_B_list[\"set_gamma_margin\"]\n\n            difference = abs(rb1[: (len(rb1) // 4)].mean() - stored_bf)\n\n            if difference &lt; epsilon:\n                break\n            else:\n                stored_bf = rb1[: (len(rb1) // 4)].mean()\n\n        out = {\"B_list\": result_B_list, \"conditional_S_list\": conditional_S}\n\n        return out\n</code></pre>"},{"location":"python_api/methods/carma/#gentropy.method.carma.CARMA.CARMA_spike_slab_noEM","title":"<code>CARMA_spike_slab_noEM(z: np.ndarray, ld: np.ndarray, lambda_val: float = 1, Max_Model_Dim: int = 200000, all_iter: int = 1, all_inner_iter: int = 10, epsilon_threshold: float = 1e-05, num_causal: int = 10, tau: float = 0.04, outlier_switch: bool = True, outlier_BF_index: float = 1 / 3.2) -&gt; dict[str, Any]</code>  <code>staticmethod</code>","text":"<p>Perform CARMA analysis using a Spike-and-Slab prior without Expectation-Maximization (EM).</p> <p>Parameters:</p> Name Type Description Default <code>z</code> <code>ndarray</code> <p>Numeric vector representing z-scores.</p> required <code>ld</code> <code>ndarray</code> <p>Numeric matrix representing the linkage disequilibrium (LD) matrix.</p> required <code>lambda_val</code> <code>float</code> <p>Regularization parameter controlling the strength of the L1 penalty.</p> <code>1</code> <code>Max_Model_Dim</code> <code>int</code> <p>Maximum allowed dimension for the causal models.</p> <code>200000</code> <code>all_iter</code> <code>int</code> <p>The total number of iterations to run the CARMA analysis.</p> <code>1</code> <code>all_inner_iter</code> <code>int</code> <p>The number of inner iterations in each CARMA iteration.</p> <code>10</code> <code>epsilon_threshold</code> <code>float</code> <p>Threshold for convergence in CARMA iterations.</p> <code>1e-05</code> <code>num_causal</code> <code>int</code> <p>Maximal number of causal variants to be selected in the final model.</p> <code>10</code> <code>tau</code> <code>float</code> <p>Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.</p> <code>0.04</code> <code>outlier_switch</code> <code>bool</code> <p>Whether to consider outlier detection in the analysis.</p> <code>True</code> <code>outlier_BF_index</code> <code>float</code> <p>Bayes Factor threshold for identifying outliers.</p> <code>1 / 3.2</code> <p>Returns:</p> Type Description <code>dict[str, Any]</code> <p>dict[str, Any]: A dictionary containing the following results: - PIPs: A numeric vector of posterior inclusion probabilities (PIPs) for all SNPs. - B_list: A dataframe containing the marginal likelihoods and the corresponding model space. - Outliers: A list of outlier SNPs.</p> Source code in <code>src/gentropy/method/carma.py</code> <pre><code>@staticmethod\ndef CARMA_spike_slab_noEM(\n    z: np.ndarray,\n    ld: np.ndarray,\n    lambda_val: float = 1,\n    Max_Model_Dim: int = 200_000,\n    all_iter: int = 1,\n    all_inner_iter: int = 10,\n    epsilon_threshold: float = 1e-5,\n    num_causal: int = 10,\n    tau: float = 0.04,\n    outlier_switch: bool = True,\n    outlier_BF_index: float = 1 / 3.2,\n) -&gt; dict[str, Any]:\n    \"\"\"Perform CARMA analysis using a Spike-and-Slab prior without Expectation-Maximization (EM).\n\n    Args:\n        z (np.ndarray): Numeric vector representing z-scores.\n        ld (np.ndarray): Numeric matrix representing the linkage disequilibrium (LD) matrix.\n        lambda_val (float): Regularization parameter controlling the strength of the L1 penalty.\n        Max_Model_Dim (int): Maximum allowed dimension for the causal models.\n        all_iter (int): The total number of iterations to run the CARMA analysis.\n        all_inner_iter (int): The number of inner iterations in each CARMA iteration.\n        epsilon_threshold (float): Threshold for convergence in CARMA iterations.\n        num_causal (int): Maximal number of causal variants to be selected in the final model.\n        tau (float): Tuning parameter controlling the degree of sparsity in the Spike-and-Slab prior.\n        outlier_switch (bool): Whether to consider outlier detection in the analysis.\n        outlier_BF_index (float): Bayes Factor threshold for identifying outliers.\n\n    Returns:\n        dict[str, Any]: A dictionary containing the following results:\n            - PIPs: A numeric vector of posterior inclusion probabilities (PIPs) for all SNPs.\n            - B_list: A dataframe containing the marginal likelihoods and the corresponding model space.\n            - Outliers: A list of outlier SNPs.\n    \"\"\"\n    p_snp = len(z)\n    epsilon_list = epsilon_threshold * p_snp\n    all_epsilon_threshold = epsilon_threshold * p_snp\n\n    # Zero step\n    all_C_list = CARMA._MCS_modified(\n        z=z,\n        ld_matrix=ld,\n        epsilon=epsilon_list,\n        Max_Model_Dim=Max_Model_Dim,\n        lambda_val=lambda_val,\n        outlier_switch=outlier_switch,\n        tau=tau,\n        num_causal=num_causal,\n        inner_all_iter=all_inner_iter,\n        outlier_BF_index=outlier_BF_index,\n    )\n\n    # Main steps\n    for _ in range(0, all_iter):\n        ac1 = all_C_list[\"B_list\"][\"set_gamma_margin\"]\n        previous_result = np.mean(ac1[0 : round(len(ac1) / 4)])\n\n        all_C_list = CARMA._MCS_modified(\n            z=z,\n            ld_matrix=ld,\n            input_conditional_S_list=all_C_list[\"conditional_S_list\"],\n            Max_Model_Dim=Max_Model_Dim,\n            num_causal=num_causal,\n            epsilon=epsilon_list,\n            outlier_switch=outlier_switch,\n            tau=tau,\n            lambda_val=lambda_val,\n            inner_all_iter=all_inner_iter,\n            outlier_BF_index=outlier_BF_index,\n        )\n\n        ac1 = all_C_list[\"B_list\"][\"set_gamma_margin\"]\n        difference = np.abs(previous_result - np.mean(ac1[0 : round(len(ac1) / 4)]))\n        if difference &lt; all_epsilon_threshold:\n            break\n\n    # Calculate PIPs and Credible Set\n    pip = CARMA._PIP_func(\n        likeli=all_C_list[\"B_list\"][\"set_gamma_margin\"],\n        model_space=all_C_list[\"B_list\"][\"matrix_gamma\"],\n        p=p_snp,\n        num_causal=num_causal,\n    )\n\n    results_list = {\n        \"PIPs\": pip,\n        \"B_list\": all_C_list[\"B_list\"],\n        \"Outliers\": all_C_list[\"conditional_S_list\"],\n    }\n\n\n    return results_list\n</code></pre>"},{"location":"python_api/methods/clumping/","title":"Clumping","text":"<p>Clumping is a commonly used post-processing method that allows for the identification of independent association signals from GWAS summary statistics and curated associations. This process is critical because of the complex linkage disequilibrium (LD) structure in human populations, which can result in multiple statistically significant associations within the same genomic region. Clumping methods help reduce redundancy in GWAS results and ensure that each reported association represents an independent signal.</p> <p>We have implemented two clumping methods:</p> <ol> <li>Distance-based clumping: Uses genomic window to clump the significant SNPs into one hit.</li> <li>LD-based clumping: Uses genomic window and LD to clump the significant SNPs into one hit.</li> </ol> <p>The algorithmic logic is similar to classic clumping approaches from PLINK (Reference: PLINK Clump Documentation). See details below:</p>"},{"location":"python_api/methods/clumping/#distance-based-clumping","title":"Distance-based clumping","text":""},{"location":"python_api/methods/clumping/#gentropy.method.window_based_clumping.WindowBasedClumping","title":"<code>gentropy.method.window_based_clumping.WindowBasedClumping</code>","text":"<p>Get semi-lead snps from summary statistics using a window based function.</p> Source code in <code>src/gentropy/method/window_based_clumping.py</code> <pre><code>class WindowBasedClumping:\n    \"\"\"Get semi-lead snps from summary statistics using a window based function.\"\"\"\n\n    @staticmethod\n    def _cluster_peaks(\n        study: Column, chromosome: Column, position: Column, window_length: int\n    ) -&gt; Column:\n        \"\"\"Cluster GWAS significant variants, were clusters are separated by a defined distance.\n\n        !! Important to note that the length of the clusters can be arbitrarily big.\n\n        Args:\n            study (Column): study identifier\n            chromosome (Column): chromosome identifier\n            position (Column): position of the variant\n            window_length (int): window length in basepair\n\n        Returns:\n            Column: containing cluster identifier\n\n        Examples:\n            &gt;&gt;&gt; data = [\n            ...     # Cluster 1:\n            ...     ('s1', 'chr1', 2),\n            ...     ('s1', 'chr1', 4),\n            ...     ('s1', 'chr1', 12),\n            ...     # Cluster 2 - Same chromosome:\n            ...     ('s1', 'chr1', 31),\n            ...     ('s1', 'chr1', 38),\n            ...     ('s1', 'chr1', 42),\n            ...     # Cluster 3 - New chromosome:\n            ...     ('s1', 'chr2', 41),\n            ...     ('s1', 'chr2', 44),\n            ...     ('s1', 'chr2', 50),\n            ...     # Cluster 4 - other study:\n            ...     ('s2', 'chr2', 55),\n            ...     ('s2', 'chr2', 62),\n            ...     ('s2', 'chr2', 70),\n            ... ]\n            &gt;&gt;&gt; window_length = 10\n            &gt;&gt;&gt; (\n            ...     spark.createDataFrame(data, ['studyId', 'chromosome', 'position'])\n            ...     .withColumn(\"cluster_id\",\n            ...         WindowBasedClumping._cluster_peaks(\n            ...             f.col('studyId'),\n            ...             f.col('chromosome'),\n            ...             f.col('position'),\n            ...             window_length\n            ...         )\n            ...     ).show()\n            ... )\n            +-------+----------+--------+----------+\n            |studyId|chromosome|position|cluster_id|\n            +-------+----------+--------+----------+\n            |     s1|      chr1|       2| s1_chr1_2|\n            |     s1|      chr1|       4| s1_chr1_2|\n            |     s1|      chr1|      12| s1_chr1_2|\n            |     s1|      chr1|      31|s1_chr1_31|\n            |     s1|      chr1|      38|s1_chr1_31|\n            |     s1|      chr1|      42|s1_chr1_31|\n            |     s1|      chr2|      41|s1_chr2_41|\n            |     s1|      chr2|      44|s1_chr2_41|\n            |     s1|      chr2|      50|s1_chr2_41|\n            |     s2|      chr2|      55|s2_chr2_55|\n            |     s2|      chr2|      62|s2_chr2_55|\n            |     s2|      chr2|      70|s2_chr2_55|\n            +-------+----------+--------+----------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        # By adding previous position, the cluster boundary can be identified:\n        previous_position = f.lag(position).over(\n            Window.partitionBy(study, chromosome).orderBy(position)\n        )\n        # We consider a cluster boudary if subsequent snps are further than the defined window:\n        cluster_id = f.when(\n            (previous_position.isNull())\n            | (position - previous_position &gt; window_length),\n            f.concat_ws(\"_\", study, chromosome, position),\n        )\n        # The cluster identifier is propagated across every variant of the cluster:\n        return f.when(\n            cluster_id.isNull(),\n            f.last(cluster_id, ignorenulls=True).over(\n                Window.partitionBy(study, chromosome)\n                .orderBy(position)\n                .rowsBetween(Window.unboundedPreceding, Window.currentRow)\n            ),\n        ).otherwise(cluster_id)\n\n    @staticmethod\n    def _prune_peak(position: NDArray[np.float64], window_size: int) -&gt; DenseVector:\n        \"\"\"Establish lead snps based on their positions listed by p-value.\n\n        The function `find_peak` assigns lead SNPs based on their positions listed by p-value within a specified window size.\n\n        Args:\n            position (NDArray[np.float64]): positions of the SNPs sorted by p-value.\n            window_size (int): the distance in bp within which associations are clumped together around the lead snp.\n\n        Returns:\n            DenseVector: binary vector where 1 indicates a lead SNP and 0 indicates a non-lead SNP.\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.ml import functions as fml\n            &gt;&gt;&gt; from pyspark.ml.linalg import DenseVector\n            &gt;&gt;&gt; WindowBasedClumping._prune_peak(np.array((3, 9, 8, 4, 6)), 2)\n            DenseVector([1.0, 1.0, 0.0, 0.0, 1.0])\n\n        \"\"\"\n        # Initializing the lead list with zeroes:\n        is_lead = np.zeros(len(position))\n\n        # List containing indices of leads:\n        lead_indices: list[int] = []\n\n        # Looping through all positions:\n        for index in range(len(position)):\n            # Looping through leads to find out if they are within a window:\n            for lead_index in lead_indices:\n                # If any of the leads within the window:\n                if abs(position[lead_index] - position[index]) &lt; window_size:\n                    # Skipping further checks:\n                    break\n            else:\n                # None of the leads were within the window:\n                lead_indices.append(index)\n                is_lead[index] = 1\n\n        return DenseVector(is_lead)\n\n    @classmethod\n    def clump(\n        cls: type[WindowBasedClumping],\n        summary_stats: SummaryStatistics,\n        window_length: int,\n        p_value_significance: float = 5e-8,\n    ) -&gt; StudyLocus:\n        \"\"\"Clump summary statistics by distance.\n\n        Args:\n            summary_stats (SummaryStatistics): summary statistics to clump\n            window_length (int): window length in basepair\n            p_value_significance (float): only more significant variants are considered\n\n        Returns:\n            StudyLocus: clumped summary statistics\n        \"\"\"\n        # Create window for locus clusters\n        # - variants where the distance between subsequent variants is below the defined threshold.\n        # - Variants are sorted by descending significance\n        cluster_window = Window.partitionBy(\n            \"studyId\", \"chromosome\", \"cluster_id\"\n        ).orderBy(f.col(\"pValueExponent\").asc(), f.col(\"pValueMantissa\").asc())\n\n        return StudyLocus(\n            _df=(\n                summary_stats\n                # Dropping snps below significance - all subsequent steps are done on significant variants:\n                .pvalue_filter(p_value_significance)\n                .df\n                # Clustering summary variants for efficient windowing (complexity reduction):\n                .withColumn(\n                    \"cluster_id\",\n                    WindowBasedClumping._cluster_peaks(\n                        f.col(\"studyId\"),\n                        f.col(\"chromosome\"),\n                        f.col(\"position\"),\n                        window_length,\n                    ),\n                )\n                # Within each cluster variants are ranked by significance:\n                .withColumn(\"pvRank\", f.row_number().over(cluster_window))\n                # Collect positions in cluster for the most significant variant (complexity reduction):\n                .withColumn(\n                    \"collectedPositions\",\n                    f.when(\n                        f.col(\"pvRank\") == 1,\n                        f.collect_list(f.col(\"position\")).over(\n                            cluster_window.rowsBetween(\n                                Window.currentRow, Window.unboundedFollowing\n                            )\n                        ),\n                    ).otherwise(f.array()),\n                )\n                # Get semi indices only ONCE per cluster:\n                .withColumn(\n                    \"semiIndices\",\n                    f.when(\n                        f.size(f.col(\"collectedPositions\")) &gt; 0,\n                        fml.vector_to_array(\n                            f.udf(WindowBasedClumping._prune_peak, VectorUDT())(\n                                fml.array_to_vector(f.col(\"collectedPositions\")),\n                                f.lit(window_length),\n                            )\n                        ),\n                    ),\n                )\n                # Propagating the result of the above calculation for all rows:\n                .withColumn(\n                    \"semiIndices\",\n                    f.when(\n                        f.col(\"semiIndices\").isNull(),\n                        f.first(f.col(\"semiIndices\"), ignorenulls=True).over(\n                            cluster_window\n                        ),\n                    ).otherwise(f.col(\"semiIndices\")),\n                )\n                # Keeping semi indices only:\n                .filter(f.col(\"semiIndices\")[f.col(\"pvRank\") - 1] &gt; 0)\n                .drop(\"pvRank\", \"collectedPositions\", \"semiIndices\", \"cluster_id\")\n                # Adding study-locus id:\n                .withColumn(\n                    \"studyLocusId\",\n                    StudyLocus.assign_study_locus_id(\n                        f.col(\"studyId\"), f.col(\"variantId\")\n                    ),\n                )\n                # Initialize QC column as array of strings:\n                .withColumn(\n                    \"qualityControls\", f.array().cast(t.ArrayType(t.StringType()))\n                )\n            ),\n            _schema=StudyLocus.get_schema(),\n        )\n\n    @classmethod\n    def clump_with_locus(\n        cls: type[WindowBasedClumping],\n        summary_stats: SummaryStatistics,\n        window_length: int,\n        p_value_significance: float = 5e-8,\n        p_value_baseline: float = 0.05,\n        locus_window_length: int | None = None,\n    ) -&gt; StudyLocus:\n        \"\"\"Clump significant associations while collecting locus around them.\n\n        Args:\n            summary_stats (SummaryStatistics): Input summary statistics dataset\n            window_length (int): Window size in  bp, used for distance based clumping.\n            p_value_significance (float): GWAS significance threshold used to filter peaks. Defaults to 5e-8.\n            p_value_baseline (float): Least significant threshold. Below this, all snps are dropped. Defaults to 0.05.\n            locus_window_length (int | None): The distance for collecting locus around the semi indices. Defaults to None.\n\n        Returns:\n            StudyLocus: StudyLocus after clumping with information about the `locus`\n        \"\"\"\n        # If no locus window provided, using the same value:\n        if locus_window_length is None:\n            locus_window_length = window_length\n\n        # Run distance based clumping on the summary stats:\n        clumped_dataframe = WindowBasedClumping.clump(\n            summary_stats,\n            window_length=window_length,\n            p_value_significance=p_value_significance,\n        ).df.alias(\"clumped\")\n\n        # Get list of columns from clumped dataset for further propagation:\n        clumped_columns = clumped_dataframe.columns\n\n        # Dropping variants not meeting the baseline criteria:\n        sumstats_baseline = summary_stats.pvalue_filter(p_value_baseline).df\n\n        # Renaming columns:\n        sumstats_baseline_renamed = sumstats_baseline.selectExpr(\n            *[f\"{col} as tag_{col}\" for col in sumstats_baseline.columns]\n        ).alias(\"sumstat\")\n\n        study_locus_df = (\n            sumstats_baseline_renamed\n            # Joining the two datasets together:\n            .join(\n                f.broadcast(clumped_dataframe),\n                on=[\n                    (f.col(\"sumstat.tag_studyId\") == f.col(\"clumped.studyId\"))\n                    &amp; (f.col(\"sumstat.tag_chromosome\") == f.col(\"clumped.chromosome\"))\n                    &amp; (\n                        f.col(\"sumstat.tag_position\")\n                        &gt;= (f.col(\"clumped.position\") - locus_window_length)\n                    )\n                    &amp; (\n                        f.col(\"sumstat.tag_position\")\n                        &lt;= (f.col(\"clumped.position\") + locus_window_length)\n                    )\n                ],\n                how=\"right\",\n            )\n            .withColumn(\n                \"locus\",\n                f.struct(\n                    f.col(\"tag_variantId\").alias(\"variantId\"),\n                    f.col(\"tag_beta\").alias(\"beta\"),\n                    f.col(\"tag_pValueMantissa\").alias(\"pValueMantissa\"),\n                    f.col(\"tag_pValueExponent\").alias(\"pValueExponent\"),\n                    f.col(\"tag_standardError\").alias(\"standardError\"),\n                ),\n            )\n            .groupby(\"studyLocusId\")\n            .agg(\n                *[\n                    f.first(col).alias(col)\n                    for col in clumped_columns\n                    if col != \"studyLocusId\"\n                ],\n                f.collect_list(f.col(\"locus\")).alias(\"locus\"),\n            )\n        )\n\n        return StudyLocus(\n            _df=study_locus_df,\n            _schema=StudyLocus.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/methods/clumping/#gentropy.method.window_based_clumping.WindowBasedClumping.clump","title":"<code>clump(summary_stats: SummaryStatistics, window_length: int, p_value_significance: float = 5e-08) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Clump summary statistics by distance.</p> <p>Parameters:</p> Name Type Description Default <code>summary_stats</code> <code>SummaryStatistics</code> <p>summary statistics to clump</p> required <code>window_length</code> <code>int</code> <p>window length in basepair</p> required <code>p_value_significance</code> <code>float</code> <p>only more significant variants are considered</p> <code>5e-08</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>clumped summary statistics</p> Source code in <code>src/gentropy/method/window_based_clumping.py</code> <pre><code>@classmethod\ndef clump(\n    cls: type[WindowBasedClumping],\n    summary_stats: SummaryStatistics,\n    window_length: int,\n    p_value_significance: float = 5e-8,\n) -&gt; StudyLocus:\n    \"\"\"Clump summary statistics by distance.\n\n    Args:\n        summary_stats (SummaryStatistics): summary statistics to clump\n        window_length (int): window length in basepair\n        p_value_significance (float): only more significant variants are considered\n\n    Returns:\n        StudyLocus: clumped summary statistics\n    \"\"\"\n    # Create window for locus clusters\n    # - variants where the distance between subsequent variants is below the defined threshold.\n    # - Variants are sorted by descending significance\n    cluster_window = Window.partitionBy(\n        \"studyId\", \"chromosome\", \"cluster_id\"\n    ).orderBy(f.col(\"pValueExponent\").asc(), f.col(\"pValueMantissa\").asc())\n\n    return StudyLocus(\n        _df=(\n            summary_stats\n            # Dropping snps below significance - all subsequent steps are done on significant variants:\n            .pvalue_filter(p_value_significance)\n            .df\n            # Clustering summary variants for efficient windowing (complexity reduction):\n            .withColumn(\n                \"cluster_id\",\n                WindowBasedClumping._cluster_peaks(\n                    f.col(\"studyId\"),\n                    f.col(\"chromosome\"),\n                    f.col(\"position\"),\n                    window_length,\n                ),\n            )\n            # Within each cluster variants are ranked by significance:\n            .withColumn(\"pvRank\", f.row_number().over(cluster_window))\n            # Collect positions in cluster for the most significant variant (complexity reduction):\n            .withColumn(\n                \"collectedPositions\",\n                f.when(\n                    f.col(\"pvRank\") == 1,\n                    f.collect_list(f.col(\"position\")).over(\n                        cluster_window.rowsBetween(\n                            Window.currentRow, Window.unboundedFollowing\n                        )\n                    ),\n                ).otherwise(f.array()),\n            )\n            # Get semi indices only ONCE per cluster:\n            .withColumn(\n                \"semiIndices\",\n                f.when(\n                    f.size(f.col(\"collectedPositions\")) &gt; 0,\n                    fml.vector_to_array(\n                        f.udf(WindowBasedClumping._prune_peak, VectorUDT())(\n                            fml.array_to_vector(f.col(\"collectedPositions\")),\n                            f.lit(window_length),\n                        )\n                    ),\n                ),\n            )\n            # Propagating the result of the above calculation for all rows:\n            .withColumn(\n                \"semiIndices\",\n                f.when(\n                    f.col(\"semiIndices\").isNull(),\n                    f.first(f.col(\"semiIndices\"), ignorenulls=True).over(\n                        cluster_window\n                    ),\n                ).otherwise(f.col(\"semiIndices\")),\n            )\n            # Keeping semi indices only:\n            .filter(f.col(\"semiIndices\")[f.col(\"pvRank\") - 1] &gt; 0)\n            .drop(\"pvRank\", \"collectedPositions\", \"semiIndices\", \"cluster_id\")\n            # Adding study-locus id:\n            .withColumn(\n                \"studyLocusId\",\n                StudyLocus.assign_study_locus_id(\n                    f.col(\"studyId\"), f.col(\"variantId\")\n                ),\n            )\n            # Initialize QC column as array of strings:\n            .withColumn(\n                \"qualityControls\", f.array().cast(t.ArrayType(t.StringType()))\n            )\n        ),\n        _schema=StudyLocus.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/methods/clumping/#gentropy.method.window_based_clumping.WindowBasedClumping.clump_with_locus","title":"<code>clump_with_locus(summary_stats: SummaryStatistics, window_length: int, p_value_significance: float = 5e-08, p_value_baseline: float = 0.05, locus_window_length: int | None = None) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Clump significant associations while collecting locus around them.</p> <p>Parameters:</p> Name Type Description Default <code>summary_stats</code> <code>SummaryStatistics</code> <p>Input summary statistics dataset</p> required <code>window_length</code> <code>int</code> <p>Window size in  bp, used for distance based clumping.</p> required <code>p_value_significance</code> <code>float</code> <p>GWAS significance threshold used to filter peaks. Defaults to 5e-8.</p> <code>5e-08</code> <code>p_value_baseline</code> <code>float</code> <p>Least significant threshold. Below this, all snps are dropped. Defaults to 0.05.</p> <code>0.05</code> <code>locus_window_length</code> <code>int | None</code> <p>The distance for collecting locus around the semi indices. Defaults to None.</p> <code>None</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>StudyLocus after clumping with information about the <code>locus</code></p> Source code in <code>src/gentropy/method/window_based_clumping.py</code> <pre><code>@classmethod\ndef clump_with_locus(\n    cls: type[WindowBasedClumping],\n    summary_stats: SummaryStatistics,\n    window_length: int,\n    p_value_significance: float = 5e-8,\n    p_value_baseline: float = 0.05,\n    locus_window_length: int | None = None,\n) -&gt; StudyLocus:\n    \"\"\"Clump significant associations while collecting locus around them.\n\n    Args:\n        summary_stats (SummaryStatistics): Input summary statistics dataset\n        window_length (int): Window size in  bp, used for distance based clumping.\n        p_value_significance (float): GWAS significance threshold used to filter peaks. Defaults to 5e-8.\n        p_value_baseline (float): Least significant threshold. Below this, all snps are dropped. Defaults to 0.05.\n        locus_window_length (int | None): The distance for collecting locus around the semi indices. Defaults to None.\n\n    Returns:\n        StudyLocus: StudyLocus after clumping with information about the `locus`\n    \"\"\"\n    # If no locus window provided, using the same value:\n    if locus_window_length is None:\n        locus_window_length = window_length\n\n    # Run distance based clumping on the summary stats:\n    clumped_dataframe = WindowBasedClumping.clump(\n        summary_stats,\n        window_length=window_length,\n        p_value_significance=p_value_significance,\n    ).df.alias(\"clumped\")\n\n    # Get list of columns from clumped dataset for further propagation:\n    clumped_columns = clumped_dataframe.columns\n\n    # Dropping variants not meeting the baseline criteria:\n    sumstats_baseline = summary_stats.pvalue_filter(p_value_baseline).df\n\n    # Renaming columns:\n    sumstats_baseline_renamed = sumstats_baseline.selectExpr(\n        *[f\"{col} as tag_{col}\" for col in sumstats_baseline.columns]\n    ).alias(\"sumstat\")\n\n    study_locus_df = (\n        sumstats_baseline_renamed\n        # Joining the two datasets together:\n        .join(\n            f.broadcast(clumped_dataframe),\n            on=[\n                (f.col(\"sumstat.tag_studyId\") == f.col(\"clumped.studyId\"))\n                &amp; (f.col(\"sumstat.tag_chromosome\") == f.col(\"clumped.chromosome\"))\n                &amp; (\n                    f.col(\"sumstat.tag_position\")\n                    &gt;= (f.col(\"clumped.position\") - locus_window_length)\n                )\n                &amp; (\n                    f.col(\"sumstat.tag_position\")\n                    &lt;= (f.col(\"clumped.position\") + locus_window_length)\n                )\n            ],\n            how=\"right\",\n        )\n        .withColumn(\n            \"locus\",\n            f.struct(\n                f.col(\"tag_variantId\").alias(\"variantId\"),\n                f.col(\"tag_beta\").alias(\"beta\"),\n                f.col(\"tag_pValueMantissa\").alias(\"pValueMantissa\"),\n                f.col(\"tag_pValueExponent\").alias(\"pValueExponent\"),\n                f.col(\"tag_standardError\").alias(\"standardError\"),\n            ),\n        )\n        .groupby(\"studyLocusId\")\n        .agg(\n            *[\n                f.first(col).alias(col)\n                for col in clumped_columns\n                if col != \"studyLocusId\"\n            ],\n            f.collect_list(f.col(\"locus\")).alias(\"locus\"),\n        )\n    )\n\n    return StudyLocus(\n        _df=study_locus_df,\n        _schema=StudyLocus.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/methods/clumping/#ld-based-clumping","title":"LD-based clumping:","text":""},{"location":"python_api/methods/clumping/#gentropy.method.clump.LDclumping","title":"<code>gentropy.method.clump.LDclumping</code>","text":"<p>LD clumping reports the most significant genetic associations in a region in terms of a smaller number of \u201cclumps\u201d of genetically linked SNPs.</p> Source code in <code>src/gentropy/method/clump.py</code> <pre><code>class LDclumping:\n    \"\"\"LD clumping reports the most significant genetic associations in a region in terms of a smaller number of \u201cclumps\u201d of genetically linked SNPs.\"\"\"\n\n    @staticmethod\n    def _is_lead_linked(\n        study_id: Column,\n        variant_id: Column,\n        p_value_exponent: Column,\n        p_value_mantissa: Column,\n        ld_set: Column,\n    ) -&gt; Column:\n        \"\"\"Evaluates whether a lead variant is linked to a tag (with lowest p-value) in the same studyLocus dataset.\n\n        Args:\n            study_id (Column): studyId\n            variant_id (Column): Lead variant id\n            p_value_exponent (Column): p-value exponent\n            p_value_mantissa (Column): p-value mantissa\n            ld_set (Column): Array of variants in LD with the lead variant\n\n        Returns:\n            Column: Boolean in which True indicates that the lead is linked to another tag in the same dataset.\n        \"\"\"\n        leads_in_study = f.collect_set(variant_id).over(Window.partitionBy(study_id))\n        tags_in_studylocus = f.array_union(\n            # Get all tag variants from the credible set per studyLocusId\n            f.transform(ld_set, lambda x: x.tagVariantId),\n            # And append the lead variant so that the intersection is the same for all studyLocusIds in a study\n            f.array(variant_id),\n        )\n        intersect_lead_tags = f.array_sort(\n            f.array_intersect(leads_in_study, tags_in_studylocus)\n        )\n        return (\n            # If the lead is in the credible set, we rank the peaks by p-value\n            f.when(\n                f.size(intersect_lead_tags) &gt; 0,\n                f.row_number().over(\n                    Window.partitionBy(study_id, intersect_lead_tags).orderBy(\n                        p_value_exponent, p_value_mantissa\n                    )\n                )\n                &gt; 1,\n            )\n            # If the intersection is empty (lead is not in the credible set or cred set is empty), the association is not linked\n            .otherwise(f.lit(False))\n        )\n\n    @classmethod\n    def clump(cls: type[LDclumping], associations: StudyLocus) -&gt; StudyLocus:\n        \"\"\"Perform clumping on studyLocus dataset.\n\n        Args:\n            associations (StudyLocus): StudyLocus dataset\n\n        Returns:\n            StudyLocus: including flag and removing locus information for LD clumped loci.\n        \"\"\"\n        return associations.clump()\n</code></pre>"},{"location":"python_api/methods/clumping/#gentropy.method.clump.LDclumping.clump","title":"<code>clump(associations: StudyLocus) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Perform clumping on studyLocus dataset.</p> <p>Parameters:</p> Name Type Description Default <code>associations</code> <code>StudyLocus</code> <p>StudyLocus dataset</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>including flag and removing locus information for LD clumped loci.</p> Source code in <code>src/gentropy/method/clump.py</code> <pre><code>@classmethod\ndef clump(cls: type[LDclumping], associations: StudyLocus) -&gt; StudyLocus:\n    \"\"\"Perform clumping on studyLocus dataset.\n\n    Args:\n        associations (StudyLocus): StudyLocus dataset\n\n    Returns:\n        StudyLocus: including flag and removing locus information for LD clumped loci.\n    \"\"\"\n    return associations.clump()\n</code></pre>"},{"location":"python_api/methods/coloc/","title":"Coloc","text":""},{"location":"python_api/methods/coloc/#gentropy.method.colocalisation.Coloc","title":"<code>gentropy.method.colocalisation.Coloc</code>","text":"<p>Calculate bayesian colocalisation based on overlapping signals from credible sets.</p> <p>Based on the R COLOC package, which uses the Bayes factors from the credible set to estimate the posterior probability of colocalisation. This method makes the simplifying assumption that only one single causal variant exists for any given trait in any genomic region.</p> Hypothesis Description H<sub>0</sub> no association with either trait in the region H<sub>1</sub> association with trait 1 only H<sub>2</sub> association with trait 2 only H<sub>3</sub> both traits are associated, but have different single causal variants H<sub>4</sub> both traits are associated and share the same single causal variant <p>Bayes factors required</p> <p>Coloc requires the availability of Bayes factors (BF) for each variant in the credible set (<code>logBF</code> column).</p> Source code in <code>src/gentropy/method/colocalisation.py</code> <pre><code>class Coloc:\n    \"\"\"Calculate bayesian colocalisation based on overlapping signals from credible sets.\n\n    Based on the [R COLOC package](https://github.com/chr1swallace/coloc/blob/main/R/claudia.R), which uses the Bayes factors from the credible set to estimate the posterior probability of colocalisation. This method makes the simplifying assumption that **only one single causal variant** exists for any given trait in any genomic region.\n\n    | Hypothesis    | Description                                                           |\n    | ------------- | --------------------------------------------------------------------- |\n    | H&lt;sub&gt;0&lt;/sub&gt; | no association with either trait in the region                        |\n    | H&lt;sub&gt;1&lt;/sub&gt; | association with trait 1 only                                         |\n    | H&lt;sub&gt;2&lt;/sub&gt; | association with trait 2 only                                         |\n    | H&lt;sub&gt;3&lt;/sub&gt; | both traits are associated, but have different single causal variants |\n    | H&lt;sub&gt;4&lt;/sub&gt; | both traits are associated and share the same single causal variant   |\n\n    !!! warning \"Bayes factors required\"\n\n        Coloc requires the availability of Bayes factors (BF) for each variant in the credible set (`logBF` column).\n\n    \"\"\"\n\n    @staticmethod\n    def _get_logsum(log_bf: NDArray[np.float64]) -&gt; float:\n        \"\"\"Calculates logsum of vector.\n\n        This function calculates the log of the sum of the exponentiated\n        logs taking out the max, i.e. insuring that the sum is not Inf\n\n        Args:\n            log_bf (NDArray[np.float64]): log bayes factor\n\n        Returns:\n            float: logsum\n\n        Example:\n            &gt;&gt;&gt; l = [0.2, 0.1, 0.05, 0]\n            &gt;&gt;&gt; round(Coloc._get_logsum(l), 6)\n            1.476557\n        \"\"\"\n        themax = np.max(log_bf)\n        result = themax + np.log(np.sum(np.exp(log_bf - themax)))\n        return float(result)\n\n    @staticmethod\n    def _get_posteriors(all_bfs: NDArray[np.float64]) -&gt; DenseVector:\n        \"\"\"Calculate posterior probabilities for each hypothesis.\n\n        Args:\n            all_bfs (NDArray[np.float64]): h0-h4 bayes factors\n\n        Returns:\n            DenseVector: Posterior\n\n        Example:\n            &gt;&gt;&gt; l = np.array([0.2, 0.1, 0.05, 0])\n            &gt;&gt;&gt; Coloc._get_posteriors(l)\n            DenseVector([0.279, 0.2524, 0.2401, 0.2284])\n        \"\"\"\n        diff = all_bfs - Coloc._get_logsum(all_bfs)\n        bfs_posteriors = np.exp(diff)\n        return Vectors.dense(bfs_posteriors)\n\n    @classmethod\n    def colocalise(\n        cls: type[Coloc],\n        overlapping_signals: StudyLocusOverlap,\n        priorc1: float = 1e-4,\n        priorc2: float = 1e-4,\n        priorc12: float = 1e-5,\n    ) -&gt; Colocalisation:\n        \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n        Args:\n            overlapping_signals (StudyLocusOverlap): overlapping peaks\n            priorc1 (float): Prior on variant being causal for trait 1. Defaults to 1e-4.\n            priorc2 (float): Prior on variant being causal for trait 2. Defaults to 1e-4.\n            priorc12 (float): Prior on variant being causal for traits 1 and 2. Defaults to 1e-5.\n\n        Returns:\n            Colocalisation: Colocalisation results\n        \"\"\"\n        # register udfs\n        logsum = f.udf(Coloc._get_logsum, DoubleType())\n        posteriors = f.udf(Coloc._get_posteriors, VectorUDT())\n        return Colocalisation(\n            _df=(\n                overlapping_signals.df\n                # Before summing log_BF columns nulls need to be filled with 0:\n                .fillna(0, subset=[\"statistics.left_logBF\", \"statistics.right_logBF\"])\n                # Sum of log_BFs for each pair of signals\n                .withColumn(\n                    \"sum_log_bf\",\n                    f.col(\"statistics.left_logBF\") + f.col(\"statistics.right_logBF\"),\n                )\n                # Group by overlapping peak and generating dense vectors of log_BF:\n                .groupBy(\"chromosome\", \"leftStudyLocusId\", \"rightStudyLocusId\")\n                .agg(\n                    f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                    fml.array_to_vector(\n                        f.collect_list(f.col(\"statistics.left_logBF\"))\n                    ).alias(\"left_logBF\"),\n                    fml.array_to_vector(\n                        f.collect_list(f.col(\"statistics.right_logBF\"))\n                    ).alias(\"right_logBF\"),\n                    fml.array_to_vector(f.collect_list(f.col(\"sum_log_bf\"))).alias(\n                        \"sum_log_bf\"\n                    ),\n                )\n                .withColumn(\"logsum1\", logsum(f.col(\"left_logBF\")))\n                .withColumn(\"logsum2\", logsum(f.col(\"right_logBF\")))\n                .withColumn(\"logsum12\", logsum(f.col(\"sum_log_bf\")))\n                .drop(\"left_logBF\", \"right_logBF\", \"sum_log_bf\")\n                # Add priors\n                # priorc1 Prior on variant being causal for trait 1\n                .withColumn(\"priorc1\", f.lit(priorc1))\n                # priorc2 Prior on variant being causal for trait 2\n                .withColumn(\"priorc2\", f.lit(priorc2))\n                # priorc12 Prior on variant being causal for traits 1 and 2\n                .withColumn(\"priorc12\", f.lit(priorc12))\n                # h0-h2\n                .withColumn(\"lH0bf\", f.lit(0))\n                .withColumn(\"lH1bf\", f.log(f.col(\"priorc1\")) + f.col(\"logsum1\"))\n                .withColumn(\"lH2bf\", f.log(f.col(\"priorc2\")) + f.col(\"logsum2\"))\n                # h3\n                .withColumn(\"sumlogsum\", f.col(\"logsum1\") + f.col(\"logsum2\"))\n                # exclude null H3/H4s: due to sumlogsum == logsum12\n                .filter(f.col(\"sumlogsum\") != f.col(\"logsum12\"))\n                .withColumn(\"max\", f.greatest(\"sumlogsum\", \"logsum12\"))\n                .withColumn(\n                    \"logdiff\",\n                    (\n                        f.col(\"max\")\n                        + f.log(\n                            f.exp(f.col(\"sumlogsum\") - f.col(\"max\"))\n                            - f.exp(f.col(\"logsum12\") - f.col(\"max\"))\n                        )\n                    ),\n                )\n                .withColumn(\n                    \"lH3bf\",\n                    f.log(f.col(\"priorc1\"))\n                    + f.log(f.col(\"priorc2\"))\n                    + f.col(\"logdiff\"),\n                )\n                .drop(\"right_logsum\", \"left_logsum\", \"sumlogsum\", \"max\", \"logdiff\")\n                # h4\n                .withColumn(\"lH4bf\", f.log(f.col(\"priorc12\")) + f.col(\"logsum12\"))\n                # cleaning\n                .drop(\n                    \"priorc1\", \"priorc2\", \"priorc12\", \"logsum1\", \"logsum2\", \"logsum12\"\n                )\n                # posteriors\n                .withColumn(\n                    \"allBF\",\n                    fml.array_to_vector(\n                        f.array(\n                            f.col(\"lH0bf\"),\n                            f.col(\"lH1bf\"),\n                            f.col(\"lH2bf\"),\n                            f.col(\"lH3bf\"),\n                            f.col(\"lH4bf\"),\n                        )\n                    ),\n                )\n                .withColumn(\n                    \"posteriors\", fml.vector_to_array(posteriors(f.col(\"allBF\")))\n                )\n                .withColumn(\"h0\", f.col(\"posteriors\").getItem(0))\n                .withColumn(\"h1\", f.col(\"posteriors\").getItem(1))\n                .withColumn(\"h2\", f.col(\"posteriors\").getItem(2))\n                .withColumn(\"h3\", f.col(\"posteriors\").getItem(3))\n                .withColumn(\"h4\", f.col(\"posteriors\").getItem(4))\n                .withColumn(\"h4h3\", f.col(\"h4\") / f.col(\"h3\"))\n                .withColumn(\"log2h4h3\", f.log2(f.col(\"h4h3\")))\n                # clean up\n                .drop(\n                    \"posteriors\",\n                    \"allBF\",\n                    \"h4h3\",\n                    \"lH0bf\",\n                    \"lH1bf\",\n                    \"lH2bf\",\n                    \"lH3bf\",\n                    \"lH4bf\",\n                )\n                .withColumn(\"colocalisationMethod\", f.lit(\"COLOC\"))\n            ),\n            _schema=Colocalisation.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/methods/coloc/#gentropy.method.colocalisation.Coloc.colocalise","title":"<code>colocalise(overlapping_signals: StudyLocusOverlap, priorc1: float = 0.0001, priorc2: float = 0.0001, priorc12: float = 1e-05) -&gt; Colocalisation</code>  <code>classmethod</code>","text":"<p>Calculate bayesian colocalisation based on overlapping signals.</p> <p>Parameters:</p> Name Type Description Default <code>overlapping_signals</code> <code>StudyLocusOverlap</code> <p>overlapping peaks</p> required <code>priorc1</code> <code>float</code> <p>Prior on variant being causal for trait 1. Defaults to 1e-4.</p> <code>0.0001</code> <code>priorc2</code> <code>float</code> <p>Prior on variant being causal for trait 2. Defaults to 1e-4.</p> <code>0.0001</code> <code>priorc12</code> <code>float</code> <p>Prior on variant being causal for traits 1 and 2. Defaults to 1e-5.</p> <code>1e-05</code> <p>Returns:</p> Name Type Description <code>Colocalisation</code> <code>Colocalisation</code> <p>Colocalisation results</p> Source code in <code>src/gentropy/method/colocalisation.py</code> <pre><code>@classmethod\ndef colocalise(\n    cls: type[Coloc],\n    overlapping_signals: StudyLocusOverlap,\n    priorc1: float = 1e-4,\n    priorc2: float = 1e-4,\n    priorc12: float = 1e-5,\n) -&gt; Colocalisation:\n    \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n    Args:\n        overlapping_signals (StudyLocusOverlap): overlapping peaks\n        priorc1 (float): Prior on variant being causal for trait 1. Defaults to 1e-4.\n        priorc2 (float): Prior on variant being causal for trait 2. Defaults to 1e-4.\n        priorc12 (float): Prior on variant being causal for traits 1 and 2. Defaults to 1e-5.\n\n    Returns:\n        Colocalisation: Colocalisation results\n    \"\"\"\n    # register udfs\n    logsum = f.udf(Coloc._get_logsum, DoubleType())\n    posteriors = f.udf(Coloc._get_posteriors, VectorUDT())\n    return Colocalisation(\n        _df=(\n            overlapping_signals.df\n            # Before summing log_BF columns nulls need to be filled with 0:\n            .fillna(0, subset=[\"statistics.left_logBF\", \"statistics.right_logBF\"])\n            # Sum of log_BFs for each pair of signals\n            .withColumn(\n                \"sum_log_bf\",\n                f.col(\"statistics.left_logBF\") + f.col(\"statistics.right_logBF\"),\n            )\n            # Group by overlapping peak and generating dense vectors of log_BF:\n            .groupBy(\"chromosome\", \"leftStudyLocusId\", \"rightStudyLocusId\")\n            .agg(\n                f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                fml.array_to_vector(\n                    f.collect_list(f.col(\"statistics.left_logBF\"))\n                ).alias(\"left_logBF\"),\n                fml.array_to_vector(\n                    f.collect_list(f.col(\"statistics.right_logBF\"))\n                ).alias(\"right_logBF\"),\n                fml.array_to_vector(f.collect_list(f.col(\"sum_log_bf\"))).alias(\n                    \"sum_log_bf\"\n                ),\n            )\n            .withColumn(\"logsum1\", logsum(f.col(\"left_logBF\")))\n            .withColumn(\"logsum2\", logsum(f.col(\"right_logBF\")))\n            .withColumn(\"logsum12\", logsum(f.col(\"sum_log_bf\")))\n            .drop(\"left_logBF\", \"right_logBF\", \"sum_log_bf\")\n            # Add priors\n            # priorc1 Prior on variant being causal for trait 1\n            .withColumn(\"priorc1\", f.lit(priorc1))\n            # priorc2 Prior on variant being causal for trait 2\n            .withColumn(\"priorc2\", f.lit(priorc2))\n            # priorc12 Prior on variant being causal for traits 1 and 2\n            .withColumn(\"priorc12\", f.lit(priorc12))\n            # h0-h2\n            .withColumn(\"lH0bf\", f.lit(0))\n            .withColumn(\"lH1bf\", f.log(f.col(\"priorc1\")) + f.col(\"logsum1\"))\n            .withColumn(\"lH2bf\", f.log(f.col(\"priorc2\")) + f.col(\"logsum2\"))\n            # h3\n            .withColumn(\"sumlogsum\", f.col(\"logsum1\") + f.col(\"logsum2\"))\n            # exclude null H3/H4s: due to sumlogsum == logsum12\n            .filter(f.col(\"sumlogsum\") != f.col(\"logsum12\"))\n            .withColumn(\"max\", f.greatest(\"sumlogsum\", \"logsum12\"))\n            .withColumn(\n                \"logdiff\",\n                (\n                    f.col(\"max\")\n                    + f.log(\n                        f.exp(f.col(\"sumlogsum\") - f.col(\"max\"))\n                        - f.exp(f.col(\"logsum12\") - f.col(\"max\"))\n                    )\n                ),\n            )\n            .withColumn(\n                \"lH3bf\",\n                f.log(f.col(\"priorc1\"))\n                + f.log(f.col(\"priorc2\"))\n                + f.col(\"logdiff\"),\n            )\n            .drop(\"right_logsum\", \"left_logsum\", \"sumlogsum\", \"max\", \"logdiff\")\n            # h4\n            .withColumn(\"lH4bf\", f.log(f.col(\"priorc12\")) + f.col(\"logsum12\"))\n            # cleaning\n            .drop(\n                \"priorc1\", \"priorc2\", \"priorc12\", \"logsum1\", \"logsum2\", \"logsum12\"\n            )\n            # posteriors\n            .withColumn(\n                \"allBF\",\n                fml.array_to_vector(\n                    f.array(\n                        f.col(\"lH0bf\"),\n                        f.col(\"lH1bf\"),\n                        f.col(\"lH2bf\"),\n                        f.col(\"lH3bf\"),\n                        f.col(\"lH4bf\"),\n                    )\n                ),\n            )\n            .withColumn(\n                \"posteriors\", fml.vector_to_array(posteriors(f.col(\"allBF\")))\n            )\n            .withColumn(\"h0\", f.col(\"posteriors\").getItem(0))\n            .withColumn(\"h1\", f.col(\"posteriors\").getItem(1))\n            .withColumn(\"h2\", f.col(\"posteriors\").getItem(2))\n            .withColumn(\"h3\", f.col(\"posteriors\").getItem(3))\n            .withColumn(\"h4\", f.col(\"posteriors\").getItem(4))\n            .withColumn(\"h4h3\", f.col(\"h4\") / f.col(\"h3\"))\n            .withColumn(\"log2h4h3\", f.log2(f.col(\"h4h3\")))\n            # clean up\n            .drop(\n                \"posteriors\",\n                \"allBF\",\n                \"h4h3\",\n                \"lH0bf\",\n                \"lH1bf\",\n                \"lH2bf\",\n                \"lH3bf\",\n                \"lH4bf\",\n            )\n            .withColumn(\"colocalisationMethod\", f.lit(\"COLOC\"))\n        ),\n        _schema=Colocalisation.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/methods/ecaviar/","title":"eCAVIAR","text":""},{"location":"python_api/methods/ecaviar/#gentropy.method.colocalisation.ECaviar","title":"<code>gentropy.method.colocalisation.ECaviar</code>","text":"<p>ECaviar-based colocalisation analysis.</p> <p>It extends CAVIAR\u00a0framework to explicitly estimate the posterior probability that the same variant is causal in 2 studies while accounting for the uncertainty of LD. eCAVIAR computes the colocalization posterior probability (CLPP) by utilizing the marginal posterior probabilities. This framework allows for multiple variants to be causal in a single locus.</p> Source code in <code>src/gentropy/method/colocalisation.py</code> <pre><code>class ECaviar:\n    \"\"\"ECaviar-based colocalisation analysis.\n\n    It extends [CAVIAR](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5142122/#bib18)\u00a0framework to explicitly estimate the posterior probability that the same variant is causal in 2 studies while accounting for the uncertainty of LD. eCAVIAR computes the colocalization posterior probability (**CLPP**) by utilizing the marginal posterior probabilities. This framework allows for **multiple variants to be causal** in a single locus.\n    \"\"\"\n\n    @staticmethod\n    def _get_clpp(left_pp: Column, right_pp: Column) -&gt; Column:\n        \"\"\"Calculate the colocalisation posterior probability (CLPP).\n\n        If the fact that the same variant is found causal for two studies are independent events,\n        CLPP is defined as the product of posterior porbabilities that a variant is causal in both studies.\n\n        Args:\n            left_pp (Column): left posterior probability\n            right_pp (Column): right posterior probability\n\n        Returns:\n            Column: CLPP\n\n        Examples:\n            &gt;&gt;&gt; d = [{\"left_pp\": 0.5, \"right_pp\": 0.5}, {\"left_pp\": 0.25, \"right_pp\": 0.75}]\n            &gt;&gt;&gt; df = spark.createDataFrame(d)\n            &gt;&gt;&gt; df.withColumn(\"clpp\", ECaviar._get_clpp(f.col(\"left_pp\"), f.col(\"right_pp\"))).show()\n            +-------+--------+------+\n            |left_pp|right_pp|  clpp|\n            +-------+--------+------+\n            |    0.5|     0.5|  0.25|\n            |   0.25|    0.75|0.1875|\n            +-------+--------+------+\n            &lt;BLANKLINE&gt;\n\n        \"\"\"\n        return left_pp * right_pp\n\n    @classmethod\n    def colocalise(\n        cls: type[ECaviar], overlapping_signals: StudyLocusOverlap\n    ) -&gt; Colocalisation:\n        \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n        Args:\n            overlapping_signals (StudyLocusOverlap): overlapping signals.\n\n        Returns:\n            Colocalisation: colocalisation results based on eCAVIAR.\n        \"\"\"\n        return Colocalisation(\n            _df=(\n                overlapping_signals.df.withColumn(\n                    \"clpp\",\n                    ECaviar._get_clpp(\n                        f.col(\"statistics.left_posteriorProbability\"),\n                        f.col(\"statistics.right_posteriorProbability\"),\n                    ),\n                )\n                .groupBy(\"leftStudyLocusId\", \"rightStudyLocusId\", \"chromosome\")\n                .agg(\n                    f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                    f.sum(f.col(\"clpp\")).alias(\"clpp\"),\n                )\n                .withColumn(\"colocalisationMethod\", f.lit(\"eCAVIAR\"))\n            ),\n            _schema=Colocalisation.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/methods/ecaviar/#gentropy.method.colocalisation.ECaviar.colocalise","title":"<code>colocalise(overlapping_signals: StudyLocusOverlap) -&gt; Colocalisation</code>  <code>classmethod</code>","text":"<p>Calculate bayesian colocalisation based on overlapping signals.</p> <p>Parameters:</p> Name Type Description Default <code>overlapping_signals</code> <code>StudyLocusOverlap</code> <p>overlapping signals.</p> required <p>Returns:</p> Name Type Description <code>Colocalisation</code> <code>Colocalisation</code> <p>colocalisation results based on eCAVIAR.</p> Source code in <code>src/gentropy/method/colocalisation.py</code> <pre><code>@classmethod\ndef colocalise(\n    cls: type[ECaviar], overlapping_signals: StudyLocusOverlap\n) -&gt; Colocalisation:\n    \"\"\"Calculate bayesian colocalisation based on overlapping signals.\n\n    Args:\n        overlapping_signals (StudyLocusOverlap): overlapping signals.\n\n    Returns:\n        Colocalisation: colocalisation results based on eCAVIAR.\n    \"\"\"\n    return Colocalisation(\n        _df=(\n            overlapping_signals.df.withColumn(\n                \"clpp\",\n                ECaviar._get_clpp(\n                    f.col(\"statistics.left_posteriorProbability\"),\n                    f.col(\"statistics.right_posteriorProbability\"),\n                ),\n            )\n            .groupBy(\"leftStudyLocusId\", \"rightStudyLocusId\", \"chromosome\")\n            .agg(\n                f.count(\"*\").alias(\"numberColocalisingVariants\"),\n                f.sum(f.col(\"clpp\")).alias(\"clpp\"),\n            )\n            .withColumn(\"colocalisationMethod\", f.lit(\"eCAVIAR\"))\n        ),\n        _schema=Colocalisation.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/methods/ld_annotator/","title":"LDAnnotator","text":""},{"location":"python_api/methods/ld_annotator/#gentropy.method.ld.LDAnnotator","title":"<code>gentropy.method.ld.LDAnnotator</code>","text":"<p>Class to annotate linkage disequilibrium (LD) operations from GnomAD.</p> Source code in <code>src/gentropy/method/ld.py</code> <pre><code>class LDAnnotator:\n    \"\"\"Class to annotate linkage disequilibrium (LD) operations from GnomAD.\"\"\"\n\n    @staticmethod\n    def _calculate_weighted_r_overall(ld_set: Column) -&gt; Column:\n        \"\"\"Aggregation of weighted R information using ancestry proportions.\n\n        Args:\n            ld_set (Column): LD set\n\n        Returns:\n            Column: LD set with added 'r2Overall' field\n        \"\"\"\n        return f.transform(\n            ld_set,\n            lambda x: f.struct(\n                x[\"tagVariantId\"].alias(\"tagVariantId\"),\n                # r2Overall is the accumulated sum of each r2 relative to the population size\n                f.aggregate(\n                    x[\"rValues\"],\n                    f.lit(0.0),\n                    lambda acc, y: acc\n                    + f.coalesce(\n                        f.pow(y[\"r\"], 2) * y[\"relativeSampleSize\"], f.lit(0.0)\n                    ),  # we use coalesce to avoid problems when r/relativeSampleSize is null\n                ).alias(\"r2Overall\"),\n            ),\n        )\n\n    @staticmethod\n    def _add_population_size(ld_set: Column, study_populations: Column) -&gt; Column:\n        \"\"\"Add population size to each rValues entry in the ldSet.\n\n        Args:\n            ld_set (Column): LD set\n            study_populations (Column): Study populations\n\n        Returns:\n            Column: LD set with added 'relativeSampleSize' field\n        \"\"\"\n        # Create a population to relativeSampleSize map from the struct\n        populations_map = f.map_from_arrays(\n            study_populations[\"ldPopulation\"],\n            study_populations[\"relativeSampleSize\"],\n        )\n        return f.transform(\n            ld_set,\n            lambda x: f.struct(\n                x[\"tagVariantId\"].alias(\"tagVariantId\"),\n                f.transform(\n                    x[\"rValues\"],\n                    lambda y: f.struct(\n                        y[\"population\"].alias(\"population\"),\n                        y[\"r\"].alias(\"r\"),\n                        populations_map[y[\"population\"]].alias(\"relativeSampleSize\"),\n                    ),\n                ).alias(\"rValues\"),\n            ),\n        )\n\n    @classmethod\n    def ld_annotate(\n        cls: type[LDAnnotator],\n        associations: StudyLocus,\n        studies: StudyIndex,\n        ld_index: LDIndex,\n    ) -&gt; StudyLocus:\n        \"\"\"Annotate linkage disequilibrium (LD) information to a set of studyLocus.\n\n        This function:\n            1. Annotates study locus with population structure information from the study index\n            2. Joins the LD index to the StudyLocus\n            3. Adds the population size of the study to each rValues entry in the ldSet\n            4. Calculates the overall R weighted by the ancestry proportions in every given study.\n\n        Args:\n            associations (StudyLocus): Dataset to be LD annotated\n            studies (StudyIndex): Dataset with study information\n            ld_index (LDIndex): Dataset with LD information for every variant present in LD matrix\n\n        Returns:\n            StudyLocus: including additional column with LD information.\n        \"\"\"\n        return (\n            StudyLocus(\n                _df=(\n                    associations.df\n                    # Drop ldSet column if already available\n                    .select(*[col for col in associations.df.columns if col != \"ldSet\"])\n                    # Annotate study locus with population structure from study index\n                    .join(\n                        studies.df.select(\"studyId\", \"ldPopulationStructure\"),\n                        on=\"studyId\",\n                        how=\"left\",\n                    )\n                    # Bring LD information from LD Index\n                    .join(\n                        ld_index.df,\n                        on=[\"variantId\", \"chromosome\"],\n                        how=\"left\",\n                    )\n                    # Add population size to each rValues entry in the ldSet if population structure available:\n                    .withColumn(\n                        \"ldSet\",\n                        f.when(\n                            f.col(\"ldPopulationStructure\").isNotNull(),\n                            cls._add_population_size(\n                                f.col(\"ldSet\"), f.col(\"ldPopulationStructure\")\n                            ),\n                        ),\n                    )\n                    # Aggregate weighted R information using ancestry proportions\n                    .withColumn(\n                        \"ldSet\",\n                        f.when(\n                            f.col(\"ldPopulationStructure\").isNotNull(),\n                            cls._calculate_weighted_r_overall(f.col(\"ldSet\")),\n                        ),\n                    )\n                    .drop(\"ldPopulationStructure\")\n                ),\n                _schema=StudyLocus.get_schema(),\n            )\n            ._qc_no_population()\n            ._qc_unresolved_ld()\n        )\n</code></pre>"},{"location":"python_api/methods/ld_annotator/#gentropy.method.ld.LDAnnotator.ld_annotate","title":"<code>ld_annotate(associations: StudyLocus, studies: StudyIndex, ld_index: LDIndex) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Annotate linkage disequilibrium (LD) information to a set of studyLocus.</p> This function <ol> <li>Annotates study locus with population structure information from the study index</li> <li>Joins the LD index to the StudyLocus</li> <li>Adds the population size of the study to each rValues entry in the ldSet</li> <li>Calculates the overall R weighted by the ancestry proportions in every given study.</li> </ol> <p>Parameters:</p> Name Type Description Default <code>associations</code> <code>StudyLocus</code> <p>Dataset to be LD annotated</p> required <code>studies</code> <code>StudyIndex</code> <p>Dataset with study information</p> required <code>ld_index</code> <code>LDIndex</code> <p>Dataset with LD information for every variant present in LD matrix</p> required <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>including additional column with LD information.</p> Source code in <code>src/gentropy/method/ld.py</code> <pre><code>@classmethod\ndef ld_annotate(\n    cls: type[LDAnnotator],\n    associations: StudyLocus,\n    studies: StudyIndex,\n    ld_index: LDIndex,\n) -&gt; StudyLocus:\n    \"\"\"Annotate linkage disequilibrium (LD) information to a set of studyLocus.\n\n    This function:\n        1. Annotates study locus with population structure information from the study index\n        2. Joins the LD index to the StudyLocus\n        3. Adds the population size of the study to each rValues entry in the ldSet\n        4. Calculates the overall R weighted by the ancestry proportions in every given study.\n\n    Args:\n        associations (StudyLocus): Dataset to be LD annotated\n        studies (StudyIndex): Dataset with study information\n        ld_index (LDIndex): Dataset with LD information for every variant present in LD matrix\n\n    Returns:\n        StudyLocus: including additional column with LD information.\n    \"\"\"\n    return (\n        StudyLocus(\n            _df=(\n                associations.df\n                # Drop ldSet column if already available\n                .select(*[col for col in associations.df.columns if col != \"ldSet\"])\n                # Annotate study locus with population structure from study index\n                .join(\n                    studies.df.select(\"studyId\", \"ldPopulationStructure\"),\n                    on=\"studyId\",\n                    how=\"left\",\n                )\n                # Bring LD information from LD Index\n                .join(\n                    ld_index.df,\n                    on=[\"variantId\", \"chromosome\"],\n                    how=\"left\",\n                )\n                # Add population size to each rValues entry in the ldSet if population structure available:\n                .withColumn(\n                    \"ldSet\",\n                    f.when(\n                        f.col(\"ldPopulationStructure\").isNotNull(),\n                        cls._add_population_size(\n                            f.col(\"ldSet\"), f.col(\"ldPopulationStructure\")\n                        ),\n                    ),\n                )\n                # Aggregate weighted R information using ancestry proportions\n                .withColumn(\n                    \"ldSet\",\n                    f.when(\n                        f.col(\"ldPopulationStructure\").isNotNull(),\n                        cls._calculate_weighted_r_overall(f.col(\"ldSet\")),\n                    ),\n                )\n                .drop(\"ldPopulationStructure\")\n            ),\n            _schema=StudyLocus.get_schema(),\n        )\n        ._qc_no_population()\n        ._qc_unresolved_ld()\n    )\n</code></pre>"},{"location":"python_api/methods/pics/","title":"PICS","text":"<p>PICS Overview:</p> <p>PICS is a fine-mapping method designed to identify the most likely causal SNPs associated with a trait or disease within a genomic region. It leverages both haplotype information and the observed association patterns from genome-wide association studies (GWAS).</p> <p>Please refer to the original publication for in-depth details: PICS Publication.</p> <p>We use PICS for both GWAS clumping results and GWAS curated studies.</p>"},{"location":"python_api/methods/pics/#gentropy.method.pics.PICS","title":"<code>gentropy.method.pics.PICS</code>","text":"<p>Probabilistic Identification of Causal SNPs (PICS), an algorithm estimating the probability that an individual variant is causal considering the haplotype structure and observed pattern of association at the genetic locus.</p> Source code in <code>src/gentropy/method/pics.py</code> <pre><code>class PICS:\n    \"\"\"Probabilistic Identification of Causal SNPs (PICS), an algorithm estimating the probability that an individual variant is causal considering the haplotype structure and observed pattern of association at the genetic locus.\"\"\"\n\n    @staticmethod\n    def _pics_relative_posterior_probability(\n        neglog_p: float, pics_snp_mu: float, pics_snp_std: float\n    ) -&gt; float:\n        \"\"\"Compute the PICS posterior probability for a given SNP.\n\n        !!! info \"This probability needs to be scaled to take into account the probabilities of the other variants in the locus.\"\n\n        Args:\n            neglog_p (float): Negative log p-value of the lead variant\n            pics_snp_mu (float): Mean P value of the association between a SNP and a trait\n            pics_snp_std (float): Standard deviation for the P value of the association between a SNP and a trait\n\n        Returns:\n            float: Posterior probability of the association between a SNP and a trait\n\n        Examples:\n            &gt;&gt;&gt; rel_prob = PICS._pics_relative_posterior_probability(neglog_p=10.0, pics_snp_mu=1.0, pics_snp_std=10.0)\n            &gt;&gt;&gt; round(rel_prob, 3)\n            0.368\n        \"\"\"\n        return float(norm(pics_snp_mu, pics_snp_std).sf(neglog_p) * 2)\n\n    @staticmethod\n    def _pics_standard_deviation(neglog_p: float, r2: float, k: float) -&gt; float | None:\n        \"\"\"Compute the PICS standard deviation.\n\n        This distribution is obtained after a series of permutation tests described in the PICS method, and it is only\n        valid when the SNP is highly linked with the lead (r2 &gt; 0.5).\n\n        Args:\n            neglog_p (float): Negative log p-value of the lead variant\n            r2 (float): LD score between a given SNP and the lead variant\n            k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n        Returns:\n            float | None: Standard deviation for the P value of the association between a SNP and a trait\n\n        Examples:\n            &gt;&gt;&gt; PICS._pics_standard_deviation(neglog_p=1.0, r2=1.0, k=6.4)\n            0.0\n            &gt;&gt;&gt; round(PICS._pics_standard_deviation(neglog_p=10.0, r2=0.5, k=6.4), 3)\n            1.493\n            &gt;&gt;&gt; print(PICS._pics_standard_deviation(neglog_p=1.0, r2=0.0, k=6.4))\n            None\n        \"\"\"\n        return (\n            abs(((1 - (r2**0.5) ** k) ** 0.5) * (neglog_p**0.5) / 2)\n            if r2 &gt;= 0.5\n            else None\n        )\n\n    @staticmethod\n    def _pics_mu(neglog_p: float, r2: float) -&gt; float | None:\n        \"\"\"Compute the PICS mu that estimates the probability of association between a given SNP and the trait.\n\n        This distribution is obtained after a series of permutation tests described in the PICS method, and it is only\n        valid when the SNP is highly linked with the lead (r2 &gt; 0.5).\n\n        Args:\n            neglog_p (float): Negative log p-value of the lead variant\n            r2 (float): LD score between a given SNP and the lead variant\n\n        Returns:\n            float | None: Mean P value of the association between a SNP and a trait\n\n        Examples:\n            &gt;&gt;&gt; PICS._pics_mu(neglog_p=1.0, r2=1.0)\n            1.0\n            &gt;&gt;&gt; PICS._pics_mu(neglog_p=10.0, r2=0.5)\n            5.0\n            &gt;&gt;&gt; print(PICS._pics_mu(neglog_p=10.0, r2=0.3))\n            None\n        \"\"\"\n        return neglog_p * r2 if r2 &gt;= 0.5 else None\n\n    @staticmethod\n    def _finemap(\n        ld_set: list[Row], lead_neglog_p: float, k: float\n    ) -&gt; list[dict[str, Any]] | None:\n        \"\"\"Calculates the probability of a variant being causal in a study-locus context by applying the PICS method.\n\n        It is intended to be applied as an UDF in `PICS.finemap`, where each row is a StudyLocus association.\n        The function iterates over every SNP in the `ldSet` array, and it returns an updated locus with\n        its association signal and causality probability as of PICS.\n\n        Args:\n            ld_set (list[Row]): list of tagging variants after expanding the locus\n            lead_neglog_p (float): P value of the association signal between the lead variant and the study in the form of -log10.\n            k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n        Returns:\n            list[dict[str, Any]] | None: List of tagging variants with an estimation of the association signal and their posterior probability as of PICS.\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.sql import Row\n            &gt;&gt;&gt; ld_set = [\n            ...     Row(variantId=\"var1\", r2Overall=0.8),\n            ...     Row(variantId=\"var2\", r2Overall=1),\n            ... ]\n            &gt;&gt;&gt; PICS._finemap(ld_set, lead_neglog_p=10.0, k=6.4)\n            [{'variantId': 'var1', 'r2Overall': 0.8, 'standardError': 0.07420896512708416, 'posteriorProbability': 0.07116959886882368}, {'variantId': 'var2', 'r2Overall': 1, 'standardError': 0.9977000638225533, 'posteriorProbability': 0.9288304011311763}]\n            &gt;&gt;&gt; empty_ld_set = []\n            &gt;&gt;&gt; PICS._finemap(empty_ld_set, lead_neglog_p=10.0, k=6.4)\n            []\n            &gt;&gt;&gt; ld_set_with_no_r2 = [\n            ...     Row(variantId=\"var1\", r2Overall=None),\n            ...     Row(variantId=\"var2\", r2Overall=None),\n            ... ]\n            &gt;&gt;&gt; PICS._finemap(ld_set_with_no_r2, lead_neglog_p=10.0, k=6.4)\n            []\n        \"\"\"\n        if ld_set is None:\n            return None\n        elif not ld_set:\n            return []\n        tmp_credible_set = []\n        new_credible_set = []\n        # First iteration: calculation of mu, standard deviation, and the relative posterior probability\n        for tag_struct in ld_set:\n            tag_dict = (\n                tag_struct.asDict()\n            )  # tag_struct is of type pyspark.Row, we'll represent it as a dict\n            if (\n                not tag_dict[\"r2Overall\"]\n                or tag_dict[\"r2Overall\"] &lt; 0.5\n                or not lead_neglog_p\n            ):\n                # If PICS cannot be calculated, we drop the variant from the credible set\n                continue\n\n            pics_snp_mu = PICS._pics_mu(lead_neglog_p, tag_dict[\"r2Overall\"])\n            pics_snp_std = PICS._pics_standard_deviation(\n                lead_neglog_p, tag_dict[\"r2Overall\"], k\n            )\n            pics_snp_std = 0.001 if pics_snp_std == 0 else pics_snp_std\n            if pics_snp_mu is not None and pics_snp_std is not None:\n                posterior_probability = PICS._pics_relative_posterior_probability(\n                    lead_neglog_p, pics_snp_mu, pics_snp_std\n                )\n                tag_dict[\"standardError\"] = 10**-pics_snp_std\n                tag_dict[\"relativePosteriorProbability\"] = posterior_probability\n\n                tmp_credible_set.append(tag_dict)\n\n        # Second iteration: calculation of the sum of all the posteriors in each study-locus, so that we scale them between 0-1\n        total_posteriors = sum(\n            tag_dict.get(\"relativePosteriorProbability\", 0)\n            for tag_dict in tmp_credible_set\n        )\n\n        # Third iteration: calculation of the final posteriorProbability\n        for tag_dict in tmp_credible_set:\n            if total_posteriors != 0:\n                tag_dict[\"posteriorProbability\"] = float(\n                    tag_dict.get(\"relativePosteriorProbability\", 0) / total_posteriors\n                )\n            tag_dict.pop(\"relativePosteriorProbability\")\n            new_credible_set.append(tag_dict)\n        return new_credible_set\n\n    @classmethod\n    def finemap(\n        cls: type[PICS], associations: StudyLocus, k: float = 6.4\n    ) -&gt; StudyLocus:\n        \"\"\"Run PICS on a study locus.\n\n        !!! info \"Study locus needs to be LD annotated\"\n\n            The study locus needs to be LD annotated before PICS can be calculated.\n\n        Args:\n            associations (StudyLocus): Study locus to finemap using PICS\n            k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n        Returns:\n            StudyLocus: Study locus with PICS results\n        \"\"\"\n        # Register UDF by defining the structure of the output locus array of structs\n        # it also renames tagVariantId to variantId\n\n        picsed_ldset_schema = t.ArrayType(\n            t.StructType(\n                [\n                    t.StructField(\"tagVariantId\", t.StringType(), True),\n                    t.StructField(\"r2Overall\", t.DoubleType(), True),\n                    t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                    t.StructField(\"standardError\", t.DoubleType(), True),\n                ]\n            )\n        )\n        picsed_study_locus_schema = t.ArrayType(\n            t.StructType(\n                [\n                    t.StructField(\"variantId\", t.StringType(), True),\n                    t.StructField(\"r2Overall\", t.DoubleType(), True),\n                    t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                    t.StructField(\"standardError\", t.DoubleType(), True),\n                ]\n            )\n        )\n        _finemap_udf = f.udf(\n            lambda locus, neglog_p: PICS._finemap(locus, neglog_p, k),\n            picsed_ldset_schema,\n        )\n        non_picsable_expr = (\n            f.size(f.filter(f.col(\"ldSet\"), lambda x: x.r2Overall &gt;= 0.5)) == 0\n        )\n        return StudyLocus(\n            _df=(\n                associations.df\n                # Old locus column will be dropped if available\n                .select(*[col for col in associations.df.columns if col != \"locus\"])\n                # Estimate neglog_pvalue for the lead variant\n                .withColumn(\"neglog_pvalue\", associations.neglog_pvalue())\n                # New locus containing the PICS results\n                .withColumn(\n                    \"locus\",\n                    f.when(\n                        f.col(\"ldSet\").isNotNull(),\n                        _finemap_udf(f.col(\"ldSet\"), f.col(\"neglog_pvalue\")).cast(\n                            picsed_study_locus_schema\n                        ),\n                    ),\n                )\n                .withColumn(\n                    \"qualityControls\",\n                    StudyLocus.update_quality_flag(\n                        f.col(\"qualityControls\"),\n                        non_picsable_expr,\n                        StudyLocusQualityCheck.NOT_QUALIFYING_LD_BLOCK,\n                    ),\n                )\n                .withColumn(\n                    \"finemappingMethod\",\n                    f.coalesce(f.col(\"finemappingMethod\"), f.lit(\"pics\")),\n                )\n                .drop(\"neglog_pvalue\")\n            ),\n            _schema=StudyLocus.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/methods/pics/#gentropy.method.pics.PICS.finemap","title":"<code>finemap(associations: StudyLocus, k: float = 6.4) -&gt; StudyLocus</code>  <code>classmethod</code>","text":"<p>Run PICS on a study locus.</p> <p>Study locus needs to be LD annotated</p> <p>The study locus needs to be LD annotated before PICS can be calculated.</p> <p>Parameters:</p> Name Type Description Default <code>associations</code> <code>StudyLocus</code> <p>Study locus to finemap using PICS</p> required <code>k</code> <code>float</code> <p>Empiric constant that can be adjusted to fit the curve, 6.4 recommended.</p> <code>6.4</code> <p>Returns:</p> Name Type Description <code>StudyLocus</code> <code>StudyLocus</code> <p>Study locus with PICS results</p> Source code in <code>src/gentropy/method/pics.py</code> <pre><code>@classmethod\ndef finemap(\n    cls: type[PICS], associations: StudyLocus, k: float = 6.4\n) -&gt; StudyLocus:\n    \"\"\"Run PICS on a study locus.\n\n    !!! info \"Study locus needs to be LD annotated\"\n\n        The study locus needs to be LD annotated before PICS can be calculated.\n\n    Args:\n        associations (StudyLocus): Study locus to finemap using PICS\n        k (float): Empiric constant that can be adjusted to fit the curve, 6.4 recommended.\n\n    Returns:\n        StudyLocus: Study locus with PICS results\n    \"\"\"\n    # Register UDF by defining the structure of the output locus array of structs\n    # it also renames tagVariantId to variantId\n\n    picsed_ldset_schema = t.ArrayType(\n        t.StructType(\n            [\n                t.StructField(\"tagVariantId\", t.StringType(), True),\n                t.StructField(\"r2Overall\", t.DoubleType(), True),\n                t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                t.StructField(\"standardError\", t.DoubleType(), True),\n            ]\n        )\n    )\n    picsed_study_locus_schema = t.ArrayType(\n        t.StructType(\n            [\n                t.StructField(\"variantId\", t.StringType(), True),\n                t.StructField(\"r2Overall\", t.DoubleType(), True),\n                t.StructField(\"posteriorProbability\", t.DoubleType(), True),\n                t.StructField(\"standardError\", t.DoubleType(), True),\n            ]\n        )\n    )\n    _finemap_udf = f.udf(\n        lambda locus, neglog_p: PICS._finemap(locus, neglog_p, k),\n        picsed_ldset_schema,\n    )\n    non_picsable_expr = (\n        f.size(f.filter(f.col(\"ldSet\"), lambda x: x.r2Overall &gt;= 0.5)) == 0\n    )\n    return StudyLocus(\n        _df=(\n            associations.df\n            # Old locus column will be dropped if available\n            .select(*[col for col in associations.df.columns if col != \"locus\"])\n            # Estimate neglog_pvalue for the lead variant\n            .withColumn(\"neglog_pvalue\", associations.neglog_pvalue())\n            # New locus containing the PICS results\n            .withColumn(\n                \"locus\",\n                f.when(\n                    f.col(\"ldSet\").isNotNull(),\n                    _finemap_udf(f.col(\"ldSet\"), f.col(\"neglog_pvalue\")).cast(\n                        picsed_study_locus_schema\n                    ),\n                ),\n            )\n            .withColumn(\n                \"qualityControls\",\n                StudyLocus.update_quality_flag(\n                    f.col(\"qualityControls\"),\n                    non_picsable_expr,\n                    StudyLocusQualityCheck.NOT_QUALIFYING_LD_BLOCK,\n                ),\n            )\n            .withColumn(\n                \"finemappingMethod\",\n                f.coalesce(f.col(\"finemappingMethod\"), f.lit(\"pics\")),\n            )\n            .drop(\"neglog_pvalue\")\n        ),\n        _schema=StudyLocus.get_schema(),\n    )\n</code></pre>"},{"location":"python_api/methods/l2g/_l2g/","title":"Locus to Gene (L2G) model","text":"<p>The \u201clocus-to-gene\u201d (L2G) model derives features to prioritize likely causal genes at each GWAS locus based on genetic and functional genomics features. The main categories of predictive features are:</p> <ul> <li>Distance: (from credible set variants to gene)</li> <li>Molecular QTL Colocalization</li> <li>Chromatin Interaction: (e.g., promoter-capture Hi-C)</li> <li>Variant Pathogenicity: (from VEP)</li> </ul> <p>The L2G model is distinct from the variant-to-gene (V2G) pipeline in that it:</p> <ul> <li>Uses a machine-learning model to learn the weights of each evidence source based on a gold standard of previously identified causal genes.</li> <li>Relies upon fine-mapping and colocalization data.</li> </ul> <p>Some of the predictive features weight variant-to-gene (or genomic region-to-gene) evidence based on the posterior probability that the variant is causal, determined through fine-mapping of the GWAS association.</p> <p>Details of the L2G model are provided in our Nature Genetics publication (ref - Nature Genetics Publication):</p> <ul> <li>Title: An open approach to systematically prioritize causal variants and genes at all published human GWAS trait-associated loci.</li> <li>Authors: Mountjoy, E., Schmidt, E.M., Carmona, M. et al.</li> <li>Journal: Nat Genet 53, 1527\u20131533 (2021).</li> <li>DOI: 10.1038/s41588-021-00945-5</li> </ul>"},{"location":"python_api/methods/l2g/evaluator/","title":"W&B evaluator","text":""},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator","title":"<code>gentropy.method.l2g.evaluator.WandbEvaluator</code>","text":"<p>             Bases: <code>Evaluator</code></p> <p>Wrapper for pyspark Evaluators. It is expected that the user will provide an Evaluators, and this wrapper will log metrics from said evaluator to W&amp;B.</p> Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>class WandbEvaluator(Evaluator):\n    \"\"\"Wrapper for pyspark Evaluators. It is expected that the user will provide an Evaluators, and this wrapper will log metrics from said evaluator to W&amp;B.\"\"\"\n\n    spark_ml_evaluator: Param[Evaluator] = Param(\n        Params._dummy(), \"spark_ml_evaluator\", \"evaluator from pyspark.ml.evaluation\"\n    )\n\n    wandb_run: Param[Run] = Param(\n        Params._dummy(),\n        \"wandb_run\",\n        \"wandb run.  Expects an already initialized run.  You should set this, or wandb_run_kwargs, NOT BOTH\",\n    )\n\n    wandb_run_kwargs: Param[Any] = Param(\n        Params._dummy(),\n        \"wandb_run_kwargs\",\n        \"kwargs to be passed to wandb.init.  You should set this, or wandb_runId, NOT BOTH.  Setting this is useful when using with WandbCrossValdidator\",\n    )\n\n    wandb_runId: Param[str] = Param(  # noqa: N815\n        Params._dummy(),\n        \"wandb_runId\",\n        \"wandb run id.  if not providing an intialized run to wandb_run, a run with id wandb_runId will be resumed\",\n    )\n\n    wandb_project_name: Param[str] = Param(\n        Params._dummy(),\n        \"wandb_project_name\",\n        \"name of W&amp;B project\",\n        typeConverter=TypeConverters.toString,\n    )\n\n    label_values: Param[list[str]] = Param(\n        Params._dummy(),\n        \"label_values\",\n        \"for classification and multiclass classification, this is a list of values the label can assume\\nIf provided Multiclass or Multilabel evaluator without label_values, we'll figure it out from dataset passed through to evaluate.\",\n    )\n\n    _input_kwargs: Dict[str, Any]\n\n    @keyword_only\n    def __init__(\n        self: WandbEvaluator,\n        label_values: list[str] | None = None,\n        **kwargs: BinaryClassificationEvaluator\n        | MulticlassClassificationEvaluator\n        | Run,\n    ) -&gt; None:\n        \"\"\"Initialize a WandbEvaluator.\n\n        Args:\n            label_values (list[str] | None): List of label values.\n            **kwargs (BinaryClassificationEvaluator | MulticlassClassificationEvaluator | Run): Keyword arguments.\n        \"\"\"\n        if label_values is None:\n            label_values = []\n        super(Evaluator, self).__init__()\n\n        self.metrics = {\n            MulticlassClassificationEvaluator: [\n                \"f1\",\n                \"accuracy\",\n                \"weightedPrecision\",\n                \"weightedRecall\",\n                \"weightedTruePositiveRate\",\n                \"weightedFalsePositiveRate\",\n                \"weightedFMeasure\",\n                \"truePositiveRateByLabel\",\n                \"falsePositiveRateByLabel\",\n                \"precisionByLabel\",\n                \"recallByLabel\",\n                \"fMeasureByLabel\",\n                \"logLoss\",\n                \"hammingLoss\",\n            ],\n            BinaryClassificationEvaluator: [\"areaUnderROC\", \"areaUnderPR\"],\n        }\n\n        self._setDefault(label_values=[])\n        kwargs = self._input_kwargs\n        self._set(**kwargs)\n\n    def setspark_ml_evaluator(self: WandbEvaluator, value: Evaluator) -&gt; None:\n        \"\"\"Set the spark_ml_evaluator parameter.\n\n        Args:\n            value (Evaluator): Spark ML evaluator.\n        \"\"\"\n        self._set(spark_ml_evaluator=value)\n\n    def setlabel_values(self: WandbEvaluator, value: list[str]) -&gt; None:\n        \"\"\"Set the label_values parameter.\n\n        Args:\n            value (list[str]): List of label values.\n        \"\"\"\n        self._set(label_values=value)\n\n    def getspark_ml_evaluator(self: WandbEvaluator) -&gt; Evaluator:\n        \"\"\"Get the spark_ml_evaluator parameter.\n\n        Returns:\n            Evaluator: Spark ML evaluator.\n        \"\"\"\n        return self.getOrDefault(self.spark_ml_evaluator)\n\n    def getwandb_run(self: WandbEvaluator) -&gt; Run:\n        \"\"\"Get the wandb_run parameter.\n\n        Returns:\n            Run: Wandb run object.\n        \"\"\"\n        return self.getOrDefault(self.wandb_run)\n\n    def getwandb_project_name(self: WandbEvaluator) -&gt; Any:\n        \"\"\"Get the wandb_project_name parameter.\n\n        Returns:\n            Any: Name of the W&amp;B project.\n        \"\"\"\n        return self.getOrDefault(self.wandb_project_name)\n\n    def getlabel_values(self: WandbEvaluator) -&gt; list[str]:\n        \"\"\"Get the label_values parameter.\n\n        Returns:\n            list[str]: List of label values.\n        \"\"\"\n        return self.getOrDefault(self.label_values)\n\n    def _evaluate(self: WandbEvaluator, dataset: DataFrame) -&gt; float:\n        \"\"\"Evaluate the model on the given dataset.\n\n        Args:\n            dataset (DataFrame): Dataset to evaluate the model on.\n\n        Returns:\n            float: Metric value.\n        \"\"\"\n        dataset.persist()\n        metric_values: list[tuple[str, Any]] = []\n        label_values = self.getlabel_values()\n        spark_ml_evaluator: BinaryClassificationEvaluator | MulticlassClassificationEvaluator = (\n            self.getspark_ml_evaluator()  # type: ignore[assignment, unused-ignore]\n        )\n        run = self.getwandb_run()\n        evaluator_type = type(spark_ml_evaluator)\n        for metric in self.metrics[evaluator_type]:\n            if \"ByLabel\" in metric and label_values == []:\n                print(  # noqa: T201\n                    \"no label_values for the target have been provided and will be determined by the dataset.  This could take some time\"\n                )\n                label_values = [\n                    r[spark_ml_evaluator.getLabelCol()]\n                    for r in dataset.select(spark_ml_evaluator.getLabelCol())\n                    .distinct()\n                    .collect()\n                ]\n                if isinstance(label_values[0], list):\n                    merged = list(itertools.chain(*label_values))\n                    label_values = list(dict.fromkeys(merged).keys())\n                    self.setlabel_values(label_values)\n            for label in label_values:\n                out = spark_ml_evaluator.evaluate(\n                    dataset,\n                    {\n                        spark_ml_evaluator.metricLabel: label,  # type: ignore[assignment, unused-ignore]\n                        spark_ml_evaluator.metricName: metric,\n                    },\n                )\n                metric_values.append((f\"{metric}:{label}\", out))\n            out = spark_ml_evaluator.evaluate(\n                dataset, {spark_ml_evaluator.metricName: metric}\n            )\n            metric_values.append((f\"{metric}\", out))\n        run.log(dict(metric_values))\n        config = [\n            (f\"{k.parent.split('_')[0]}.{k.name}\", v)\n            for k, v in spark_ml_evaluator.extractParamMap().items()\n            if \"metric\" not in k.name\n        ]\n        run.config.update(dict(config))\n        return_metric = spark_ml_evaluator.evaluate(dataset)\n        dataset.unpersist()\n        return return_metric\n</code></pre>"},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator.__init__","title":"<code>__init__(label_values: list[str] | None = None, **kwargs: BinaryClassificationEvaluator | MulticlassClassificationEvaluator | Run) -&gt; None</code>","text":"<p>Initialize a WandbEvaluator.</p> <p>Parameters:</p> Name Type Description Default <code>label_values</code> <code>list[str] | None</code> <p>List of label values.</p> <code>None</code> <code>**kwargs</code> <code>BinaryClassificationEvaluator | MulticlassClassificationEvaluator | Run</code> <p>Keyword arguments.</p> <code>{}</code> Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>@keyword_only\ndef __init__(\n    self: WandbEvaluator,\n    label_values: list[str] | None = None,\n    **kwargs: BinaryClassificationEvaluator\n    | MulticlassClassificationEvaluator\n    | Run,\n) -&gt; None:\n    \"\"\"Initialize a WandbEvaluator.\n\n    Args:\n        label_values (list[str] | None): List of label values.\n        **kwargs (BinaryClassificationEvaluator | MulticlassClassificationEvaluator | Run): Keyword arguments.\n    \"\"\"\n    if label_values is None:\n        label_values = []\n    super(Evaluator, self).__init__()\n\n    self.metrics = {\n        MulticlassClassificationEvaluator: [\n            \"f1\",\n            \"accuracy\",\n            \"weightedPrecision\",\n            \"weightedRecall\",\n            \"weightedTruePositiveRate\",\n            \"weightedFalsePositiveRate\",\n            \"weightedFMeasure\",\n            \"truePositiveRateByLabel\",\n            \"falsePositiveRateByLabel\",\n            \"precisionByLabel\",\n            \"recallByLabel\",\n            \"fMeasureByLabel\",\n            \"logLoss\",\n            \"hammingLoss\",\n        ],\n        BinaryClassificationEvaluator: [\"areaUnderROC\", \"areaUnderPR\"],\n    }\n\n    self._setDefault(label_values=[])\n    kwargs = self._input_kwargs\n    self._set(**kwargs)\n</code></pre>"},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator.getlabel_values","title":"<code>getlabel_values() -&gt; list[str]</code>","text":"<p>Get the label_values parameter.</p> <p>Returns:</p> Type Description <code>list[str]</code> <p>list[str]: List of label values.</p> Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>def getlabel_values(self: WandbEvaluator) -&gt; list[str]:\n    \"\"\"Get the label_values parameter.\n\n    Returns:\n        list[str]: List of label values.\n    \"\"\"\n    return self.getOrDefault(self.label_values)\n</code></pre>"},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator.getspark_ml_evaluator","title":"<code>getspark_ml_evaluator() -&gt; Evaluator</code>","text":"<p>Get the spark_ml_evaluator parameter.</p> <p>Returns:</p> Name Type Description <code>Evaluator</code> <code>Evaluator</code> <p>Spark ML evaluator.</p> Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>def getspark_ml_evaluator(self: WandbEvaluator) -&gt; Evaluator:\n    \"\"\"Get the spark_ml_evaluator parameter.\n\n    Returns:\n        Evaluator: Spark ML evaluator.\n    \"\"\"\n    return self.getOrDefault(self.spark_ml_evaluator)\n</code></pre>"},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_project_name","title":"<code>getwandb_project_name() -&gt; Any</code>","text":"<p>Get the wandb_project_name parameter.</p> <p>Returns:</p> Name Type Description <code>Any</code> <code>Any</code> <p>Name of the W&amp;B project.</p> Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>def getwandb_project_name(self: WandbEvaluator) -&gt; Any:\n    \"\"\"Get the wandb_project_name parameter.\n\n    Returns:\n        Any: Name of the W&amp;B project.\n    \"\"\"\n    return self.getOrDefault(self.wandb_project_name)\n</code></pre>"},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator.getwandb_run","title":"<code>getwandb_run() -&gt; Run</code>","text":"<p>Get the wandb_run parameter.</p> <p>Returns:</p> Name Type Description <code>Run</code> <code>Run</code> <p>Wandb run object.</p> Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>def getwandb_run(self: WandbEvaluator) -&gt; Run:\n    \"\"\"Get the wandb_run parameter.\n\n    Returns:\n        Run: Wandb run object.\n    \"\"\"\n    return self.getOrDefault(self.wandb_run)\n</code></pre>"},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator.setlabel_values","title":"<code>setlabel_values(value: list[str]) -&gt; None</code>","text":"<p>Set the label_values parameter.</p> <p>Parameters:</p> Name Type Description Default <code>value</code> <code>list[str]</code> <p>List of label values.</p> required Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>def setlabel_values(self: WandbEvaluator, value: list[str]) -&gt; None:\n    \"\"\"Set the label_values parameter.\n\n    Args:\n        value (list[str]): List of label values.\n    \"\"\"\n    self._set(label_values=value)\n</code></pre>"},{"location":"python_api/methods/l2g/evaluator/#gentropy.method.l2g.evaluator.WandbEvaluator.setspark_ml_evaluator","title":"<code>setspark_ml_evaluator(value: Evaluator) -&gt; None</code>","text":"<p>Set the spark_ml_evaluator parameter.</p> <p>Parameters:</p> Name Type Description Default <code>value</code> <code>Evaluator</code> <p>Spark ML evaluator.</p> required Source code in <code>src/gentropy/method/l2g/evaluator.py</code> <pre><code>def setspark_ml_evaluator(self: WandbEvaluator, value: Evaluator) -&gt; None:\n    \"\"\"Set the spark_ml_evaluator parameter.\n\n    Args:\n        value (Evaluator): Spark ML evaluator.\n    \"\"\"\n    self._set(spark_ml_evaluator=value)\n</code></pre>"},{"location":"python_api/methods/l2g/feature_factory/","title":"L2G Feature Factory","text":""},{"location":"python_api/methods/l2g/feature_factory/#gentropy.method.l2g.feature_factory.ColocalisationFactory","title":"<code>gentropy.method.l2g.feature_factory.ColocalisationFactory</code>","text":"<p>Feature extraction in colocalisation.</p> Source code in <code>src/gentropy/method/l2g/feature_factory.py</code> <pre><code>class ColocalisationFactory:\n    \"\"\"Feature extraction in colocalisation.\"\"\"\n\n    @staticmethod\n    def _get_max_coloc_per_study_locus(\n        study_locus: StudyLocus,\n        studies: StudyIndex,\n        colocalisation: Colocalisation,\n        colocalisation_method: str,\n    ) -&gt; L2GFeature:\n        \"\"\"Get the maximum colocalisation posterior probability for each pair of overlapping study-locus per type of colocalisation method and QTL type.\n\n        Args:\n            study_locus (StudyLocus): Study locus dataset\n            studies (StudyIndex): Study index dataset\n            colocalisation (Colocalisation): Colocalisation dataset\n            colocalisation_method (str): Colocalisation method to extract the max from\n\n        Returns:\n            L2GFeature: Stores the features with the max coloc probabilities for each pair of study-locus\n\n        Raises:\n            ValueError: If the colocalisation method is not supported\n        \"\"\"\n        if colocalisation_method not in [\"COLOC\", \"eCAVIAR\"]:\n            raise ValueError(\n                f\"Colocalisation method {colocalisation_method} not supported\"\n            )\n        if colocalisation_method == \"COLOC\":\n            coloc_score_col_name = \"log2h4h3\"\n            coloc_feature_col_template = \"ColocLlrMaximum\"\n\n        elif colocalisation_method == \"eCAVIAR\":\n            coloc_score_col_name = \"clpp\"\n            coloc_feature_col_template = \"ColocClppMaximum\"\n\n        colocalising_study_locus = (\n            study_locus.df.select(\"studyLocusId\", \"studyId\")\n            # annotate studyLoci with overlapping IDs on the left - to just keep GWAS associations\n            .join(\n                colocalisation.df.selectExpr(\n                    \"leftStudyLocusId as studyLocusId\",\n                    \"rightStudyLocusId\",\n                    \"colocalisationMethod\",\n                    f\"{coloc_score_col_name} as coloc_score\",\n                ),\n                on=\"studyLocusId\",\n                how=\"inner\",\n            )\n            # bring study metadata to just keep QTL studies on the right\n            .join(\n                study_locus.df.selectExpr(\n                    \"studyLocusId as rightStudyLocusId\", \"studyId as right_studyId\"\n                ),\n                on=\"rightStudyLocusId\",\n                how=\"inner\",\n            )\n            .join(\n                f.broadcast(\n                    studies.df.selectExpr(\n                        \"studyId as right_studyId\",\n                        \"studyType as right_studyType\",\n                        \"geneId\",\n                    )\n                ),\n                on=\"right_studyId\",\n                how=\"inner\",\n            )\n            .filter(\n                (f.col(\"colocalisationMethod\") == colocalisation_method)\n                &amp; (f.col(\"right_studyType\") != \"gwas\")\n            )\n            .select(\"studyLocusId\", \"right_studyType\", \"geneId\", \"coloc_score\")\n        )\n\n        # Max PP calculation per studyLocus AND type of QTL\n        local_max = get_record_with_maximum_value(\n            colocalising_study_locus,\n            [\"studyLocusId\", \"right_studyType\", \"geneId\"],\n            \"coloc_score\",\n        ).persist()\n\n        intercept = 0.0001\n        neighbourhood_max = (\n            (\n                local_max.selectExpr(\n                    \"studyLocusId\", \"coloc_score as coloc_local_max\", \"geneId\"\n                )\n                .join(\n                    # Add maximum in the neighborhood\n                    get_record_with_maximum_value(\n                        colocalising_study_locus.withColumnRenamed(\n                            \"coloc_score\", \"coloc_neighborhood_max\"\n                        ),\n                        [\"studyLocusId\", \"right_studyType\"],\n                        \"coloc_neighborhood_max\",\n                    ).drop(\"geneId\"),\n                    on=\"studyLocusId\",\n                )\n                .withColumn(\n                    f\"{coloc_feature_col_template}Neighborhood\",\n                    f.log10(\n                        f.abs(\n                            f.col(\"coloc_local_max\")\n                            - f.col(\"coloc_neighborhood_max\")\n                            + f.lit(intercept)\n                        )\n                    ),\n                )\n            )\n            .drop(\"coloc_neighborhood_max\", \"coloc_local_max\")\n            .persist()\n        )\n\n        # Split feature per molQTL\n        local_dfs = []\n        nbh_dfs = []\n        qtl_types: list[str] = (\n            colocalising_study_locus.select(\"right_studyType\")\n            .distinct()\n            .toPandas()[\"right_studyType\"]\n            .tolist()\n        ) or [\"eqtl\", \"pqtl\", \"sqtl\"]\n        for qtl_type in qtl_types:\n            filtered_local_max = (\n                local_max.filter(f.col(\"right_studyType\") == qtl_type)\n                .withColumnRenamed(\n                    \"coloc_score\",\n                    f\"{qtl_type}{coloc_feature_col_template}\",\n                )\n                .drop(\"right_studyType\")\n            )\n            local_dfs.append(filtered_local_max)\n\n            filtered_neighbourhood_max = (\n                neighbourhood_max.filter(f.col(\"right_studyType\") == qtl_type)\n                .withColumnRenamed(\n                    f\"{coloc_feature_col_template}Neighborhood\",\n                    f\"{qtl_type}{coloc_feature_col_template}Neighborhood\",\n                )\n                .drop(\"right_studyType\")\n            )\n            nbh_dfs.append(filtered_neighbourhood_max)\n\n        wide_dfs = reduce(\n            lambda x, y: x.unionByName(y, allowMissingColumns=True),\n            local_dfs + nbh_dfs,\n        )\n\n        return L2GFeature(\n            _df=convert_from_wide_to_long(\n                wide_dfs.groupBy(\"studyLocusId\", \"geneId\").agg(\n                    *(\n                        f.first(f.col(c), ignorenulls=True).alias(c)\n                        for c in wide_dfs.columns\n                        if c\n                        not in [\n                            \"studyLocusId\",\n                            \"geneId\",\n                        ]\n                    )\n                ),\n                id_vars=(\"studyLocusId\", \"geneId\"),\n                var_name=\"featureName\",\n                value_name=\"featureValue\",\n            ),\n            _schema=L2GFeature.get_schema(),\n        )\n\n    @staticmethod\n    def _get_coloc_features(\n        study_locus: StudyLocus, studies: StudyIndex, colocalisation: Colocalisation\n    ) -&gt; L2GFeature:\n        \"\"\"Calls _get_max_coloc_per_study_locus for both methods and concatenates the results.\n\n        !!! note \"Colocalisation features are only available for the eCAVIAR results for now.\"\n\n        Args:\n            study_locus (StudyLocus): Study locus dataset\n            studies (StudyIndex): Study index dataset\n            colocalisation (Colocalisation): Colocalisation dataset\n\n        Returns:\n            L2GFeature: Stores the features with the max coloc probabilities for each pair of study-locus\n        \"\"\"\n        coloc_clpp = ColocalisationFactory._get_max_coloc_per_study_locus(\n            study_locus,\n            studies,\n            colocalisation,\n            \"eCAVIAR\",\n        )\n\n        return L2GFeature(\n            _df=coloc_clpp.df,\n            _schema=L2GFeature.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/methods/l2g/feature_factory/#gentropy.method.l2g.feature_factory.StudyLocusFactory","title":"<code>gentropy.method.l2g.feature_factory.StudyLocusFactory</code>","text":"<p>             Bases: <code>StudyLocus</code></p> <p>Feature extraction in study locus.</p> Source code in <code>src/gentropy/method/l2g/feature_factory.py</code> <pre><code>class StudyLocusFactory(StudyLocus):\n    \"\"\"Feature extraction in study locus.\"\"\"\n\n    @staticmethod\n    def _get_tss_distance_features(\n        study_locus: StudyLocus, distances: V2G\n    ) -&gt; L2GFeature:\n        \"\"\"Joins StudyLocus with the V2G to extract the minimum distance to a gene TSS of all variants in a StudyLocus credible set.\n\n        Args:\n            study_locus (StudyLocus): Study locus dataset\n            distances (V2G): Dataframe containing the distances of all variants to all genes TSS within a region\n\n        Returns:\n            L2GFeature: Stores the features with the minimum distance among all variants in the credible set and a gene TSS.\n\n        \"\"\"\n        wide_df = (\n            study_locus.filter_credible_set(CredibleInterval.IS95)\n            .df.select(\n                \"studyLocusId\",\n                \"variantId\",\n                f.explode(\"locus.variantId\").alias(\"tagVariantId\"),\n            )\n            .join(\n                distances.df.selectExpr(\n                    \"variantId as tagVariantId\", \"geneId\", \"distance\"\n                ),\n                on=\"tagVariantId\",\n                how=\"inner\",\n            )\n            .groupBy(\"studyLocusId\", \"geneId\")\n            .agg(\n                f.min(\"distance\").alias(\"distanceTssMinimum\"),\n                f.mean(\"distance\").alias(\"distanceTssMean\"),\n            )\n        )\n\n        return L2GFeature(\n            _df=convert_from_wide_to_long(\n                wide_df,\n                id_vars=(\"studyLocusId\", \"geneId\"),\n                var_name=\"featureName\",\n                value_name=\"featureValue\",\n            ),\n            _schema=L2GFeature.get_schema(),\n        )\n\n    @staticmethod\n    def _get_vep_features(\n        credible_set: StudyLocus,\n        v2g: V2G,\n    ) -&gt; L2GFeature:\n        \"\"\"Get the maximum VEP score for all variants in a locus's 95% credible set.\n\n        This informs about functional impact of the variants in the locus. For more information on variant consequences, see: https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html\n        Two metrics: max VEP score per study locus and gene, and max VEP score per study locus.\n\n\n        Args:\n            credible_set (StudyLocus): Study locus dataset with the associations to be annotated\n            v2g (V2G): V2G dataset with the variant/gene relationships and their consequences\n\n        Returns:\n            L2GFeature: Stores the features with the max VEP score.\n        \"\"\"\n\n        def _aggregate_vep_feature(\n            df: DataFrame,\n            aggregation_expr: Column,\n            aggregation_cols: list[str],\n            feature_name: str,\n        ) -&gt; DataFrame:\n            \"\"\"Extracts the maximum or average VEP score after grouping by the given columns. Different aggregations return different predictive annotations.\n\n            If the group_cols include \"geneId\", the maximum/mean VEP score per gene is returned.\n            Otherwise, the maximum/mean VEP score for all genes in the neighborhood of the locus is returned.\n\n            Args:\n                df (DataFrame): DataFrame with the VEP scores for each variant in a studyLocus\n                aggregation_expr (Column): Aggregation expression to apply\n                aggregation_cols (list[str]): Columns to group by\n                feature_name (str): Name of the feature to be returned\n\n            Returns:\n                DataFrame: DataFrame with the maximum VEP score per locus or per locus/gene\n            \"\"\"\n            if \"geneId\" in aggregation_cols:\n                return df.groupBy(aggregation_cols).agg(\n                    aggregation_expr.alias(feature_name)\n                )\n            return (\n                df.groupBy(aggregation_cols)\n                .agg(\n                    aggregation_expr.alias(feature_name),\n                    f.collect_set(\"geneId\").alias(\"geneId\"),\n                )\n                .withColumn(\"geneId\", f.explode(\"geneId\"))\n            )\n\n        credible_set_w_variant_consequences = (\n            credible_set.filter_credible_set(CredibleInterval.IS95)\n            .df.withColumn(\"variantInLocusId\", f.explode(f.col(\"locus.variantId\")))\n            .withColumn(\n                \"variantInLocusPosteriorProbability\",\n                f.explode(f.col(\"locus.posteriorProbability\")),\n            )\n            .join(\n                # Join with V2G to get variant consequences\n                v2g.df.filter(\n                    f.col(\"datasourceId\") == \"variantConsequence\"\n                ).withColumnRenamed(\"variantId\", \"variantInLocusId\"),\n                on=\"variantInLocusId\",\n            )\n            .withColumn(\n                \"weightedScore\",\n                f.col(\"score\") * f.col(\"variantInLocusPosteriorProbability\"),\n            )\n            .select(\n                \"studyLocusId\",\n                \"variantId\",\n                \"studyId\",\n                \"geneId\",\n                \"score\",\n                \"weightedScore\",\n            )\n            .distinct()\n            .persist()\n        )\n\n        return L2GFeature(\n            _df=convert_from_wide_to_long(\n                reduce(\n                    lambda x, y: x.unionByName(y, allowMissingColumns=True),\n                    [\n                        # Calculate overall max VEP score for all genes in the vicinity\n                        credible_set_w_variant_consequences.transform(\n                            _aggregate_vep_feature,\n                            f.max(\"score\"),\n                            [\"studyLocusId\"],\n                            \"vepMaximumNeighborhood\",\n                        ),\n                        # Calculate overall max VEP score per gene\n                        credible_set_w_variant_consequences.transform(\n                            _aggregate_vep_feature,\n                            f.max(\"score\"),\n                            [\"studyLocusId\", \"geneId\"],\n                            \"vepMaximum\",\n                        ),\n                        # Calculate mean VEP score for all genes in the vicinity\n                        credible_set_w_variant_consequences.transform(\n                            _aggregate_vep_feature,\n                            f.mean(\"weightedScore\"),\n                            [\"studyLocusId\"],\n                            \"vepMeanNeighborhood\",\n                        ),\n                        # Calculate mean VEP score per gene\n                        credible_set_w_variant_consequences.transform(\n                            _aggregate_vep_feature,\n                            f.mean(\"weightedScore\"),\n                            [\"studyLocusId\", \"geneId\"],\n                            \"vepMean\",\n                        ),\n                    ],\n                ),\n                id_vars=(\"studyLocusId\", \"geneId\"),\n                var_name=\"featureName\",\n                value_name=\"featureValue\",\n            ).filter(f.col(\"featureValue\").isNotNull()),\n            _schema=L2GFeature.get_schema(),\n        )\n</code></pre>"},{"location":"python_api/methods/l2g/model/","title":"L2G Model","text":""},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel","title":"<code>gentropy.method.l2g.model.LocusToGeneModel</code>  <code>dataclass</code>","text":"<p>Wrapper for the Locus to Gene classifier.</p> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>@dataclass\nclass LocusToGeneModel:\n    \"\"\"Wrapper for the Locus to Gene classifier.\"\"\"\n\n    features_list: list[str]\n    estimator: Any = None\n    pipeline: Pipeline = Pipeline(stages=[])\n    model: PipelineModel | None = None\n    wandb_l2g_project_name: str = \"otg_l2g\"\n\n    def __post_init__(self: LocusToGeneModel) -&gt; None:\n        \"\"\"Post init that adds the model to the ML pipeline.\"\"\"\n        label_indexer = StringIndexer(\n            inputCol=\"goldStandardSet\", outputCol=\"label\", handleInvalid=\"keep\"\n        )\n        vector_assembler = LocusToGeneModel.features_vector_assembler(\n            self.features_list\n        )\n\n        self.pipeline = Pipeline(\n            stages=[\n                label_indexer,\n                vector_assembler,\n            ]\n        )\n\n    def save(self: LocusToGeneModel, path: str) -&gt; None:\n        \"\"\"Saves fitted pipeline model to disk.\n\n        Args:\n            path (str): Path to save the model to\n\n        Raises:\n            ValueError: If the model has not been fitted yet\n        \"\"\"\n        if self.model is None:\n            raise ValueError(\"Model has not been fitted yet.\")\n        self.model.write().overwrite().save(path)\n\n    @property\n    def classifier(self: LocusToGeneModel) -&gt; Any:\n        \"\"\"Return the model.\n\n        Returns:\n            Any: An estimator object from Spark ML\n        \"\"\"\n        return self.estimator\n\n    @staticmethod\n    def features_vector_assembler(features_cols: list[str]) -&gt; VectorAssembler:\n        \"\"\"Spark transformer to assemble the feature columns into a vector.\n\n        Args:\n            features_cols (list[str]): List of feature columns to assemble\n\n        Returns:\n            VectorAssembler: Spark transformer to assemble the feature columns into a vector\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.ml.feature import VectorAssembler\n            &gt;&gt;&gt; df = spark.createDataFrame([(5.2, 3.5)], schema=\"feature_1 FLOAT, feature_2 FLOAT\")\n            &gt;&gt;&gt; assembler = LocusToGeneModel.features_vector_assembler([\"feature_1\", \"feature_2\"])\n            &gt;&gt;&gt; assembler.transform(df).show()\n            +---------+---------+--------------------+\n            |feature_1|feature_2|            features|\n            +---------+---------+--------------------+\n            |      5.2|      3.5|[5.19999980926513...|\n            +---------+---------+--------------------+\n            &lt;BLANKLINE&gt;\n        \"\"\"\n        return (\n            VectorAssembler(handleInvalid=\"error\")\n            .setInputCols(features_cols)\n            .setOutputCol(\"features\")\n        )\n\n    def log_to_wandb(\n        self: LocusToGeneModel,\n        results: DataFrame,\n        training_data: L2GFeatureMatrix,\n        evaluators: list[\n            BinaryClassificationEvaluator | MulticlassClassificationEvaluator\n        ],\n        wandb_run: Run,\n    ) -&gt; None:\n        \"\"\"Log evaluation results and feature importance to W&amp;B.\n\n        Args:\n            results (DataFrame): Dataframe containing the predictions\n            training_data (L2GFeatureMatrix): Training data used for the model. If provided, the table and the number of positive and negative labels will be logged to W&amp;B\n            evaluators (list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator]): List of Spark ML evaluators to use for evaluation\n            wandb_run (Run): W&amp;B run to log the results to\n        \"\"\"\n        ## Track evaluation metrics\n        for evaluator in evaluators:\n            wandb_evaluator = WandbEvaluator(\n                spark_ml_evaluator=evaluator, wandb_run=wandb_run\n            )\n            wandb_evaluator.evaluate(results)\n        ## Track feature importance\n        wandb_run.log({\"importances\": self.get_feature_importance()})\n        ## Track training set\n        training_table = Table(dataframe=training_data.df.toPandas())\n        wandb_run.log({\"trainingSet\": training_table})\n        # Count number of positive and negative labels\n        gs_counts_dict = {\n            \"goldStandard\" + row[\"goldStandardSet\"].capitalize(): row[\"count\"]\n            for row in training_data.df.groupBy(\"goldStandardSet\").count().collect()\n        }\n        wandb_run.log(gs_counts_dict)\n        # Missingness rates\n        wandb_run.log(\n            {\"missingnessRates\": training_data.calculate_feature_missingness_rate()}\n        )\n\n    @classmethod\n    def load_from_disk(\n        cls: Type[LocusToGeneModel], path: str, features_list: list[str]\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Load a fitted pipeline model from disk.\n\n        Args:\n            path (str): Path to the model\n            features_list (list[str]): List of features used for the model\n\n        Returns:\n            LocusToGeneModel: L2G model loaded from disk\n        \"\"\"\n        return cls(model=PipelineModel.load(path), features_list=features_list)\n\n    @classifier.setter  # type: ignore\n    def classifier(self: LocusToGeneModel, new_estimator: Any) -&gt; None:\n        \"\"\"Set the model.\n\n        Args:\n            new_estimator (Any): An estimator object from Spark ML\n        \"\"\"\n        self.estimator = new_estimator\n\n    def get_param_grid(self: LocusToGeneModel) -&gt; list[Any]:\n        \"\"\"Return the parameter grid for the model.\n\n        Returns:\n            list[Any]: List of parameter maps to use for cross validation\n        \"\"\"\n        return (\n            ParamGridBuilder()\n            .addGrid(self.estimator.max_depth, [3, 5, 7])\n            .addGrid(self.estimator.learning_rate, [0.01, 0.1, 1.0])\n            .build()\n        )\n\n    def add_pipeline_stage(\n        self: LocusToGeneModel, transformer: Transformer\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Adds a stage to the L2G pipeline.\n\n        Args:\n            transformer (Transformer): Spark transformer to add to the pipeline\n\n        Returns:\n            LocusToGeneModel: L2G model with the new transformer\n\n        Examples:\n            &gt;&gt;&gt; from pyspark.ml.regression import LinearRegression\n            &gt;&gt;&gt; estimator = LinearRegression()\n            &gt;&gt;&gt; test_model = LocusToGeneModel(features_list=[\"a\", \"b\"])\n            &gt;&gt;&gt; print(len(test_model.pipeline.getStages()))\n            2\n            &gt;&gt;&gt; print(len(test_model.add_pipeline_stage(estimator).pipeline.getStages()))\n            3\n        \"\"\"\n        pipeline_stages = self.pipeline.getStages()\n        new_stages = pipeline_stages + [transformer]\n        self.pipeline = Pipeline(stages=new_stages)\n        return self\n\n    def evaluate(\n        self: LocusToGeneModel,\n        results: DataFrame,\n        hyperparameters: dict[str, Any],\n        wandb_run_name: str | None,\n        training_data: L2GFeatureMatrix | None = None,\n    ) -&gt; None:\n        \"\"\"Perform evaluation of the model predictions for the test set and track the results with W&amp;B.\n\n        Args:\n            results (DataFrame): Dataframe containing the predictions\n            hyperparameters (dict[str, Any]): Hyperparameters used for the model\n            wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n            training_data (L2GFeatureMatrix | None): Training data used for the model. If provided, the ratio of positive to negative labels will be logged to W&amp;B\n        \"\"\"\n        binary_evaluator = BinaryClassificationEvaluator(\n            rawPredictionCol=\"rawPrediction\", labelCol=\"label\"\n        )\n        multi_evaluator = MulticlassClassificationEvaluator(\n            labelCol=\"label\", predictionCol=\"prediction\"\n        )\n\n        if wandb_run_name and training_data:\n            run = wandb_init(\n                project=self.wandb_l2g_project_name,\n                config=hyperparameters,\n                name=wandb_run_name,\n            )\n            if isinstance(run, Run):\n                self.log_to_wandb(\n                    results, training_data, [binary_evaluator, multi_evaluator], run\n                )\n                run.finish()\n\n    @property\n    def feature_name_map(self: LocusToGeneModel) -&gt; dict[str, str]:\n        \"\"\"Return a dictionary mapping encoded feature names to the original names.\n\n        Returns:\n            dict[str, str]: Feature name map of the model\n\n        Raises:\n            ValueError: If the model has not been fitted yet\n        \"\"\"\n        if not self.model:\n            raise ValueError(\"Model not fitted yet. `fit()` has to be called first.\")\n        elif isinstance(self.model.stages[1], VectorAssembler):\n            feature_names = self.model.stages[1].getInputCols()\n        return {f\"f{i}\": feature_name for i, feature_name in enumerate(feature_names)}\n\n    def get_feature_importance(self: LocusToGeneModel) -&gt; dict[str, float]:\n        \"\"\"Return dictionary with relative importances of every feature in the model. Feature names are encoded and have to be mapped back to their original names.\n\n        Returns:\n            dict[str, float]: Dictionary mapping feature names to their importance\n\n        Raises:\n            ValueError: If the model has not been fitted yet or is not an XGBoost model\n        \"\"\"\n        if not self.model or not isinstance(\n            self.model.stages[-1], SparkXGBClassifierModel\n        ):\n            raise ValueError(\n                f\"Model type {type(self.model)} not supported for feature importance.\"\n            )\n        importance_map = self.model.stages[-1].get_feature_importances()\n        return {self.feature_name_map[k]: v for k, v in importance_map.items()}\n\n    def fit(\n        self: LocusToGeneModel,\n        feature_matrix: L2GFeatureMatrix,\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Fit the pipeline to the feature matrix dataframe.\n\n        Args:\n            feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to fit the model to\n\n        Returns:\n            LocusToGeneModel: Fitted model\n        \"\"\"\n        self.model = self.pipeline.fit(feature_matrix.df)\n        return self\n\n    def predict(\n        self: LocusToGeneModel,\n        feature_matrix: L2GFeatureMatrix,\n    ) -&gt; DataFrame:\n        \"\"\"Apply the model to a given feature matrix dataframe. The feature matrix needs to be preprocessed first.\n\n        Args:\n            feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to apply the model to\n\n        Returns:\n            DataFrame: Dataframe with predictions\n\n        Raises:\n            ValueError: If the model has not been fitted yet\n        \"\"\"\n        if not self.model:\n            raise ValueError(\"Model not fitted yet. `fit()` has to be called first.\")\n        return self.model.transform(feature_matrix.df)\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.classifier","title":"<code>classifier: Any</code>  <code>property</code> <code>writable</code>","text":"<p>Return the model.</p> <p>Returns:</p> Name Type Description <code>Any</code> <code>Any</code> <p>An estimator object from Spark ML</p>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.feature_name_map","title":"<code>feature_name_map: dict[str, str]</code>  <code>property</code>","text":"<p>Return a dictionary mapping encoded feature names to the original names.</p> <p>Returns:</p> Type Description <code>dict[str, str]</code> <p>dict[str, str]: Feature name map of the model</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet</p>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.add_pipeline_stage","title":"<code>add_pipeline_stage(transformer: Transformer) -&gt; LocusToGeneModel</code>","text":"<p>Adds a stage to the L2G pipeline.</p> <p>Parameters:</p> Name Type Description Default <code>transformer</code> <code>Transformer</code> <p>Spark transformer to add to the pipeline</p> required <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>L2G model with the new transformer</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; from pyspark.ml.regression import LinearRegression\n&gt;&gt;&gt; estimator = LinearRegression()\n&gt;&gt;&gt; test_model = LocusToGeneModel(features_list=[\"a\", \"b\"])\n&gt;&gt;&gt; print(len(test_model.pipeline.getStages()))\n2\n&gt;&gt;&gt; print(len(test_model.add_pipeline_stage(estimator).pipeline.getStages()))\n3\n</code></pre> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def add_pipeline_stage(\n    self: LocusToGeneModel, transformer: Transformer\n) -&gt; LocusToGeneModel:\n    \"\"\"Adds a stage to the L2G pipeline.\n\n    Args:\n        transformer (Transformer): Spark transformer to add to the pipeline\n\n    Returns:\n        LocusToGeneModel: L2G model with the new transformer\n\n    Examples:\n        &gt;&gt;&gt; from pyspark.ml.regression import LinearRegression\n        &gt;&gt;&gt; estimator = LinearRegression()\n        &gt;&gt;&gt; test_model = LocusToGeneModel(features_list=[\"a\", \"b\"])\n        &gt;&gt;&gt; print(len(test_model.pipeline.getStages()))\n        2\n        &gt;&gt;&gt; print(len(test_model.add_pipeline_stage(estimator).pipeline.getStages()))\n        3\n    \"\"\"\n    pipeline_stages = self.pipeline.getStages()\n    new_stages = pipeline_stages + [transformer]\n    self.pipeline = Pipeline(stages=new_stages)\n    return self\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.evaluate","title":"<code>evaluate(results: DataFrame, hyperparameters: dict[str, Any], wandb_run_name: str | None, training_data: L2GFeatureMatrix | None = None) -&gt; None</code>","text":"<p>Perform evaluation of the model predictions for the test set and track the results with W&amp;B.</p> <p>Parameters:</p> Name Type Description Default <code>results</code> <code>DataFrame</code> <p>Dataframe containing the predictions</p> required <code>hyperparameters</code> <code>dict[str, Any]</code> <p>Hyperparameters used for the model</p> required <code>wandb_run_name</code> <code>str | None</code> <p>Descriptive name for the run to be tracked with W&amp;B</p> required <code>training_data</code> <code>L2GFeatureMatrix | None</code> <p>Training data used for the model. If provided, the ratio of positive to negative labels will be logged to W&amp;B</p> <code>None</code> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def evaluate(\n    self: LocusToGeneModel,\n    results: DataFrame,\n    hyperparameters: dict[str, Any],\n    wandb_run_name: str | None,\n    training_data: L2GFeatureMatrix | None = None,\n) -&gt; None:\n    \"\"\"Perform evaluation of the model predictions for the test set and track the results with W&amp;B.\n\n    Args:\n        results (DataFrame): Dataframe containing the predictions\n        hyperparameters (dict[str, Any]): Hyperparameters used for the model\n        wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n        training_data (L2GFeatureMatrix | None): Training data used for the model. If provided, the ratio of positive to negative labels will be logged to W&amp;B\n    \"\"\"\n    binary_evaluator = BinaryClassificationEvaluator(\n        rawPredictionCol=\"rawPrediction\", labelCol=\"label\"\n    )\n    multi_evaluator = MulticlassClassificationEvaluator(\n        labelCol=\"label\", predictionCol=\"prediction\"\n    )\n\n    if wandb_run_name and training_data:\n        run = wandb_init(\n            project=self.wandb_l2g_project_name,\n            config=hyperparameters,\n            name=wandb_run_name,\n        )\n        if isinstance(run, Run):\n            self.log_to_wandb(\n                results, training_data, [binary_evaluator, multi_evaluator], run\n            )\n            run.finish()\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.features_vector_assembler","title":"<code>features_vector_assembler(features_cols: list[str]) -&gt; VectorAssembler</code>  <code>staticmethod</code>","text":"<p>Spark transformer to assemble the feature columns into a vector.</p> <p>Parameters:</p> Name Type Description Default <code>features_cols</code> <code>list[str]</code> <p>List of feature columns to assemble</p> required <p>Returns:</p> Name Type Description <code>VectorAssembler</code> <code>VectorAssembler</code> <p>Spark transformer to assemble the feature columns into a vector</p> <p>Examples:</p> <pre><code>&gt;&gt;&gt; from pyspark.ml.feature import VectorAssembler\n&gt;&gt;&gt; df = spark.createDataFrame([(5.2, 3.5)], schema=\"feature_1 FLOAT, feature_2 FLOAT\")\n&gt;&gt;&gt; assembler = LocusToGeneModel.features_vector_assembler([\"feature_1\", \"feature_2\"])\n&gt;&gt;&gt; assembler.transform(df).show()\n+---------+---------+--------------------+\n|feature_1|feature_2|            features|\n+---------+---------+--------------------+\n|      5.2|      3.5|[5.19999980926513...|\n+---------+---------+--------------------+\n</code></pre> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>@staticmethod\ndef features_vector_assembler(features_cols: list[str]) -&gt; VectorAssembler:\n    \"\"\"Spark transformer to assemble the feature columns into a vector.\n\n    Args:\n        features_cols (list[str]): List of feature columns to assemble\n\n    Returns:\n        VectorAssembler: Spark transformer to assemble the feature columns into a vector\n\n    Examples:\n        &gt;&gt;&gt; from pyspark.ml.feature import VectorAssembler\n        &gt;&gt;&gt; df = spark.createDataFrame([(5.2, 3.5)], schema=\"feature_1 FLOAT, feature_2 FLOAT\")\n        &gt;&gt;&gt; assembler = LocusToGeneModel.features_vector_assembler([\"feature_1\", \"feature_2\"])\n        &gt;&gt;&gt; assembler.transform(df).show()\n        +---------+---------+--------------------+\n        |feature_1|feature_2|            features|\n        +---------+---------+--------------------+\n        |      5.2|      3.5|[5.19999980926513...|\n        +---------+---------+--------------------+\n        &lt;BLANKLINE&gt;\n    \"\"\"\n    return (\n        VectorAssembler(handleInvalid=\"error\")\n        .setInputCols(features_cols)\n        .setOutputCol(\"features\")\n    )\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.fit","title":"<code>fit(feature_matrix: L2GFeatureMatrix) -&gt; LocusToGeneModel</code>","text":"<p>Fit the pipeline to the feature matrix dataframe.</p> <p>Parameters:</p> Name Type Description Default <code>feature_matrix</code> <code>L2GFeatureMatrix</code> <p>Feature matrix dataframe to fit the model to</p> required <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>Fitted model</p> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def fit(\n    self: LocusToGeneModel,\n    feature_matrix: L2GFeatureMatrix,\n) -&gt; LocusToGeneModel:\n    \"\"\"Fit the pipeline to the feature matrix dataframe.\n\n    Args:\n        feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to fit the model to\n\n    Returns:\n        LocusToGeneModel: Fitted model\n    \"\"\"\n    self.model = self.pipeline.fit(feature_matrix.df)\n    return self\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.get_feature_importance","title":"<code>get_feature_importance() -&gt; dict[str, float]</code>","text":"<p>Return dictionary with relative importances of every feature in the model. Feature names are encoded and have to be mapped back to their original names.</p> <p>Returns:</p> Type Description <code>dict[str, float]</code> <p>dict[str, float]: Dictionary mapping feature names to their importance</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet or is not an XGBoost model</p> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def get_feature_importance(self: LocusToGeneModel) -&gt; dict[str, float]:\n    \"\"\"Return dictionary with relative importances of every feature in the model. Feature names are encoded and have to be mapped back to their original names.\n\n    Returns:\n        dict[str, float]: Dictionary mapping feature names to their importance\n\n    Raises:\n        ValueError: If the model has not been fitted yet or is not an XGBoost model\n    \"\"\"\n    if not self.model or not isinstance(\n        self.model.stages[-1], SparkXGBClassifierModel\n    ):\n        raise ValueError(\n            f\"Model type {type(self.model)} not supported for feature importance.\"\n        )\n    importance_map = self.model.stages[-1].get_feature_importances()\n    return {self.feature_name_map[k]: v for k, v in importance_map.items()}\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.get_param_grid","title":"<code>get_param_grid() -&gt; list[Any]</code>","text":"<p>Return the parameter grid for the model.</p> <p>Returns:</p> Type Description <code>list[Any]</code> <p>list[Any]: List of parameter maps to use for cross validation</p> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def get_param_grid(self: LocusToGeneModel) -&gt; list[Any]:\n    \"\"\"Return the parameter grid for the model.\n\n    Returns:\n        list[Any]: List of parameter maps to use for cross validation\n    \"\"\"\n    return (\n        ParamGridBuilder()\n        .addGrid(self.estimator.max_depth, [3, 5, 7])\n        .addGrid(self.estimator.learning_rate, [0.01, 0.1, 1.0])\n        .build()\n    )\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.load_from_disk","title":"<code>load_from_disk(path: str, features_list: list[str]) -&gt; LocusToGeneModel</code>  <code>classmethod</code>","text":"<p>Load a fitted pipeline model from disk.</p> <p>Parameters:</p> Name Type Description Default <code>path</code> <code>str</code> <p>Path to the model</p> required <code>features_list</code> <code>list[str]</code> <p>List of features used for the model</p> required <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>L2G model loaded from disk</p> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>@classmethod\ndef load_from_disk(\n    cls: Type[LocusToGeneModel], path: str, features_list: list[str]\n) -&gt; LocusToGeneModel:\n    \"\"\"Load a fitted pipeline model from disk.\n\n    Args:\n        path (str): Path to the model\n        features_list (list[str]): List of features used for the model\n\n    Returns:\n        LocusToGeneModel: L2G model loaded from disk\n    \"\"\"\n    return cls(model=PipelineModel.load(path), features_list=features_list)\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.log_to_wandb","title":"<code>log_to_wandb(results: DataFrame, training_data: L2GFeatureMatrix, evaluators: list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator], wandb_run: Run) -&gt; None</code>","text":"<p>Log evaluation results and feature importance to W&amp;B.</p> <p>Parameters:</p> Name Type Description Default <code>results</code> <code>DataFrame</code> <p>Dataframe containing the predictions</p> required <code>training_data</code> <code>L2GFeatureMatrix</code> <p>Training data used for the model. If provided, the table and the number of positive and negative labels will be logged to W&amp;B</p> required <code>evaluators</code> <code>list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator]</code> <p>List of Spark ML evaluators to use for evaluation</p> required <code>wandb_run</code> <code>Run</code> <p>W&amp;B run to log the results to</p> required Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def log_to_wandb(\n    self: LocusToGeneModel,\n    results: DataFrame,\n    training_data: L2GFeatureMatrix,\n    evaluators: list[\n        BinaryClassificationEvaluator | MulticlassClassificationEvaluator\n    ],\n    wandb_run: Run,\n) -&gt; None:\n    \"\"\"Log evaluation results and feature importance to W&amp;B.\n\n    Args:\n        results (DataFrame): Dataframe containing the predictions\n        training_data (L2GFeatureMatrix): Training data used for the model. If provided, the table and the number of positive and negative labels will be logged to W&amp;B\n        evaluators (list[BinaryClassificationEvaluator | MulticlassClassificationEvaluator]): List of Spark ML evaluators to use for evaluation\n        wandb_run (Run): W&amp;B run to log the results to\n    \"\"\"\n    ## Track evaluation metrics\n    for evaluator in evaluators:\n        wandb_evaluator = WandbEvaluator(\n            spark_ml_evaluator=evaluator, wandb_run=wandb_run\n        )\n        wandb_evaluator.evaluate(results)\n    ## Track feature importance\n    wandb_run.log({\"importances\": self.get_feature_importance()})\n    ## Track training set\n    training_table = Table(dataframe=training_data.df.toPandas())\n    wandb_run.log({\"trainingSet\": training_table})\n    # Count number of positive and negative labels\n    gs_counts_dict = {\n        \"goldStandard\" + row[\"goldStandardSet\"].capitalize(): row[\"count\"]\n        for row in training_data.df.groupBy(\"goldStandardSet\").count().collect()\n    }\n    wandb_run.log(gs_counts_dict)\n    # Missingness rates\n    wandb_run.log(\n        {\"missingnessRates\": training_data.calculate_feature_missingness_rate()}\n    )\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.predict","title":"<code>predict(feature_matrix: L2GFeatureMatrix) -&gt; DataFrame</code>","text":"<p>Apply the model to a given feature matrix dataframe. The feature matrix needs to be preprocessed first.</p> <p>Parameters:</p> Name Type Description Default <code>feature_matrix</code> <code>L2GFeatureMatrix</code> <p>Feature matrix dataframe to apply the model to</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>Dataframe with predictions</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet</p> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def predict(\n    self: LocusToGeneModel,\n    feature_matrix: L2GFeatureMatrix,\n) -&gt; DataFrame:\n    \"\"\"Apply the model to a given feature matrix dataframe. The feature matrix needs to be preprocessed first.\n\n    Args:\n        feature_matrix (L2GFeatureMatrix): Feature matrix dataframe to apply the model to\n\n    Returns:\n        DataFrame: Dataframe with predictions\n\n    Raises:\n        ValueError: If the model has not been fitted yet\n    \"\"\"\n    if not self.model:\n        raise ValueError(\"Model not fitted yet. `fit()` has to be called first.\")\n    return self.model.transform(feature_matrix.df)\n</code></pre>"},{"location":"python_api/methods/l2g/model/#gentropy.method.l2g.model.LocusToGeneModel.save","title":"<code>save(path: str) -&gt; None</code>","text":"<p>Saves fitted pipeline model to disk.</p> <p>Parameters:</p> Name Type Description Default <code>path</code> <code>str</code> <p>Path to save the model to</p> required <p>Raises:</p> Type Description <code>ValueError</code> <p>If the model has not been fitted yet</p> Source code in <code>src/gentropy/method/l2g/model.py</code> <pre><code>def save(self: LocusToGeneModel, path: str) -&gt; None:\n    \"\"\"Saves fitted pipeline model to disk.\n\n    Args:\n        path (str): Path to save the model to\n\n    Raises:\n        ValueError: If the model has not been fitted yet\n    \"\"\"\n    if self.model is None:\n        raise ValueError(\"Model has not been fitted yet.\")\n    self.model.write().overwrite().save(path)\n</code></pre>"},{"location":"python_api/methods/l2g/trainer/","title":"L2G Trainer","text":""},{"location":"python_api/methods/l2g/trainer/#gentropy.method.l2g.trainer.LocusToGeneTrainer","title":"<code>gentropy.method.l2g.trainer.LocusToGeneTrainer</code>  <code>dataclass</code>","text":"<p>Modelling of what is the most likely causal gene associated with a given locus.</p> Source code in <code>src/gentropy/method/l2g/trainer.py</code> <pre><code>@dataclass\nclass LocusToGeneTrainer:\n    \"\"\"Modelling of what is the most likely causal gene associated with a given locus.\"\"\"\n\n    _model: LocusToGeneModel\n    train_set: L2GFeatureMatrix\n\n    @classmethod\n    def train(\n        cls: type[LocusToGeneTrainer],\n        data: L2GFeatureMatrix,\n        l2g_model: LocusToGeneModel,\n        features_list: list[str],\n        evaluate: bool,\n        wandb_run_name: str | None = None,\n        model_path: str | None = None,\n        **hyperparams: dict[str, Any],\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Train the Locus to Gene model.\n\n        Args:\n            data (L2GFeatureMatrix): Feature matrix containing the data\n            l2g_model (LocusToGeneModel): Model to fit to the data on\n            features_list (list[str]): List of features to use for the model\n            evaluate (bool): Whether to evaluate the model on a test set\n            wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n            model_path (str | None): Path to save the model to\n            **hyperparams (dict[str, Any]): Hyperparameters to use for the model\n\n        Returns:\n            LocusToGeneModel: Trained model\n        \"\"\"\n        train, test = data.select_features(features_list).train_test_split(fraction=0.8)\n\n        model = l2g_model.add_pipeline_stage(l2g_model.estimator).fit(train)\n\n        if evaluate:\n            l2g_model.evaluate(\n                results=model.predict(test),\n                hyperparameters=hyperparams,\n                wandb_run_name=wandb_run_name,\n                training_data=train,\n            )\n        if model_path:\n            l2g_model.save(model_path)\n        return l2g_model\n\n    @classmethod\n    def cross_validate(\n        cls: type[LocusToGeneTrainer],\n        l2g_model: LocusToGeneModel,\n        data: L2GFeatureMatrix,\n        num_folds: int,\n        param_grid: Optional[list] = None,  # type: ignore\n    ) -&gt; LocusToGeneModel:\n        \"\"\"Perform k-fold cross validation on the model.\n\n        By providing a model with a parameter grid, this method will perform k-fold cross validation on the model for each\n        combination of parameters and return the best model.\n\n        Args:\n            l2g_model (LocusToGeneModel): Model to fit to the data on\n            data (L2GFeatureMatrix): Data to perform cross validation on\n            num_folds (int): Number of folds to use for cross validation\n            param_grid (Optional[list]): List of parameter maps to use for cross validation\n\n        Returns:\n            LocusToGeneModel: Trained model fitted with the best hyperparameters\n\n        Raises:\n            ValueError: Parameter grid is empty. Cannot perform cross-validation.\n            ValueError: Unable to retrieve the best model.\n        \"\"\"\n        evaluator = MulticlassClassificationEvaluator()\n        params_grid = param_grid or l2g_model.get_param_grid()\n        if not param_grid:\n            raise ValueError(\n                \"Parameter grid is empty. Cannot perform cross-validation.\"\n            )\n        cv = CrossValidator(\n            numFolds=num_folds,\n            estimator=l2g_model.estimator,\n            estimatorParamMaps=params_grid,\n            evaluator=evaluator,\n            parallelism=2,\n            collectSubModels=False,\n            seed=42,\n        )\n\n        l2g_model.add_pipeline_stage(cv)  # type: ignore[assignment, unused-ignore]\n\n        # Integrate the best model from the last stage of the pipeline\n        if (full_pipeline_model := l2g_model.fit(data).model) is None or not hasattr(\n            full_pipeline_model, \"stages\"\n        ):\n            raise ValueError(\"Unable to retrieve the best model.\")\n        l2g_model.model = full_pipeline_model.stages[-1].bestModel  # type: ignore[assignment, unused-ignore]\n        return l2g_model\n</code></pre>"},{"location":"python_api/methods/l2g/trainer/#gentropy.method.l2g.trainer.LocusToGeneTrainer.cross_validate","title":"<code>cross_validate(l2g_model: LocusToGeneModel, data: L2GFeatureMatrix, num_folds: int, param_grid: Optional[list] = None) -&gt; LocusToGeneModel</code>  <code>classmethod</code>","text":"<p>Perform k-fold cross validation on the model.</p> <p>By providing a model with a parameter grid, this method will perform k-fold cross validation on the model for each combination of parameters and return the best model.</p> <p>Parameters:</p> Name Type Description Default <code>l2g_model</code> <code>LocusToGeneModel</code> <p>Model to fit to the data on</p> required <code>data</code> <code>L2GFeatureMatrix</code> <p>Data to perform cross validation on</p> required <code>num_folds</code> <code>int</code> <p>Number of folds to use for cross validation</p> required <code>param_grid</code> <code>Optional[list]</code> <p>List of parameter maps to use for cross validation</p> <code>None</code> <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>Trained model fitted with the best hyperparameters</p> <p>Raises:</p> Type Description <code>ValueError</code> <p>Parameter grid is empty. Cannot perform cross-validation.</p> <code>ValueError</code> <p>Unable to retrieve the best model.</p> Source code in <code>src/gentropy/method/l2g/trainer.py</code> <pre><code>@classmethod\ndef cross_validate(\n    cls: type[LocusToGeneTrainer],\n    l2g_model: LocusToGeneModel,\n    data: L2GFeatureMatrix,\n    num_folds: int,\n    param_grid: Optional[list] = None,  # type: ignore\n) -&gt; LocusToGeneModel:\n    \"\"\"Perform k-fold cross validation on the model.\n\n    By providing a model with a parameter grid, this method will perform k-fold cross validation on the model for each\n    combination of parameters and return the best model.\n\n    Args:\n        l2g_model (LocusToGeneModel): Model to fit to the data on\n        data (L2GFeatureMatrix): Data to perform cross validation on\n        num_folds (int): Number of folds to use for cross validation\n        param_grid (Optional[list]): List of parameter maps to use for cross validation\n\n    Returns:\n        LocusToGeneModel: Trained model fitted with the best hyperparameters\n\n    Raises:\n        ValueError: Parameter grid is empty. Cannot perform cross-validation.\n        ValueError: Unable to retrieve the best model.\n    \"\"\"\n    evaluator = MulticlassClassificationEvaluator()\n    params_grid = param_grid or l2g_model.get_param_grid()\n    if not param_grid:\n        raise ValueError(\n            \"Parameter grid is empty. Cannot perform cross-validation.\"\n        )\n    cv = CrossValidator(\n        numFolds=num_folds,\n        estimator=l2g_model.estimator,\n        estimatorParamMaps=params_grid,\n        evaluator=evaluator,\n        parallelism=2,\n        collectSubModels=False,\n        seed=42,\n    )\n\n    l2g_model.add_pipeline_stage(cv)  # type: ignore[assignment, unused-ignore]\n\n    # Integrate the best model from the last stage of the pipeline\n    if (full_pipeline_model := l2g_model.fit(data).model) is None or not hasattr(\n        full_pipeline_model, \"stages\"\n    ):\n        raise ValueError(\"Unable to retrieve the best model.\")\n    l2g_model.model = full_pipeline_model.stages[-1].bestModel  # type: ignore[assignment, unused-ignore]\n    return l2g_model\n</code></pre>"},{"location":"python_api/methods/l2g/trainer/#gentropy.method.l2g.trainer.LocusToGeneTrainer.train","title":"<code>train(data: L2GFeatureMatrix, l2g_model: LocusToGeneModel, features_list: list[str], evaluate: bool, wandb_run_name: str | None = None, model_path: str | None = None, **hyperparams: dict[str, Any]) -&gt; LocusToGeneModel</code>  <code>classmethod</code>","text":"<p>Train the Locus to Gene model.</p> <p>Parameters:</p> Name Type Description Default <code>data</code> <code>L2GFeatureMatrix</code> <p>Feature matrix containing the data</p> required <code>l2g_model</code> <code>LocusToGeneModel</code> <p>Model to fit to the data on</p> required <code>features_list</code> <code>list[str]</code> <p>List of features to use for the model</p> required <code>evaluate</code> <code>bool</code> <p>Whether to evaluate the model on a test set</p> required <code>wandb_run_name</code> <code>str | None</code> <p>Descriptive name for the run to be tracked with W&amp;B</p> <code>None</code> <code>model_path</code> <code>str | None</code> <p>Path to save the model to</p> <code>None</code> <code>**hyperparams</code> <code>dict[str, Any]</code> <p>Hyperparameters to use for the model</p> <code>{}</code> <p>Returns:</p> Name Type Description <code>LocusToGeneModel</code> <code>LocusToGeneModel</code> <p>Trained model</p> Source code in <code>src/gentropy/method/l2g/trainer.py</code> <pre><code>@classmethod\ndef train(\n    cls: type[LocusToGeneTrainer],\n    data: L2GFeatureMatrix,\n    l2g_model: LocusToGeneModel,\n    features_list: list[str],\n    evaluate: bool,\n    wandb_run_name: str | None = None,\n    model_path: str | None = None,\n    **hyperparams: dict[str, Any],\n) -&gt; LocusToGeneModel:\n    \"\"\"Train the Locus to Gene model.\n\n    Args:\n        data (L2GFeatureMatrix): Feature matrix containing the data\n        l2g_model (LocusToGeneModel): Model to fit to the data on\n        features_list (list[str]): List of features to use for the model\n        evaluate (bool): Whether to evaluate the model on a test set\n        wandb_run_name (str | None): Descriptive name for the run to be tracked with W&amp;B\n        model_path (str | None): Path to save the model to\n        **hyperparams (dict[str, Any]): Hyperparameters to use for the model\n\n    Returns:\n        LocusToGeneModel: Trained model\n    \"\"\"\n    train, test = data.select_features(features_list).train_test_split(fraction=0.8)\n\n    model = l2g_model.add_pipeline_stage(l2g_model.estimator).fit(train)\n\n    if evaluate:\n        l2g_model.evaluate(\n            results=model.predict(test),\n            hyperparameters=hyperparams,\n            wandb_run_name=wandb_run_name,\n            training_data=train,\n        )\n    if model_path:\n        l2g_model.save(model_path)\n    return l2g_model\n</code></pre>"},{"location":"python_api/steps/_steps/","title":"Step","text":"<p>This section provides description for the <code>Step</code> class. Each <code>Step</code> uses its own set of Methods and Datasets and implements the logic necessary to read a set of inputs, perform the transformation and write the outputs. All steps are available through the command line interface when running the <code>gentropy</code> command.</p>"},{"location":"python_api/steps/colocalisation/","title":"colocalisation","text":""},{"location":"python_api/steps/colocalisation/#gentropy.colocalisation.ColocalisationStep","title":"<code>gentropy.colocalisation.ColocalisationStep</code>","text":"<p>Colocalisation step.</p> <p>This workflow runs colocalisation analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).</p> Source code in <code>src/gentropy/colocalisation.py</code> <pre><code>class ColocalisationStep:\n    \"\"\"Colocalisation step.\n\n    This workflow runs colocalisation analyses that assess the degree to which independent signals of the association share the same causal variant in a region of the genome, typically limited by linkage disequilibrium (LD).\n    \"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        credible_set_path: str,\n        study_index_path: str,\n        coloc_path: str,\n    ) -&gt; None:\n        \"\"\"Run Colocalisation step.\n\n        Args:\n            session (Session): Session object.\n            credible_set_path (str): Input credible sets path.\n            study_index_path (str): Input study index path.\n            coloc_path (str): Output Colocalisation path.\n        \"\"\"\n        # Extract\n        credible_set = StudyLocus.from_parquet(\n            session, credible_set_path, recursiveFileLookup=True\n        )\n        si = StudyIndex.from_parquet(\n            session, study_index_path, recursiveFileLookup=True\n        )\n\n        # Transform\n        overlaps = credible_set.filter_credible_set(\n            CredibleInterval.IS95\n        ).find_overlaps(si)\n        ecaviar_results = ECaviar.colocalise(overlaps)\n\n        # Load\n        ecaviar_results.df.write.mode(session.write_mode).parquet(coloc_path)\n</code></pre>"},{"location":"python_api/steps/colocalisation/#gentropy.colocalisation.ColocalisationStep.__init__","title":"<code>__init__(session: Session, credible_set_path: str, study_index_path: str, coloc_path: str) -&gt; None</code>","text":"<p>Run Colocalisation step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>credible_set_path</code> <code>str</code> <p>Input credible sets path.</p> required <code>study_index_path</code> <code>str</code> <p>Input study index path.</p> required <code>coloc_path</code> <code>str</code> <p>Output Colocalisation path.</p> required Source code in <code>src/gentropy/colocalisation.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    credible_set_path: str,\n    study_index_path: str,\n    coloc_path: str,\n) -&gt; None:\n    \"\"\"Run Colocalisation step.\n\n    Args:\n        session (Session): Session object.\n        credible_set_path (str): Input credible sets path.\n        study_index_path (str): Input study index path.\n        coloc_path (str): Output Colocalisation path.\n    \"\"\"\n    # Extract\n    credible_set = StudyLocus.from_parquet(\n        session, credible_set_path, recursiveFileLookup=True\n    )\n    si = StudyIndex.from_parquet(\n        session, study_index_path, recursiveFileLookup=True\n    )\n\n    # Transform\n    overlaps = credible_set.filter_credible_set(\n        CredibleInterval.IS95\n    ).find_overlaps(si)\n    ecaviar_results = ECaviar.colocalise(overlaps)\n\n    # Load\n    ecaviar_results.df.write.mode(session.write_mode).parquet(coloc_path)\n</code></pre>"},{"location":"python_api/steps/eqtl_catalogue/","title":"eqtl_catalogue","text":""},{"location":"python_api/steps/eqtl_catalogue/#gentropy.eqtl_catalogue.EqtlCatalogueStep","title":"<code>gentropy.eqtl_catalogue.EqtlCatalogueStep</code>","text":"<p>eQTL Catalogue ingestion step.</p> Source code in <code>src/gentropy/eqtl_catalogue.py</code> <pre><code>class EqtlCatalogueStep:\n    \"\"\"eQTL Catalogue ingestion step.\"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        eqtl_catalogue_paths_imported: str,\n        eqtl_catalogue_study_index_out: str,\n        eqtl_catalogue_summary_stats_out: str,\n    ) -&gt; None:\n        \"\"\"Run eQTL Catalogue ingestion step.\n\n        Args:\n            session (Session): Session object.\n            eqtl_catalogue_paths_imported (str): Input eQTL Catalogue study index path.\n            eqtl_catalogue_study_index_out (str): Output eQTL Catalogue study index path.\n            eqtl_catalogue_summary_stats_out (str): Output eQTL Catalogue summary stats path.\n        \"\"\"\n        # Fetch study index.\n        df = session.spark.read.option(\"delimiter\", \"\\t\").csv(\n            eqtl_catalogue_paths_imported, header=True\n        )\n        # Process partial study index.  At this point, it is not complete because we don't have the gene IDs, which we\n        # will only get once the summary stats are ingested.\n        study_index_df = EqtlCatalogueStudyIndex.from_source(df).df\n\n        # Fetch summary stats.\n        input_filenames = [row.summarystatsLocation for row in study_index_df.collect()]\n        summary_stats_df = (\n            session.spark.read.option(\"delimiter\", \"\\t\")\n            .csv(input_filenames, header=True)\n            .repartition(1280)\n        )\n        # Process summary stats.\n        summary_stats_df = EqtlCatalogueSummaryStats.from_source(summary_stats_df).df\n\n        # Add geneId column to the study index.\n        study_index_df = EqtlCatalogueStudyIndex.add_gene_to_study_id(\n            study_index_df,\n            summary_stats_df,\n        ).df\n\n        # Write study index.\n        study_index_df.write.mode(session.write_mode).parquet(\n            eqtl_catalogue_study_index_out\n        )\n        # Write summary stats.\n        (\n            summary_stats_df.sortWithinPartitions(\"position\")\n            .write.partitionBy(\"chromosome\")\n            .mode(session.write_mode)\n            .parquet(eqtl_catalogue_summary_stats_out)\n        )\n</code></pre>"},{"location":"python_api/steps/eqtl_catalogue/#gentropy.eqtl_catalogue.EqtlCatalogueStep.__init__","title":"<code>__init__(session: Session, eqtl_catalogue_paths_imported: str, eqtl_catalogue_study_index_out: str, eqtl_catalogue_summary_stats_out: str) -&gt; None</code>","text":"<p>Run eQTL Catalogue ingestion step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>eqtl_catalogue_paths_imported</code> <code>str</code> <p>Input eQTL Catalogue study index path.</p> required <code>eqtl_catalogue_study_index_out</code> <code>str</code> <p>Output eQTL Catalogue study index path.</p> required <code>eqtl_catalogue_summary_stats_out</code> <code>str</code> <p>Output eQTL Catalogue summary stats path.</p> required Source code in <code>src/gentropy/eqtl_catalogue.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    eqtl_catalogue_paths_imported: str,\n    eqtl_catalogue_study_index_out: str,\n    eqtl_catalogue_summary_stats_out: str,\n) -&gt; None:\n    \"\"\"Run eQTL Catalogue ingestion step.\n\n    Args:\n        session (Session): Session object.\n        eqtl_catalogue_paths_imported (str): Input eQTL Catalogue study index path.\n        eqtl_catalogue_study_index_out (str): Output eQTL Catalogue study index path.\n        eqtl_catalogue_summary_stats_out (str): Output eQTL Catalogue summary stats path.\n    \"\"\"\n    # Fetch study index.\n    df = session.spark.read.option(\"delimiter\", \"\\t\").csv(\n        eqtl_catalogue_paths_imported, header=True\n    )\n    # Process partial study index.  At this point, it is not complete because we don't have the gene IDs, which we\n    # will only get once the summary stats are ingested.\n    study_index_df = EqtlCatalogueStudyIndex.from_source(df).df\n\n    # Fetch summary stats.\n    input_filenames = [row.summarystatsLocation for row in study_index_df.collect()]\n    summary_stats_df = (\n        session.spark.read.option(\"delimiter\", \"\\t\")\n        .csv(input_filenames, header=True)\n        .repartition(1280)\n    )\n    # Process summary stats.\n    summary_stats_df = EqtlCatalogueSummaryStats.from_source(summary_stats_df).df\n\n    # Add geneId column to the study index.\n    study_index_df = EqtlCatalogueStudyIndex.add_gene_to_study_id(\n        study_index_df,\n        summary_stats_df,\n    ).df\n\n    # Write study index.\n    study_index_df.write.mode(session.write_mode).parquet(\n        eqtl_catalogue_study_index_out\n    )\n    # Write summary stats.\n    (\n        summary_stats_df.sortWithinPartitions(\"position\")\n        .write.partitionBy(\"chromosome\")\n        .mode(session.write_mode)\n        .parquet(eqtl_catalogue_summary_stats_out)\n    )\n</code></pre>"},{"location":"python_api/steps/finngen_studies/","title":"finngen_studies","text":""},{"location":"python_api/steps/finngen_studies/#gentropy.finngen_studies.FinnGenStudiesStep","title":"<code>gentropy.finngen_studies.FinnGenStudiesStep</code>","text":"<p>FinnGen study index generation step.</p> Source code in <code>src/gentropy/finngen_studies.py</code> <pre><code>class FinnGenStudiesStep:\n    \"\"\"FinnGen study index generation step.\"\"\"\n\n    def __init__(self, session: Session, finngen_study_index_out: str) -&gt; None:\n        \"\"\"Run FinnGen study index generation step.\n\n        Args:\n            session (Session): Session object.\n            finngen_study_index_out (str): Output FinnGen study index path.\n        \"\"\"\n        # Fetch study index.\n        FinnGenStudyIndex.from_source(session.spark).df.write.mode(\n            session.write_mode\n        ).parquet(finngen_study_index_out)\n</code></pre>"},{"location":"python_api/steps/finngen_studies/#gentropy.finngen_studies.FinnGenStudiesStep.__init__","title":"<code>__init__(session: Session, finngen_study_index_out: str) -&gt; None</code>","text":"<p>Run FinnGen study index generation step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>finngen_study_index_out</code> <code>str</code> <p>Output FinnGen study index path.</p> required Source code in <code>src/gentropy/finngen_studies.py</code> <pre><code>def __init__(self, session: Session, finngen_study_index_out: str) -&gt; None:\n    \"\"\"Run FinnGen study index generation step.\n\n    Args:\n        session (Session): Session object.\n        finngen_study_index_out (str): Output FinnGen study index path.\n    \"\"\"\n    # Fetch study index.\n    FinnGenStudyIndex.from_source(session.spark).df.write.mode(\n        session.write_mode\n    ).parquet(finngen_study_index_out)\n</code></pre>"},{"location":"python_api/steps/finngen_sumstat_preprocess/","title":"finngen_sumstat_preprocess","text":""},{"location":"python_api/steps/finngen_sumstat_preprocess/#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep","title":"<code>gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep</code>","text":"<p>FinnGen sumstats preprocessing.</p> Source code in <code>src/gentropy/finngen_sumstat_preprocess.py</code> <pre><code>class FinnGenSumstatPreprocessStep:\n    \"\"\"FinnGen sumstats preprocessing.\"\"\"\n\n    def __init__(\n        self, session: Session, raw_sumstats_path: str, out_sumstats_path: str\n    ) -&gt; None:\n        \"\"\"Run FinnGen summary stats preprocessing step.\n\n        Args:\n            session (Session): Session object.\n            raw_sumstats_path (str): Input raw summary stats path.\n            out_sumstats_path (str): Output summary stats path.\n        \"\"\"\n        # Process summary stats.\n        (\n            FinnGenSummaryStats.from_source(session.spark, raw_file=raw_sumstats_path)\n            .df.write.mode(session.write_mode)\n            .parquet(out_sumstats_path)\n        )\n</code></pre>"},{"location":"python_api/steps/finngen_sumstat_preprocess/#gentropy.finngen_sumstat_preprocess.FinnGenSumstatPreprocessStep.__init__","title":"<code>__init__(session: Session, raw_sumstats_path: str, out_sumstats_path: str) -&gt; None</code>","text":"<p>Run FinnGen summary stats preprocessing step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>raw_sumstats_path</code> <code>str</code> <p>Input raw summary stats path.</p> required <code>out_sumstats_path</code> <code>str</code> <p>Output summary stats path.</p> required Source code in <code>src/gentropy/finngen_sumstat_preprocess.py</code> <pre><code>def __init__(\n    self, session: Session, raw_sumstats_path: str, out_sumstats_path: str\n) -&gt; None:\n    \"\"\"Run FinnGen summary stats preprocessing step.\n\n    Args:\n        session (Session): Session object.\n        raw_sumstats_path (str): Input raw summary stats path.\n        out_sumstats_path (str): Output summary stats path.\n    \"\"\"\n    # Process summary stats.\n    (\n        FinnGenSummaryStats.from_source(session.spark, raw_file=raw_sumstats_path)\n        .df.write.mode(session.write_mode)\n        .parquet(out_sumstats_path)\n    )\n</code></pre>"},{"location":"python_api/steps/gene_index/","title":"gene_index","text":""},{"location":"python_api/steps/gene_index/#gentropy.gene_index.GeneIndexStep","title":"<code>gentropy.gene_index.GeneIndexStep</code>","text":"<p>Gene index step.</p> <p>This step generates a gene index dataset from an Open Targets Platform target dataset.</p> Source code in <code>src/gentropy/gene_index.py</code> <pre><code>class GeneIndexStep:\n    \"\"\"Gene index step.\n\n    This step generates a gene index dataset from an Open Targets Platform target dataset.\n    \"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        target_path: str,\n        gene_index_path: str,\n    ) -&gt; None:\n        \"\"\"Initialize step.\n\n        Args:\n            session (Session): Session object.\n            target_path (str): Input Open Targets Platform target dataset path.\n            gene_index_path (str): Output gene index dataset path.\n        \"\"\"\n        platform_target = session.spark.read.parquet(target_path)\n        # Transform\n        gene_index = OpenTargetsTarget.as_gene_index(platform_target)\n        # Load\n        gene_index.df.write.mode(session.write_mode).parquet(gene_index_path)\n</code></pre>"},{"location":"python_api/steps/gene_index/#gentropy.gene_index.GeneIndexStep.__init__","title":"<code>__init__(session: Session, target_path: str, gene_index_path: str) -&gt; None</code>","text":"<p>Initialize step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>target_path</code> <code>str</code> <p>Input Open Targets Platform target dataset path.</p> required <code>gene_index_path</code> <code>str</code> <p>Output gene index dataset path.</p> required Source code in <code>src/gentropy/gene_index.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    target_path: str,\n    gene_index_path: str,\n) -&gt; None:\n    \"\"\"Initialize step.\n\n    Args:\n        session (Session): Session object.\n        target_path (str): Input Open Targets Platform target dataset path.\n        gene_index_path (str): Output gene index dataset path.\n    \"\"\"\n    platform_target = session.spark.read.parquet(target_path)\n    # Transform\n    gene_index = OpenTargetsTarget.as_gene_index(platform_target)\n    # Load\n    gene_index.df.write.mode(session.write_mode).parquet(gene_index_path)\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_curation/","title":"gwas_catalog_study_curation","text":""},{"location":"python_api/steps/gwas_catalog_curation/#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep","title":"<code>gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep</code>","text":"<p>Annotate GWAS Catalog studies with additional curation and create a curation backlog.</p> Source code in <code>src/gentropy/gwas_catalog_study_curation.py</code> <pre><code>class GWASCatalogStudyCurationStep:\n    \"\"\"Annotate GWAS Catalog studies with additional curation and create a curation backlog.\"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        catalog_study_files: list[str],\n        catalog_ancestry_files: list[str],\n        catalog_sumstats_lut: str,\n        gwas_catalog_study_curation_out: str,\n        gwas_catalog_study_curation_file: str | None,\n    ) -&gt; None:\n        \"\"\"Run step to annotate and create backlog.\n\n        Args:\n            session (Session): Session object.\n            catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n            catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.\n            gwas_catalog_study_curation_out (str): Path for the updated curation table.\n            gwas_catalog_study_curation_file (str | None): Path to the original curation table. Optinal\n        \"\"\"\n        catalog_studies = session.spark.read.csv(\n            list(catalog_study_files), sep=\"\\t\", header=True\n        )\n        ancestry_lut = session.spark.read.csv(\n            list(catalog_ancestry_files), sep=\"\\t\", header=True\n        )\n        sumstats_lut = session.spark.read.csv(\n            catalog_sumstats_lut, sep=\"\\t\", header=False\n        )\n        gwas_catalog_study_curation = read_curation_table(\n            gwas_catalog_study_curation_file, session\n        )\n\n        # Process GWAS Catalog studies and get list of studies for curation:\n        (\n            StudyIndexGWASCatalogParser.from_source(\n                catalog_studies, ancestry_lut, sumstats_lut\n            )\n            # Adding existing curation:\n            .annotate_from_study_curation(gwas_catalog_study_curation)\n            # Extract new studies for curation:\n            .extract_studies_for_curation(gwas_catalog_study_curation)\n            # Save table:\n            .toPandas()\n            .to_csv(gwas_catalog_study_curation_out, sep=\"\\t\", index=False)\n        )\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_curation/#gentropy.gwas_catalog_study_curation.GWASCatalogStudyCurationStep.__init__","title":"<code>__init__(session: Session, catalog_study_files: list[str], catalog_ancestry_files: list[str], catalog_sumstats_lut: str, gwas_catalog_study_curation_out: str, gwas_catalog_study_curation_file: str | None) -&gt; None</code>","text":"<p>Run step to annotate and create backlog.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>catalog_study_files</code> <code>list[str]</code> <p>List of raw GWAS catalog studies file.</p> required <code>catalog_ancestry_files</code> <code>list[str]</code> <p>List of raw ancestry annotations files from GWAS Catalog.</p> required <code>catalog_sumstats_lut</code> <code>str</code> <p>GWAS Catalog summary statistics lookup table.</p> required <code>gwas_catalog_study_curation_out</code> <code>str</code> <p>Path for the updated curation table.</p> required <code>gwas_catalog_study_curation_file</code> <code>str | None</code> <p>Path to the original curation table. Optinal</p> required Source code in <code>src/gentropy/gwas_catalog_study_curation.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    catalog_study_files: list[str],\n    catalog_ancestry_files: list[str],\n    catalog_sumstats_lut: str,\n    gwas_catalog_study_curation_out: str,\n    gwas_catalog_study_curation_file: str | None,\n) -&gt; None:\n    \"\"\"Run step to annotate and create backlog.\n\n    Args:\n        session (Session): Session object.\n        catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n        catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.\n        gwas_catalog_study_curation_out (str): Path for the updated curation table.\n        gwas_catalog_study_curation_file (str | None): Path to the original curation table. Optinal\n    \"\"\"\n    catalog_studies = session.spark.read.csv(\n        list(catalog_study_files), sep=\"\\t\", header=True\n    )\n    ancestry_lut = session.spark.read.csv(\n        list(catalog_ancestry_files), sep=\"\\t\", header=True\n    )\n    sumstats_lut = session.spark.read.csv(\n        catalog_sumstats_lut, sep=\"\\t\", header=False\n    )\n    gwas_catalog_study_curation = read_curation_table(\n        gwas_catalog_study_curation_file, session\n    )\n\n    # Process GWAS Catalog studies and get list of studies for curation:\n    (\n        StudyIndexGWASCatalogParser.from_source(\n            catalog_studies, ancestry_lut, sumstats_lut\n        )\n        # Adding existing curation:\n        .annotate_from_study_curation(gwas_catalog_study_curation)\n        # Extract new studies for curation:\n        .extract_studies_for_curation(gwas_catalog_study_curation)\n        # Save table:\n        .toPandas()\n        .to_csv(gwas_catalog_study_curation_out, sep=\"\\t\", index=False)\n    )\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_inclusion/","title":"gwas_catalog_study_inclusion","text":""},{"location":"python_api/steps/gwas_catalog_inclusion/#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator","title":"<code>gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator</code>","text":"<p>GWAS Catalog study eligibility for ingestion based on curation and the provided criteria.</p> Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code> <pre><code>class GWASCatalogStudyInclusionGenerator:\n    \"\"\"GWAS Catalog study eligibility for ingestion based on curation and the provided criteria.\"\"\"\n\n    @staticmethod\n    def flag_eligible_studies(\n        study_index: StudyIndexGWASCatalog, criteria: str\n    ) -&gt; DataFrame:\n        \"\"\"Apply filter on GWAS Catalog studies based on the provided criteria.\n\n        Args:\n            study_index (StudyIndexGWASCatalog): complete study index to be filtered based on the provided filter set\n            criteria (str): name of the filter set to be applied.\n\n        Raises:\n            ValueError: if the provided filter set is not in the accepted values.\n\n        Returns:\n            DataFrame: filtered dataframe containing only eligible studies.\n        \"\"\"\n        filters: dict[str, Column] = {\n            # Filters applied on studies for ingesting curated associations:\n            \"curation\": (study_index.is_gwas() &amp; study_index.has_mapped_trait()),\n            # Filters applied on studies for ingesting summary statistics:\n            \"summary_stats\": (\n                study_index.is_gwas()\n                &amp; study_index.has_mapped_trait()\n                &amp; (~study_index.is_quality_flagged())\n                &amp; study_index.has_summarystats()\n            ),\n        }\n\n        if criteria not in filters:\n            raise ValueError(\n                f'Wrong value as filter set ({criteria}). Accepted: {\",\".join(filters.keys())}'\n            )\n\n        # Applying the relevant filter to the study:\n        return study_index.df.select(\n            \"studyId\",\n            \"studyType\",\n            \"traitFromSource\",\n            \"traitFromSourceMappedIds\",\n            \"qualityControls\",\n            \"hasSumstats\",\n            filters[criteria].alias(\"isEligible\"),\n        )\n\n    @staticmethod\n    def process_harmonised_list(studies: list[str], session: Session) -&gt; DataFrame:\n        \"\"\"Generate spark dataframe from the provided list.\n\n        Args:\n            studies (list[str]): list of path pointing to harmonised summary statistics.\n            session (Session): session\n\n        Returns:\n            DataFrame: column name is consistent with original implementatin\n        \"\"\"\n        return session.spark.createDataFrame([{\"_c0\": path} for path in studies])\n\n    @staticmethod\n    def get_gwas_catalog_study_index(\n        session: Session,\n        variant_annotation_path: str,\n        catalog_study_files: list[str],\n        catalog_ancestry_files: list[str],\n        harmonised_study_file: str,\n        catalog_associations_file: str,\n        gwas_catalog_study_curation_file: str,\n    ) -&gt; StudyIndexGWASCatalog:\n        \"\"\"Return GWAS Catalog study index.\n\n        Args:\n            session (Session): Session object.\n            variant_annotation_path (str): Input variant annotation path.\n            catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n            harmonised_study_file (str): GWAS Catalog summary statistics lookup table.\n            catalog_associations_file (str): Raw GWAS catalog associations file.\n            gwas_catalog_study_curation_file (str): file of the curation table. Optional.\n\n        Returns:\n            StudyIndexGWASCatalog: Completely processed and fully annotated study index.\n        \"\"\"\n        # Extract\n        va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n        catalog_studies = session.spark.read.csv(\n            list(catalog_study_files), sep=\"\\t\", header=True\n        )\n        ancestry_lut = session.spark.read.csv(\n            list(catalog_ancestry_files), sep=\"\\t\", header=True\n        )\n        sumstats_lut = session.spark.read.csv(\n            harmonised_study_file, sep=\"\\t\", header=False\n        )\n        catalog_associations = session.spark.read.csv(\n            catalog_associations_file, sep=\"\\t\", header=True\n        ).persist()\n        gwas_catalog_study_curation = read_curation_table(\n            gwas_catalog_study_curation_file, session\n        )\n\n        # Transform\n        study_index, _ = GWASCatalogStudySplitter.split(\n            StudyIndexGWASCatalogParser.from_source(\n                catalog_studies,\n                ancestry_lut,\n                sumstats_lut,\n            ).annotate_from_study_curation(gwas_catalog_study_curation),\n            GWASCatalogCuratedAssociationsParser.from_source(catalog_associations, va),\n        )\n\n        return study_index\n\n    def __init__(\n        self,\n        session: Session,\n        catalog_study_files: list[str],\n        catalog_ancestry_files: list[str],\n        catalog_associations_file: str,\n        gwas_catalog_study_curation_file: str,\n        variant_annotation_path: str,\n        harmonised_study_file: str,\n        criteria: str,\n        inclusion_list_path: str,\n        exclusion_list_path: str,\n    ) -&gt; None:\n        \"\"\"Run step.\n\n        Args:\n            session (Session): Session object.\n            catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n            catalog_associations_file (str): Raw GWAS catalog associations file.\n            gwas_catalog_study_curation_file (str): file of the curation table. Optional.\n            variant_annotation_path (str): Input variant annotation path.\n            harmonised_study_file (str): GWAS Catalog summary statistics lookup table.\n            criteria (str): name of the filter set to be applied.\n            inclusion_list_path (str): Output path for the inclusion list.\n            exclusion_list_path (str): Output path for the exclusion list.\n        \"\"\"\n        # Create study index:\n        study_index = self.get_gwas_catalog_study_index(\n            session,\n            variant_annotation_path,\n            catalog_study_files,\n            catalog_ancestry_files,\n            harmonised_study_file,\n            catalog_associations_file,\n            gwas_catalog_study_curation_file,\n        )\n\n        # Get study indices for inclusion:\n        flagged_studies = self.flag_eligible_studies(study_index, criteria)\n\n        # Output inclusion list:\n        eligible = (\n            flagged_studies.filter(f.col(\"isEligible\")).select(\"studyId\").persist()\n        )\n        eligible.write.mode(session.write_mode).parquet(inclusion_list_path)\n\n        # Output exclusion list:\n        excluded = flagged_studies.filter(~f.col(\"isEligible\")).persist()\n        excluded.write.mode(session.write_mode).parquet(exclusion_list_path)\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_inclusion/#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.__init__","title":"<code>__init__(session: Session, catalog_study_files: list[str], catalog_ancestry_files: list[str], catalog_associations_file: str, gwas_catalog_study_curation_file: str, variant_annotation_path: str, harmonised_study_file: str, criteria: str, inclusion_list_path: str, exclusion_list_path: str) -&gt; None</code>","text":"<p>Run step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>catalog_study_files</code> <code>list[str]</code> <p>List of raw GWAS catalog studies file.</p> required <code>catalog_ancestry_files</code> <code>list[str]</code> <p>List of raw ancestry annotations files from GWAS Catalog.</p> required <code>catalog_associations_file</code> <code>str</code> <p>Raw GWAS catalog associations file.</p> required <code>gwas_catalog_study_curation_file</code> <code>str</code> <p>file of the curation table. Optional.</p> required <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> required <code>harmonised_study_file</code> <code>str</code> <p>GWAS Catalog summary statistics lookup table.</p> required <code>criteria</code> <code>str</code> <p>name of the filter set to be applied.</p> required <code>inclusion_list_path</code> <code>str</code> <p>Output path for the inclusion list.</p> required <code>exclusion_list_path</code> <code>str</code> <p>Output path for the exclusion list.</p> required Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    catalog_study_files: list[str],\n    catalog_ancestry_files: list[str],\n    catalog_associations_file: str,\n    gwas_catalog_study_curation_file: str,\n    variant_annotation_path: str,\n    harmonised_study_file: str,\n    criteria: str,\n    inclusion_list_path: str,\n    exclusion_list_path: str,\n) -&gt; None:\n    \"\"\"Run step.\n\n    Args:\n        session (Session): Session object.\n        catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n        catalog_associations_file (str): Raw GWAS catalog associations file.\n        gwas_catalog_study_curation_file (str): file of the curation table. Optional.\n        variant_annotation_path (str): Input variant annotation path.\n        harmonised_study_file (str): GWAS Catalog summary statistics lookup table.\n        criteria (str): name of the filter set to be applied.\n        inclusion_list_path (str): Output path for the inclusion list.\n        exclusion_list_path (str): Output path for the exclusion list.\n    \"\"\"\n    # Create study index:\n    study_index = self.get_gwas_catalog_study_index(\n        session,\n        variant_annotation_path,\n        catalog_study_files,\n        catalog_ancestry_files,\n        harmonised_study_file,\n        catalog_associations_file,\n        gwas_catalog_study_curation_file,\n    )\n\n    # Get study indices for inclusion:\n    flagged_studies = self.flag_eligible_studies(study_index, criteria)\n\n    # Output inclusion list:\n    eligible = (\n        flagged_studies.filter(f.col(\"isEligible\")).select(\"studyId\").persist()\n    )\n    eligible.write.mode(session.write_mode).parquet(inclusion_list_path)\n\n    # Output exclusion list:\n    excluded = flagged_studies.filter(~f.col(\"isEligible\")).persist()\n    excluded.write.mode(session.write_mode).parquet(exclusion_list_path)\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_inclusion/#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.flag_eligible_studies","title":"<code>flag_eligible_studies(study_index: StudyIndexGWASCatalog, criteria: str) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Apply filter on GWAS Catalog studies based on the provided criteria.</p> <p>Parameters:</p> Name Type Description Default <code>study_index</code> <code>StudyIndexGWASCatalog</code> <p>complete study index to be filtered based on the provided filter set</p> required <code>criteria</code> <code>str</code> <p>name of the filter set to be applied.</p> required <p>Raises:</p> Type Description <code>ValueError</code> <p>if the provided filter set is not in the accepted values.</p> <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>filtered dataframe containing only eligible studies.</p> Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code> <pre><code>@staticmethod\ndef flag_eligible_studies(\n    study_index: StudyIndexGWASCatalog, criteria: str\n) -&gt; DataFrame:\n    \"\"\"Apply filter on GWAS Catalog studies based on the provided criteria.\n\n    Args:\n        study_index (StudyIndexGWASCatalog): complete study index to be filtered based on the provided filter set\n        criteria (str): name of the filter set to be applied.\n\n    Raises:\n        ValueError: if the provided filter set is not in the accepted values.\n\n    Returns:\n        DataFrame: filtered dataframe containing only eligible studies.\n    \"\"\"\n    filters: dict[str, Column] = {\n        # Filters applied on studies for ingesting curated associations:\n        \"curation\": (study_index.is_gwas() &amp; study_index.has_mapped_trait()),\n        # Filters applied on studies for ingesting summary statistics:\n        \"summary_stats\": (\n            study_index.is_gwas()\n            &amp; study_index.has_mapped_trait()\n            &amp; (~study_index.is_quality_flagged())\n            &amp; study_index.has_summarystats()\n        ),\n    }\n\n    if criteria not in filters:\n        raise ValueError(\n            f'Wrong value as filter set ({criteria}). Accepted: {\",\".join(filters.keys())}'\n        )\n\n    # Applying the relevant filter to the study:\n    return study_index.df.select(\n        \"studyId\",\n        \"studyType\",\n        \"traitFromSource\",\n        \"traitFromSourceMappedIds\",\n        \"qualityControls\",\n        \"hasSumstats\",\n        filters[criteria].alias(\"isEligible\"),\n    )\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_inclusion/#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.get_gwas_catalog_study_index","title":"<code>get_gwas_catalog_study_index(session: Session, variant_annotation_path: str, catalog_study_files: list[str], catalog_ancestry_files: list[str], harmonised_study_file: str, catalog_associations_file: str, gwas_catalog_study_curation_file: str) -&gt; StudyIndexGWASCatalog</code>  <code>staticmethod</code>","text":"<p>Return GWAS Catalog study index.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> required <code>catalog_study_files</code> <code>list[str]</code> <p>List of raw GWAS catalog studies file.</p> required <code>catalog_ancestry_files</code> <code>list[str]</code> <p>List of raw ancestry annotations files from GWAS Catalog.</p> required <code>harmonised_study_file</code> <code>str</code> <p>GWAS Catalog summary statistics lookup table.</p> required <code>catalog_associations_file</code> <code>str</code> <p>Raw GWAS catalog associations file.</p> required <code>gwas_catalog_study_curation_file</code> <code>str</code> <p>file of the curation table. Optional.</p> required <p>Returns:</p> Name Type Description <code>StudyIndexGWASCatalog</code> <code>StudyIndexGWASCatalog</code> <p>Completely processed and fully annotated study index.</p> Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code> <pre><code>@staticmethod\ndef get_gwas_catalog_study_index(\n    session: Session,\n    variant_annotation_path: str,\n    catalog_study_files: list[str],\n    catalog_ancestry_files: list[str],\n    harmonised_study_file: str,\n    catalog_associations_file: str,\n    gwas_catalog_study_curation_file: str,\n) -&gt; StudyIndexGWASCatalog:\n    \"\"\"Return GWAS Catalog study index.\n\n    Args:\n        session (Session): Session object.\n        variant_annotation_path (str): Input variant annotation path.\n        catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n        harmonised_study_file (str): GWAS Catalog summary statistics lookup table.\n        catalog_associations_file (str): Raw GWAS catalog associations file.\n        gwas_catalog_study_curation_file (str): file of the curation table. Optional.\n\n    Returns:\n        StudyIndexGWASCatalog: Completely processed and fully annotated study index.\n    \"\"\"\n    # Extract\n    va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n    catalog_studies = session.spark.read.csv(\n        list(catalog_study_files), sep=\"\\t\", header=True\n    )\n    ancestry_lut = session.spark.read.csv(\n        list(catalog_ancestry_files), sep=\"\\t\", header=True\n    )\n    sumstats_lut = session.spark.read.csv(\n        harmonised_study_file, sep=\"\\t\", header=False\n    )\n    catalog_associations = session.spark.read.csv(\n        catalog_associations_file, sep=\"\\t\", header=True\n    ).persist()\n    gwas_catalog_study_curation = read_curation_table(\n        gwas_catalog_study_curation_file, session\n    )\n\n    # Transform\n    study_index, _ = GWASCatalogStudySplitter.split(\n        StudyIndexGWASCatalogParser.from_source(\n            catalog_studies,\n            ancestry_lut,\n            sumstats_lut,\n        ).annotate_from_study_curation(gwas_catalog_study_curation),\n        GWASCatalogCuratedAssociationsParser.from_source(catalog_associations, va),\n    )\n\n    return study_index\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_inclusion/#gentropy.gwas_catalog_study_inclusion.GWASCatalogStudyInclusionGenerator.process_harmonised_list","title":"<code>process_harmonised_list(studies: list[str], session: Session) -&gt; DataFrame</code>  <code>staticmethod</code>","text":"<p>Generate spark dataframe from the provided list.</p> <p>Parameters:</p> Name Type Description Default <code>studies</code> <code>list[str]</code> <p>list of path pointing to harmonised summary statistics.</p> required <code>session</code> <code>Session</code> <p>session</p> required <p>Returns:</p> Name Type Description <code>DataFrame</code> <code>DataFrame</code> <p>column name is consistent with original implementatin</p> Source code in <code>src/gentropy/gwas_catalog_study_inclusion.py</code> <pre><code>@staticmethod\ndef process_harmonised_list(studies: list[str], session: Session) -&gt; DataFrame:\n    \"\"\"Generate spark dataframe from the provided list.\n\n    Args:\n        studies (list[str]): list of path pointing to harmonised summary statistics.\n        session (Session): session\n\n    Returns:\n        DataFrame: column name is consistent with original implementatin\n    \"\"\"\n    return session.spark.createDataFrame([{\"_c0\": path} for path in studies])\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_ingestion/","title":"gwas_catalog_ingestion","text":""},{"location":"python_api/steps/gwas_catalog_ingestion/#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep","title":"<code>gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep</code>","text":"<p>GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.</p> <p>!!! note This step currently only processes the GWAS Catalog curated list of top hits.</p> Source code in <code>src/gentropy/gwas_catalog_ingestion.py</code> <pre><code>class GWASCatalogIngestionStep:\n    \"\"\"GWAS Catalog ingestion step to extract GWASCatalog Study and StudyLocus tables.\n\n    !!! note This step currently only processes the GWAS Catalog curated list of top hits.\n    \"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        catalog_study_files: list[str],\n        catalog_ancestry_files: list[str],\n        catalog_sumstats_lut: str,\n        catalog_associations_file: str,\n        variant_annotation_path: str,\n        catalog_studies_out: str,\n        catalog_associations_out: str,\n        gwas_catalog_study_curation_file: str | None = None,\n        inclusion_list_path: str | None = None,\n    ) -&gt; None:\n        \"\"\"Run step.\n\n        Args:\n            session (Session): Session object.\n            catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n            catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n            catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.\n            catalog_associations_file (str): Raw GWAS catalog associations file.\n            variant_annotation_path (str): Input variant annotation path.\n            catalog_studies_out (str): Output GWAS catalog studies path.\n            catalog_associations_out (str): Output GWAS catalog associations path.\n            gwas_catalog_study_curation_file (str | None): file of the curation table. Optional.\n            inclusion_list_path (str | None): optional inclusion list (parquet)\n        \"\"\"\n        # Extract\n        va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n        catalog_studies = session.spark.read.csv(\n            list(catalog_study_files), sep=\"\\t\", header=True\n        )\n        ancestry_lut = session.spark.read.csv(\n            list(catalog_ancestry_files), sep=\"\\t\", header=True\n        )\n        sumstats_lut = session.spark.read.csv(\n            catalog_sumstats_lut, sep=\"\\t\", header=False\n        )\n        catalog_associations = session.spark.read.csv(\n            catalog_associations_file, sep=\"\\t\", header=True\n        ).persist()\n        gwas_catalog_study_curation = read_curation_table(\n            gwas_catalog_study_curation_file, session\n        )\n\n        # Transform\n        study_index, study_locus = GWASCatalogStudySplitter.split(\n            StudyIndexGWASCatalogParser.from_source(\n                catalog_studies, ancestry_lut, sumstats_lut\n            ).annotate_from_study_curation(gwas_catalog_study_curation),\n            GWASCatalogCuratedAssociationsParser.from_source(catalog_associations, va),\n        )\n\n        # if inclusion list is provided apply filter:\n        if inclusion_list_path:\n            inclusion_list = session.spark.read.parquet(\n                inclusion_list_path, sep=\"\\t\", header=True\n            )\n\n            study_index = study_index.apply_inclusion_list(inclusion_list)\n            study_locus = study_locus.apply_inclusion_list(inclusion_list)\n\n        # Load\n        study_index.df.write.mode(session.write_mode).parquet(catalog_studies_out)\n        study_locus.df.write.mode(session.write_mode).parquet(catalog_associations_out)\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_ingestion/#gentropy.gwas_catalog_ingestion.GWASCatalogIngestionStep.__init__","title":"<code>__init__(session: Session, catalog_study_files: list[str], catalog_ancestry_files: list[str], catalog_sumstats_lut: str, catalog_associations_file: str, variant_annotation_path: str, catalog_studies_out: str, catalog_associations_out: str, gwas_catalog_study_curation_file: str | None = None, inclusion_list_path: str | None = None) -&gt; None</code>","text":"<p>Run step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>catalog_study_files</code> <code>list[str]</code> <p>List of raw GWAS catalog studies file.</p> required <code>catalog_ancestry_files</code> <code>list[str]</code> <p>List of raw ancestry annotations files from GWAS Catalog.</p> required <code>catalog_sumstats_lut</code> <code>str</code> <p>GWAS Catalog summary statistics lookup table.</p> required <code>catalog_associations_file</code> <code>str</code> <p>Raw GWAS catalog associations file.</p> required <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> required <code>catalog_studies_out</code> <code>str</code> <p>Output GWAS catalog studies path.</p> required <code>catalog_associations_out</code> <code>str</code> <p>Output GWAS catalog associations path.</p> required <code>gwas_catalog_study_curation_file</code> <code>str | None</code> <p>file of the curation table. Optional.</p> <code>None</code> <code>inclusion_list_path</code> <code>str | None</code> <p>optional inclusion list (parquet)</p> <code>None</code> Source code in <code>src/gentropy/gwas_catalog_ingestion.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    catalog_study_files: list[str],\n    catalog_ancestry_files: list[str],\n    catalog_sumstats_lut: str,\n    catalog_associations_file: str,\n    variant_annotation_path: str,\n    catalog_studies_out: str,\n    catalog_associations_out: str,\n    gwas_catalog_study_curation_file: str | None = None,\n    inclusion_list_path: str | None = None,\n) -&gt; None:\n    \"\"\"Run step.\n\n    Args:\n        session (Session): Session object.\n        catalog_study_files (list[str]): List of raw GWAS catalog studies file.\n        catalog_ancestry_files (list[str]): List of raw ancestry annotations files from GWAS Catalog.\n        catalog_sumstats_lut (str): GWAS Catalog summary statistics lookup table.\n        catalog_associations_file (str): Raw GWAS catalog associations file.\n        variant_annotation_path (str): Input variant annotation path.\n        catalog_studies_out (str): Output GWAS catalog studies path.\n        catalog_associations_out (str): Output GWAS catalog associations path.\n        gwas_catalog_study_curation_file (str | None): file of the curation table. Optional.\n        inclusion_list_path (str | None): optional inclusion list (parquet)\n    \"\"\"\n    # Extract\n    va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n    catalog_studies = session.spark.read.csv(\n        list(catalog_study_files), sep=\"\\t\", header=True\n    )\n    ancestry_lut = session.spark.read.csv(\n        list(catalog_ancestry_files), sep=\"\\t\", header=True\n    )\n    sumstats_lut = session.spark.read.csv(\n        catalog_sumstats_lut, sep=\"\\t\", header=False\n    )\n    catalog_associations = session.spark.read.csv(\n        catalog_associations_file, sep=\"\\t\", header=True\n    ).persist()\n    gwas_catalog_study_curation = read_curation_table(\n        gwas_catalog_study_curation_file, session\n    )\n\n    # Transform\n    study_index, study_locus = GWASCatalogStudySplitter.split(\n        StudyIndexGWASCatalogParser.from_source(\n            catalog_studies, ancestry_lut, sumstats_lut\n        ).annotate_from_study_curation(gwas_catalog_study_curation),\n        GWASCatalogCuratedAssociationsParser.from_source(catalog_associations, va),\n    )\n\n    # if inclusion list is provided apply filter:\n    if inclusion_list_path:\n        inclusion_list = session.spark.read.parquet(\n            inclusion_list_path, sep=\"\\t\", header=True\n        )\n\n        study_index = study_index.apply_inclusion_list(inclusion_list)\n        study_locus = study_locus.apply_inclusion_list(inclusion_list)\n\n    # Load\n    study_index.df.write.mode(session.write_mode).parquet(catalog_studies_out)\n    study_locus.df.write.mode(session.write_mode).parquet(catalog_associations_out)\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_sumstat_preprocess/","title":"gwas_catalog_sumstat_preprocess","text":""},{"location":"python_api/steps/gwas_catalog_sumstat_preprocess/#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep","title":"<code>gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep</code>","text":"<p>Step to preprocess GWAS Catalog harmonised summary stats.</p> Source code in <code>src/gentropy/gwas_catalog_sumstat_preprocess.py</code> <pre><code>class GWASCatalogSumstatsPreprocessStep:\n    \"\"\"Step to preprocess GWAS Catalog harmonised summary stats.\"\"\"\n\n    def __init__(\n        self, session: Session, raw_sumstats_path: str, out_sumstats_path: str\n    ) -&gt; None:\n        \"\"\"Run step to preprocess GWAS Catalog harmonised summary stats and produce SummaryStatistics dataset.\n\n        Args:\n            session (Session): Session object.\n            raw_sumstats_path (str): Input GWAS Catalog harmonised summary stats path.\n            out_sumstats_path (str): Output SummaryStatistics dataset path.\n        \"\"\"\n        # Processing dataset:\n        GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats(\n            session.spark, raw_sumstats_path\n        ).df.write.mode(session.write_mode).parquet(out_sumstats_path)\n        session.logger.info(\"Processing dataset successfully completed.\")\n</code></pre>"},{"location":"python_api/steps/gwas_catalog_sumstat_preprocess/#gentropy.gwas_catalog_sumstat_preprocess.GWASCatalogSumstatsPreprocessStep.__init__","title":"<code>__init__(session: Session, raw_sumstats_path: str, out_sumstats_path: str) -&gt; None</code>","text":"<p>Run step to preprocess GWAS Catalog harmonised summary stats and produce SummaryStatistics dataset.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>raw_sumstats_path</code> <code>str</code> <p>Input GWAS Catalog harmonised summary stats path.</p> required <code>out_sumstats_path</code> <code>str</code> <p>Output SummaryStatistics dataset path.</p> required Source code in <code>src/gentropy/gwas_catalog_sumstat_preprocess.py</code> <pre><code>def __init__(\n    self, session: Session, raw_sumstats_path: str, out_sumstats_path: str\n) -&gt; None:\n    \"\"\"Run step to preprocess GWAS Catalog harmonised summary stats and produce SummaryStatistics dataset.\n\n    Args:\n        session (Session): Session object.\n        raw_sumstats_path (str): Input GWAS Catalog harmonised summary stats path.\n        out_sumstats_path (str): Output SummaryStatistics dataset path.\n    \"\"\"\n    # Processing dataset:\n    GWASCatalogSummaryStatistics.from_gwas_harmonized_summary_stats(\n        session.spark, raw_sumstats_path\n    ).df.write.mode(session.write_mode).parquet(out_sumstats_path)\n    session.logger.info(\"Processing dataset successfully completed.\")\n</code></pre>"},{"location":"python_api/steps/l2g/","title":"locus_to_gene","text":""},{"location":"python_api/steps/l2g/#gentropy.l2g.LocusToGeneStep","title":"<code>gentropy.l2g.LocusToGeneStep</code>","text":"<p>Locus to gene step.</p> Source code in <code>src/gentropy/l2g.py</code> <pre><code>class LocusToGeneStep:\n    \"\"\"Locus to gene step.\"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        run_mode: str,\n        model_path: str,\n        predictions_path: str,\n        credible_set_path: str,\n        variant_gene_path: str,\n        colocalisation_path: str,\n        study_index_path: str,\n        gold_standard_curation_path: str,\n        gene_interactions_path: str,\n        features_list: list[str],\n        hyperparameters: dict[str, Any],\n        wandb_run_name: str | None = None,\n        perform_cross_validation: bool = False,\n    ) -&gt; None:\n        \"\"\"Run step.\n\n        Args:\n            session (Session): Session object.\n            run_mode (str): One of \"train\" or \"predict\".\n            model_path (str): Path to save the model.\n            predictions_path (str): Path to save the predictions.\n            credible_set_path (str): Path to credible set Parquet files.\n            variant_gene_path (str): Path to variant to gene Parquet files.\n            colocalisation_path (str): Path to colocalisation Parquet files.\n            study_index_path (str): Path to study index Parquet files.\n            gold_standard_curation_path (str): Path to gold standard curation JSON files.\n            gene_interactions_path (str): Path to gene interactions Parquet files.\n            features_list (list[str]): List of features to use.\n            hyperparameters (dict[str, Any]): Hyperparameters for the model.\n            wandb_run_name (str | None): Name of the run to be tracked on W&amp;B.\n            perform_cross_validation (bool): Whether to perform cross validation.\n\n        Raises:\n            ValueError: if run_mode is not one of \"train\" or \"predict\".\n        \"\"\"\n        print(\"Sci-kit learn version: \", sklearn.__version__)  # noqa: T201\n        if run_mode not in [\"train\", \"predict\"]:\n            raise ValueError(\n                f\"run_mode must be one of 'train' or 'predict', got {run_mode}\"\n            )\n        # Load common inputs\n        credible_set = StudyLocus.from_parquet(\n            session, credible_set_path, recursiveFileLookup=True\n        )\n        studies = StudyIndex.from_parquet(\n            session, study_index_path, recursiveFileLookup=True\n        )\n        v2g = V2G.from_parquet(session, variant_gene_path)\n        coloc = Colocalisation.from_parquet(session, colocalisation_path)\n\n        if run_mode == \"predict\":\n            if not model_path or not predictions_path:\n                raise ValueError(\n                    \"model_path and predictions_path must be set for predict mode.\"\n                )\n            predictions = L2GPrediction.from_credible_set(\n                model_path, list(features_list), credible_set, studies, v2g, coloc\n            )\n            predictions.df.write.mode(session.write_mode).parquet(predictions_path)\n            session.logger.info(predictions_path)\n        elif (\n            run_mode == \"train\"\n            and gold_standard_curation_path\n            and gene_interactions_path\n        ):\n            # Process gold standard and L2G features\n            gs_curation = session.spark.read.json(gold_standard_curation_path).persist()\n            interactions = session.spark.read.parquet(gene_interactions_path)\n            study_locus_overlap = StudyLocus(\n                # We just extract overlaps of associations in the gold standard. This parsing is a duplication of the one in the gold standard curation,\n                # but we need to do it here to be able to parse gold standards later\n                _df=credible_set.df.join(\n                    f.broadcast(\n                        gs_curation.select(\n                            StudyLocus.assign_study_locus_id(\n                                f.col(\"association_info.otg_id\"),  # studyId\n                                f.concat_ws(  # variantId\n                                    \"_\",\n                                    f.col(\"sentinel_variant.locus_GRCh38.chromosome\"),\n                                    f.col(\"sentinel_variant.locus_GRCh38.position\"),\n                                    f.col(\"sentinel_variant.alleles.reference\"),\n                                    f.col(\"sentinel_variant.alleles.alternative\"),\n                                ),\n                            ).alias(\"studyLocusId\"),\n                        )\n                    ),\n                    \"studyLocusId\",\n                    \"inner\",\n                ),\n                _schema=StudyLocus.get_schema(),\n            ).find_overlaps(studies)\n\n            gold_standards = L2GGoldStandard.from_otg_curation(\n                gold_standard_curation=gs_curation,\n                v2g=v2g,\n                study_locus_overlap=study_locus_overlap,\n                interactions=interactions,\n            )\n\n            fm = L2GFeatureMatrix.generate_features(\n                features_list=features_list,\n                study_locus=credible_set,\n                study_index=studies,\n                variant_gene=v2g,\n                colocalisation=coloc,\n            )\n\n            # Join and fill null values with 0\n            data = L2GFeatureMatrix(\n                _df=fm.df.join(\n                    f.broadcast(\n                        gold_standards.df.drop(\"variantId\", \"studyId\", \"sources\")\n                    ),\n                    on=[\"studyLocusId\", \"geneId\"],\n                    how=\"inner\",\n                ),\n                _schema=L2GFeatureMatrix.get_schema(),\n            ).fill_na()\n\n            # Instantiate classifier\n            estimator = SparkXGBClassifier(\n                eval_metric=\"logloss\",\n                features_col=\"features\",\n                label_col=\"label\",\n                max_depth=5,\n            )\n            l2g_model = LocusToGeneModel(\n                features_list=list(features_list), estimator=estimator\n            )\n            if perform_cross_validation:\n                # Perform cross validation to extract what are the best hyperparameters\n                cv_folds = hyperparameters.get(\"cross_validation_folds\", 5)\n                LocusToGeneTrainer.cross_validate(\n                    l2g_model=l2g_model,\n                    data=data,\n                    num_folds=cv_folds,\n                )\n            else:\n                # Train model\n                LocusToGeneTrainer.train(\n                    data=data,\n                    l2g_model=l2g_model,\n                    features_list=list(features_list),\n                    model_path=model_path,\n                    evaluate=True,\n                    wandb_run_name=wandb_run_name,\n                    **hyperparameters,\n                )\n                session.logger.info(model_path)\n</code></pre>"},{"location":"python_api/steps/l2g/#gentropy.l2g.LocusToGeneStep.__init__","title":"<code>__init__(session: Session, run_mode: str, model_path: str, predictions_path: str, credible_set_path: str, variant_gene_path: str, colocalisation_path: str, study_index_path: str, gold_standard_curation_path: str, gene_interactions_path: str, features_list: list[str], hyperparameters: dict[str, Any], wandb_run_name: str | None = None, perform_cross_validation: bool = False) -&gt; None</code>","text":"<p>Run step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>run_mode</code> <code>str</code> <p>One of \"train\" or \"predict\".</p> required <code>model_path</code> <code>str</code> <p>Path to save the model.</p> required <code>predictions_path</code> <code>str</code> <p>Path to save the predictions.</p> required <code>credible_set_path</code> <code>str</code> <p>Path to credible set Parquet files.</p> required <code>variant_gene_path</code> <code>str</code> <p>Path to variant to gene Parquet files.</p> required <code>colocalisation_path</code> <code>str</code> <p>Path to colocalisation Parquet files.</p> required <code>study_index_path</code> <code>str</code> <p>Path to study index Parquet files.</p> required <code>gold_standard_curation_path</code> <code>str</code> <p>Path to gold standard curation JSON files.</p> required <code>gene_interactions_path</code> <code>str</code> <p>Path to gene interactions Parquet files.</p> required <code>features_list</code> <code>list[str]</code> <p>List of features to use.</p> required <code>hyperparameters</code> <code>dict[str, Any]</code> <p>Hyperparameters for the model.</p> required <code>wandb_run_name</code> <code>str | None</code> <p>Name of the run to be tracked on W&amp;B.</p> <code>None</code> <code>perform_cross_validation</code> <code>bool</code> <p>Whether to perform cross validation.</p> <code>False</code> <p>Raises:</p> Type Description <code>ValueError</code> <p>if run_mode is not one of \"train\" or \"predict\".</p> Source code in <code>src/gentropy/l2g.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    run_mode: str,\n    model_path: str,\n    predictions_path: str,\n    credible_set_path: str,\n    variant_gene_path: str,\n    colocalisation_path: str,\n    study_index_path: str,\n    gold_standard_curation_path: str,\n    gene_interactions_path: str,\n    features_list: list[str],\n    hyperparameters: dict[str, Any],\n    wandb_run_name: str | None = None,\n    perform_cross_validation: bool = False,\n) -&gt; None:\n    \"\"\"Run step.\n\n    Args:\n        session (Session): Session object.\n        run_mode (str): One of \"train\" or \"predict\".\n        model_path (str): Path to save the model.\n        predictions_path (str): Path to save the predictions.\n        credible_set_path (str): Path to credible set Parquet files.\n        variant_gene_path (str): Path to variant to gene Parquet files.\n        colocalisation_path (str): Path to colocalisation Parquet files.\n        study_index_path (str): Path to study index Parquet files.\n        gold_standard_curation_path (str): Path to gold standard curation JSON files.\n        gene_interactions_path (str): Path to gene interactions Parquet files.\n        features_list (list[str]): List of features to use.\n        hyperparameters (dict[str, Any]): Hyperparameters for the model.\n        wandb_run_name (str | None): Name of the run to be tracked on W&amp;B.\n        perform_cross_validation (bool): Whether to perform cross validation.\n\n    Raises:\n        ValueError: if run_mode is not one of \"train\" or \"predict\".\n    \"\"\"\n    print(\"Sci-kit learn version: \", sklearn.__version__)  # noqa: T201\n    if run_mode not in [\"train\", \"predict\"]:\n        raise ValueError(\n            f\"run_mode must be one of 'train' or 'predict', got {run_mode}\"\n        )\n    # Load common inputs\n    credible_set = StudyLocus.from_parquet(\n        session, credible_set_path, recursiveFileLookup=True\n    )\n    studies = StudyIndex.from_parquet(\n        session, study_index_path, recursiveFileLookup=True\n    )\n    v2g = V2G.from_parquet(session, variant_gene_path)\n    coloc = Colocalisation.from_parquet(session, colocalisation_path)\n\n    if run_mode == \"predict\":\n        if not model_path or not predictions_path:\n            raise ValueError(\n                \"model_path and predictions_path must be set for predict mode.\"\n            )\n        predictions = L2GPrediction.from_credible_set(\n            model_path, list(features_list), credible_set, studies, v2g, coloc\n        )\n        predictions.df.write.mode(session.write_mode).parquet(predictions_path)\n        session.logger.info(predictions_path)\n    elif (\n        run_mode == \"train\"\n        and gold_standard_curation_path\n        and gene_interactions_path\n    ):\n        # Process gold standard and L2G features\n        gs_curation = session.spark.read.json(gold_standard_curation_path).persist()\n        interactions = session.spark.read.parquet(gene_interactions_path)\n        study_locus_overlap = StudyLocus(\n            # We just extract overlaps of associations in the gold standard. This parsing is a duplication of the one in the gold standard curation,\n            # but we need to do it here to be able to parse gold standards later\n            _df=credible_set.df.join(\n                f.broadcast(\n                    gs_curation.select(\n                        StudyLocus.assign_study_locus_id(\n                            f.col(\"association_info.otg_id\"),  # studyId\n                            f.concat_ws(  # variantId\n                                \"_\",\n                                f.col(\"sentinel_variant.locus_GRCh38.chromosome\"),\n                                f.col(\"sentinel_variant.locus_GRCh38.position\"),\n                                f.col(\"sentinel_variant.alleles.reference\"),\n                                f.col(\"sentinel_variant.alleles.alternative\"),\n                            ),\n                        ).alias(\"studyLocusId\"),\n                    )\n                ),\n                \"studyLocusId\",\n                \"inner\",\n            ),\n            _schema=StudyLocus.get_schema(),\n        ).find_overlaps(studies)\n\n        gold_standards = L2GGoldStandard.from_otg_curation(\n            gold_standard_curation=gs_curation,\n            v2g=v2g,\n            study_locus_overlap=study_locus_overlap,\n            interactions=interactions,\n        )\n\n        fm = L2GFeatureMatrix.generate_features(\n            features_list=features_list,\n            study_locus=credible_set,\n            study_index=studies,\n            variant_gene=v2g,\n            colocalisation=coloc,\n        )\n\n        # Join and fill null values with 0\n        data = L2GFeatureMatrix(\n            _df=fm.df.join(\n                f.broadcast(\n                    gold_standards.df.drop(\"variantId\", \"studyId\", \"sources\")\n                ),\n                on=[\"studyLocusId\", \"geneId\"],\n                how=\"inner\",\n            ),\n            _schema=L2GFeatureMatrix.get_schema(),\n        ).fill_na()\n\n        # Instantiate classifier\n        estimator = SparkXGBClassifier(\n            eval_metric=\"logloss\",\n            features_col=\"features\",\n            label_col=\"label\",\n            max_depth=5,\n        )\n        l2g_model = LocusToGeneModel(\n            features_list=list(features_list), estimator=estimator\n        )\n        if perform_cross_validation:\n            # Perform cross validation to extract what are the best hyperparameters\n            cv_folds = hyperparameters.get(\"cross_validation_folds\", 5)\n            LocusToGeneTrainer.cross_validate(\n                l2g_model=l2g_model,\n                data=data,\n                num_folds=cv_folds,\n            )\n        else:\n            # Train model\n            LocusToGeneTrainer.train(\n                data=data,\n                l2g_model=l2g_model,\n                features_list=list(features_list),\n                model_path=model_path,\n                evaluate=True,\n                wandb_run_name=wandb_run_name,\n                **hyperparameters,\n            )\n            session.logger.info(model_path)\n</code></pre>"},{"location":"python_api/steps/ld_clump/","title":"ld_based_clumping","text":""},{"location":"python_api/steps/ld_clump/#gentropy.ld_based_clumping.LDBasedClumpingStep","title":"<code>gentropy.ld_based_clumping.LDBasedClumpingStep</code>","text":"<p>Step to perform LD-based clumping on study locus dataset.</p> <p>As a first step, study locus is enriched with population specific linked-variants. That's why the study index and the ld index is required for this step. Study loci are flaggged in the resulting dataset, which can be explained by a more significant association from the same study.</p> Source code in <code>src/gentropy/ld_based_clumping.py</code> <pre><code>class LDBasedClumpingStep:\n    \"\"\"Step to perform LD-based clumping on study locus dataset.\n\n    As a first step, study locus is enriched with population specific linked-variants.\n    That's why the study index and the ld index is required for this step. Study loci are flaggged\n    in the resulting dataset, which can be explained by a more significant association\n    from the same study.\n    \"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        study_locus_input_path: str,\n        study_index_path: str,\n        ld_index_path: str,\n        clumped_study_locus_output_path: str,\n    ) -&gt; None:\n        \"\"\"Run LD-based clumping step.\n\n        Args:\n            session (Session): Session object.\n            study_locus_input_path (str): Path to the input study locus.\n            study_index_path (str): Path to the study index.\n            ld_index_path (str): Path to the LD index.\n            clumped_study_locus_output_path (str): path of the resulting, clumped study-locus dataset.\n        \"\"\"\n        study_locus = StudyLocus.from_parquet(session, study_locus_input_path)\n        ld_index = LDIndex.from_parquet(session, ld_index_path)\n        study_index = StudyIndex.from_parquet(session, study_index_path)\n\n        (\n            study_locus\n            # Annotating study locus with LD information:\n            .annotate_ld(study_index, ld_index)\n            .clump()\n            # Save result:\n            .df.write.mode(session.write_mode)\n            .parquet(clumped_study_locus_output_path)\n        )\n</code></pre>"},{"location":"python_api/steps/ld_clump/#gentropy.ld_based_clumping.LDBasedClumpingStep.__init__","title":"<code>__init__(session: Session, study_locus_input_path: str, study_index_path: str, ld_index_path: str, clumped_study_locus_output_path: str) -&gt; None</code>","text":"<p>Run LD-based clumping step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>study_locus_input_path</code> <code>str</code> <p>Path to the input study locus.</p> required <code>study_index_path</code> <code>str</code> <p>Path to the study index.</p> required <code>ld_index_path</code> <code>str</code> <p>Path to the LD index.</p> required <code>clumped_study_locus_output_path</code> <code>str</code> <p>path of the resulting, clumped study-locus dataset.</p> required Source code in <code>src/gentropy/ld_based_clumping.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    study_locus_input_path: str,\n    study_index_path: str,\n    ld_index_path: str,\n    clumped_study_locus_output_path: str,\n) -&gt; None:\n    \"\"\"Run LD-based clumping step.\n\n    Args:\n        session (Session): Session object.\n        study_locus_input_path (str): Path to the input study locus.\n        study_index_path (str): Path to the study index.\n        ld_index_path (str): Path to the LD index.\n        clumped_study_locus_output_path (str): path of the resulting, clumped study-locus dataset.\n    \"\"\"\n    study_locus = StudyLocus.from_parquet(session, study_locus_input_path)\n    ld_index = LDIndex.from_parquet(session, ld_index_path)\n    study_index = StudyIndex.from_parquet(session, study_index_path)\n\n    (\n        study_locus\n        # Annotating study locus with LD information:\n        .annotate_ld(study_index, ld_index)\n        .clump()\n        # Save result:\n        .df.write.mode(session.write_mode)\n        .parquet(clumped_study_locus_output_path)\n    )\n</code></pre>"},{"location":"python_api/steps/ld_index/","title":"ld_index","text":""},{"location":"python_api/steps/ld_index/#gentropy.ld_index.LDIndexStep","title":"<code>gentropy.ld_index.LDIndexStep</code>","text":"<p>LD index step.</p> <p>This step is resource intensive</p> <p>Suggested params: high memory machine, 5TB of boot disk, no SSDs.</p> Source code in <code>src/gentropy/ld_index.py</code> <pre><code>class LDIndexStep:\n    \"\"\"LD index step.\n\n    !!! warning \"This step is resource intensive\"\n\n        Suggested params: high memory machine, 5TB of boot disk, no SSDs.\n    \"\"\"\n\n    def __init__(self, session: Session, min_r2: float, ld_index_out: str) -&gt; None:\n        \"\"\"Run step.\n\n        Args:\n            session (Session): Session object.\n            min_r2 (float): Minimum r2 to consider when considering variants within a window.\n            ld_index_out (str): Output LD index path.\n        \"\"\"\n        hl.init(sc=session.spark.sparkContext, log=\"/dev/null\")\n        (\n            GnomADLDMatrix()\n            .as_ld_index(min_r2)\n            .df.write.partitionBy(\"chromosome\")\n            .mode(session.write_mode)\n            .parquet(ld_index_out)\n        )\n        session.logger.info(ld_index_out)\n</code></pre>"},{"location":"python_api/steps/ld_index/#gentropy.ld_index.LDIndexStep.__init__","title":"<code>__init__(session: Session, min_r2: float, ld_index_out: str) -&gt; None</code>","text":"<p>Run step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>min_r2</code> <code>float</code> <p>Minimum r2 to consider when considering variants within a window.</p> required <code>ld_index_out</code> <code>str</code> <p>Output LD index path.</p> required Source code in <code>src/gentropy/ld_index.py</code> <pre><code>def __init__(self, session: Session, min_r2: float, ld_index_out: str) -&gt; None:\n    \"\"\"Run step.\n\n    Args:\n        session (Session): Session object.\n        min_r2 (float): Minimum r2 to consider when considering variants within a window.\n        ld_index_out (str): Output LD index path.\n    \"\"\"\n    hl.init(sc=session.spark.sparkContext, log=\"/dev/null\")\n    (\n        GnomADLDMatrix()\n        .as_ld_index(min_r2)\n        .df.write.partitionBy(\"chromosome\")\n        .mode(session.write_mode)\n        .parquet(ld_index_out)\n    )\n    session.logger.info(ld_index_out)\n</code></pre>"},{"location":"python_api/steps/pics/","title":"pics","text":""},{"location":"python_api/steps/pics/#gentropy.pics.PICSStep","title":"<code>gentropy.pics.PICSStep</code>","text":"<p>PICS finemapping of LD-annotated StudyLocus.</p> Source code in <code>src/gentropy/pics.py</code> <pre><code>class PICSStep:\n    \"\"\"PICS finemapping of LD-annotated StudyLocus.\"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        study_locus_ld_annotated_in: str,\n        picsed_study_locus_out: str,\n    ) -&gt; None:\n        \"\"\"Run PICS on LD annotated study-locus.\n\n        Args:\n            session (Session): Session object.\n            study_locus_ld_annotated_in (str): Input LD annotated study-locus path.\n            picsed_study_locus_out (str): Output PICSed study-locus path.\n        \"\"\"\n        # Extract\n        study_locus_ld_annotated = StudyLocus.from_parquet(\n            session, study_locus_ld_annotated_in\n        )\n        # PICS\n        picsed_sl = PICS.finemap(study_locus_ld_annotated).annotate_credible_sets()\n        # Write\n        picsed_sl.df.write.mode(session.write_mode).parquet(picsed_study_locus_out)\n</code></pre>"},{"location":"python_api/steps/pics/#gentropy.pics.PICSStep.__init__","title":"<code>__init__(session: Session, study_locus_ld_annotated_in: str, picsed_study_locus_out: str) -&gt; None</code>","text":"<p>Run PICS on LD annotated study-locus.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>study_locus_ld_annotated_in</code> <code>str</code> <p>Input LD annotated study-locus path.</p> required <code>picsed_study_locus_out</code> <code>str</code> <p>Output PICSed study-locus path.</p> required Source code in <code>src/gentropy/pics.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    study_locus_ld_annotated_in: str,\n    picsed_study_locus_out: str,\n) -&gt; None:\n    \"\"\"Run PICS on LD annotated study-locus.\n\n    Args:\n        session (Session): Session object.\n        study_locus_ld_annotated_in (str): Input LD annotated study-locus path.\n        picsed_study_locus_out (str): Output PICSed study-locus path.\n    \"\"\"\n    # Extract\n    study_locus_ld_annotated = StudyLocus.from_parquet(\n        session, study_locus_ld_annotated_in\n    )\n    # PICS\n    picsed_sl = PICS.finemap(study_locus_ld_annotated).annotate_credible_sets()\n    # Write\n    picsed_sl.df.write.mode(session.write_mode).parquet(picsed_study_locus_out)\n</code></pre>"},{"location":"python_api/steps/variant_annotation_step/","title":"variant_annotation","text":""},{"location":"python_api/steps/variant_annotation_step/#gentropy.variant_annotation.VariantAnnotationStep","title":"<code>gentropy.variant_annotation.VariantAnnotationStep</code>","text":"<p>Variant annotation step.</p> <p>Variant annotation step produces a dataset of the type <code>VariantAnnotation</code> derived from gnomADs <code>gnomad.genomes.vX.X.X.sites.ht</code> Hail's table. This dataset is used to validate variants and as a source of annotation.</p> Source code in <code>src/gentropy/variant_annotation.py</code> <pre><code>class VariantAnnotationStep:\n    \"\"\"Variant annotation step.\n\n    Variant annotation step produces a dataset of the type `VariantAnnotation` derived from gnomADs `gnomad.genomes.vX.X.X.sites.ht` Hail's table. This dataset is used to validate variants and as a source of annotation.\n    \"\"\"\n\n    def __init__(self, session: Session, variant_annotation_path: str) -&gt; None:\n        \"\"\"Run Variant Annotation step.\n\n        Args:\n            session (Session): Session object.\n            variant_annotation_path (str): Variant annotation dataset path.\n        \"\"\"\n        # Initialise hail session.\n        hl.init(sc=session.spark.sparkContext, log=\"/dev/null\")\n        # Run variant annotation.\n        variant_annotation = GnomADVariants().as_variant_annotation()\n        # Write data partitioned by chromosome and position.\n        (\n            variant_annotation.df.write.mode(session.write_mode).parquet(\n                variant_annotation_path\n            )\n        )\n</code></pre>"},{"location":"python_api/steps/variant_annotation_step/#gentropy.variant_annotation.VariantAnnotationStep.__init__","title":"<code>__init__(session: Session, variant_annotation_path: str) -&gt; None</code>","text":"<p>Run Variant Annotation step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>variant_annotation_path</code> <code>str</code> <p>Variant annotation dataset path.</p> required Source code in <code>src/gentropy/variant_annotation.py</code> <pre><code>def __init__(self, session: Session, variant_annotation_path: str) -&gt; None:\n    \"\"\"Run Variant Annotation step.\n\n    Args:\n        session (Session): Session object.\n        variant_annotation_path (str): Variant annotation dataset path.\n    \"\"\"\n    # Initialise hail session.\n    hl.init(sc=session.spark.sparkContext, log=\"/dev/null\")\n    # Run variant annotation.\n    variant_annotation = GnomADVariants().as_variant_annotation()\n    # Write data partitioned by chromosome and position.\n    (\n        variant_annotation.df.write.mode(session.write_mode).parquet(\n            variant_annotation_path\n        )\n    )\n</code></pre>"},{"location":"python_api/steps/variant_index_step/","title":"variant_index","text":""},{"location":"python_api/steps/variant_index_step/#gentropy.variant_index.VariantIndexStep","title":"<code>gentropy.variant_index.VariantIndexStep</code>","text":"<p>Run variant index step to only variants in study-locus sets.</p> <p>Using a <code>VariantAnnotation</code> dataset as a reference, this step creates and writes a dataset of the type <code>VariantIndex</code> that includes only variants that have disease-association data with a reduced set of annotations.</p> Source code in <code>src/gentropy/variant_index.py</code> <pre><code>class VariantIndexStep:\n    \"\"\"Run variant index step to only variants in study-locus sets.\n\n    Using a `VariantAnnotation` dataset as a reference, this step creates and writes a dataset of the type `VariantIndex` that includes only variants that have disease-association data with a reduced set of annotations.\n    \"\"\"\n\n    def __init__(\n        self: VariantIndexStep,\n        session: Session,\n        variant_annotation_path: str,\n        credible_set_path: str,\n        variant_index_path: str,\n    ) -&gt; None:\n        \"\"\"Run VariantIndex step.\n\n        Args:\n            session (Session): Session object.\n            variant_annotation_path (str): Variant annotation dataset path.\n            credible_set_path (str): Credible set dataset path.\n            variant_index_path (str): Variant index dataset path.\n        \"\"\"\n        # Extract\n        va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n        credible_set = StudyLocus.from_parquet(\n            session, credible_set_path, recursiveFileLookup=True\n        )\n\n        # Transform\n        vi = VariantIndex.from_variant_annotation(va, credible_set)\n\n        (\n            vi.df.write.partitionBy(\"chromosome\")\n            .mode(session.write_mode)\n            .parquet(variant_index_path)\n        )\n</code></pre>"},{"location":"python_api/steps/variant_index_step/#gentropy.variant_index.VariantIndexStep.__init__","title":"<code>__init__(session: Session, variant_annotation_path: str, credible_set_path: str, variant_index_path: str) -&gt; None</code>","text":"<p>Run VariantIndex step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>variant_annotation_path</code> <code>str</code> <p>Variant annotation dataset path.</p> required <code>credible_set_path</code> <code>str</code> <p>Credible set dataset path.</p> required <code>variant_index_path</code> <code>str</code> <p>Variant index dataset path.</p> required Source code in <code>src/gentropy/variant_index.py</code> <pre><code>def __init__(\n    self: VariantIndexStep,\n    session: Session,\n    variant_annotation_path: str,\n    credible_set_path: str,\n    variant_index_path: str,\n) -&gt; None:\n    \"\"\"Run VariantIndex step.\n\n    Args:\n        session (Session): Session object.\n        variant_annotation_path (str): Variant annotation dataset path.\n        credible_set_path (str): Credible set dataset path.\n        variant_index_path (str): Variant index dataset path.\n    \"\"\"\n    # Extract\n    va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n    credible_set = StudyLocus.from_parquet(\n        session, credible_set_path, recursiveFileLookup=True\n    )\n\n    # Transform\n    vi = VariantIndex.from_variant_annotation(va, credible_set)\n\n    (\n        vi.df.write.partitionBy(\"chromosome\")\n        .mode(session.write_mode)\n        .parquet(variant_index_path)\n    )\n</code></pre>"},{"location":"python_api/steps/variant_to_gene_step/","title":"variant_to_gene","text":""},{"location":"python_api/steps/variant_to_gene_step/#gentropy.v2g.V2GStep","title":"<code>gentropy.v2g.V2GStep</code>","text":"<p>Variant-to-gene (V2G) step.</p> <p>This step aims to generate a dataset that contains multiple pieces of evidence supporting the functional association of specific variants with genes. Some of the evidence types include:</p> <ol> <li>Chromatin interaction experiments, e.g. Promoter Capture Hi-C (PCHi-C).</li> <li>In silico functional predictions, e.g. Variant Effect Predictor (VEP) from Ensembl.</li> <li>Distance between the variant and each gene's canonical transcription start site (TSS).</li> </ol> <p>Attributes:</p> Name Type Description <code>session</code> <code>Session</code> <p>Session object.</p> <code>variant_index_path</code> <code>str</code> <p>Input variant index path.</p> <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> <code>gene_index_path</code> <code>str</code> <p>Input gene index path.</p> <code>vep_consequences_path</code> <code>str</code> <p>Input VEP consequences path.</p> <code>liftover_chain_file_path</code> <code>str</code> <p>Path to GRCh37 to GRCh38 chain file.</p> <code>liftover_max_length_difference</code> <code>str</code> <p>Maximum length difference for liftover.</p> <code>max_distance</code> <code>int</code> <p>Maximum distance to consider.</p> <code>approved_biotypes</code> <code>list[str]</code> <p>List of approved biotypes.</p> <code>intervals</code> <code>dict</code> <p>Dictionary of interval sources.</p> <code>v2g_path</code> <code>str</code> <p>Output V2G path.</p> Source code in <code>src/gentropy/v2g.py</code> <pre><code>class V2GStep:\n    \"\"\"Variant-to-gene (V2G) step.\n\n    This step aims to generate a dataset that contains multiple pieces of evidence supporting the functional association of specific variants with genes. Some of the evidence types include:\n\n    1. Chromatin interaction experiments, e.g. Promoter Capture Hi-C (PCHi-C).\n    2. In silico functional predictions, e.g. Variant Effect Predictor (VEP) from Ensembl.\n    3. Distance between the variant and each gene's canonical transcription start site (TSS).\n\n    Attributes:\n        session (Session): Session object.\n        variant_index_path (str): Input variant index path.\n        variant_annotation_path (str): Input variant annotation path.\n        gene_index_path (str): Input gene index path.\n        vep_consequences_path (str): Input VEP consequences path.\n        liftover_chain_file_path (str): Path to GRCh37 to GRCh38 chain file.\n        liftover_max_length_difference: Maximum length difference for liftover.\n        max_distance (int): Maximum distance to consider.\n        approved_biotypes (list[str]): List of approved biotypes.\n        intervals (dict): Dictionary of interval sources.\n        v2g_path (str): Output V2G path.\n    \"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        variant_index_path: str,\n        variant_annotation_path: str,\n        gene_index_path: str,\n        vep_consequences_path: str,\n        liftover_chain_file_path: str,\n        approved_biotypes: list[str],\n        interval_sources: dict[str, str],\n        v2g_path: str,\n        max_distance: int = 500_000,\n        liftover_max_length_difference: int = 100,\n    ) -&gt; None:\n        \"\"\"Run Variant-to-gene (V2G) step.\n\n        Args:\n            session (Session): Session object.\n            variant_index_path (str): Input variant index path.\n            variant_annotation_path (str): Input variant annotation path.\n            gene_index_path (str): Input gene index path.\n            vep_consequences_path (str): Input VEP consequences path.\n            liftover_chain_file_path (str): Path to GRCh37 to GRCh38 chain file.\n            approved_biotypes (list[str]): List of approved biotypes.\n            interval_sources (dict[str, str]): Dictionary of interval sources.\n            v2g_path (str): Output V2G path.\n            max_distance (int): Maximum distance to consider.\n            liftover_max_length_difference (int): Maximum length difference for liftover.\n        \"\"\"\n        # Read\n        gene_index = GeneIndex.from_parquet(session, gene_index_path)\n        vi = VariantIndex.from_parquet(session, variant_index_path).persist()\n        va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n        vep_consequences = session.spark.read.csv(\n            vep_consequences_path, sep=\"\\t\", header=True\n        ).select(\n            f.element_at(f.split(\"Accession\", r\"/\"), -1).alias(\n                \"variantFunctionalConsequenceId\"\n            ),\n            f.col(\"Term\").alias(\"label\"),\n            f.col(\"v2g_score\").cast(\"double\").alias(\"score\"),\n        )\n\n        # Transform\n        lift = LiftOverSpark(\n            # lift over variants to hg38\n            liftover_chain_file_path,\n            liftover_max_length_difference,\n        )\n        gene_index_filtered = gene_index.filter_by_biotypes(\n            # Filter gene index by approved biotypes to define V2G gene universe\n            list(approved_biotypes)\n        )\n        va_slimmed = va.filter_by_variant_df(\n            # Variant annotation reduced to the variant index to define V2G variant universe\n            vi.df\n        ).persist()\n        intervals = Intervals(\n            _df=reduce(\n                lambda x, y: x.unionByName(y, allowMissingColumns=True),\n                # create interval instances by parsing each source\n                [\n                    Intervals.from_source(\n                        session.spark, source_name, source_path, gene_index, lift\n                    ).df\n                    for source_name, source_path in interval_sources.items()\n                ],\n            ),\n            _schema=Intervals.get_schema(),\n        )\n        v2g_datasets = [\n            va_slimmed.get_distance_to_tss(gene_index_filtered, max_distance),\n            va_slimmed.get_most_severe_vep_v2g(vep_consequences, gene_index_filtered),\n            va_slimmed.get_plof_v2g(gene_index_filtered),\n            intervals.v2g(vi),\n        ]\n        v2g = V2G(\n            _df=reduce(\n                lambda x, y: x.unionByName(y, allowMissingColumns=True),\n                [dataset.df for dataset in v2g_datasets],\n            ).repartition(\"chromosome\"),\n            _schema=V2G.get_schema(),\n        )\n\n        # Load\n        (\n            v2g.df.write.partitionBy(\"chromosome\")\n            .mode(session.write_mode)\n            .parquet(v2g_path)\n        )\n</code></pre>"},{"location":"python_api/steps/variant_to_gene_step/#gentropy.v2g.V2GStep.__init__","title":"<code>__init__(session: Session, variant_index_path: str, variant_annotation_path: str, gene_index_path: str, vep_consequences_path: str, liftover_chain_file_path: str, approved_biotypes: list[str], interval_sources: dict[str, str], v2g_path: str, max_distance: int = 500000, liftover_max_length_difference: int = 100) -&gt; None</code>","text":"<p>Run Variant-to-gene (V2G) step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>variant_index_path</code> <code>str</code> <p>Input variant index path.</p> required <code>variant_annotation_path</code> <code>str</code> <p>Input variant annotation path.</p> required <code>gene_index_path</code> <code>str</code> <p>Input gene index path.</p> required <code>vep_consequences_path</code> <code>str</code> <p>Input VEP consequences path.</p> required <code>liftover_chain_file_path</code> <code>str</code> <p>Path to GRCh37 to GRCh38 chain file.</p> required <code>approved_biotypes</code> <code>list[str]</code> <p>List of approved biotypes.</p> required <code>interval_sources</code> <code>dict[str, str]</code> <p>Dictionary of interval sources.</p> required <code>v2g_path</code> <code>str</code> <p>Output V2G path.</p> required <code>max_distance</code> <code>int</code> <p>Maximum distance to consider.</p> <code>500000</code> <code>liftover_max_length_difference</code> <code>int</code> <p>Maximum length difference for liftover.</p> <code>100</code> Source code in <code>src/gentropy/v2g.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    variant_index_path: str,\n    variant_annotation_path: str,\n    gene_index_path: str,\n    vep_consequences_path: str,\n    liftover_chain_file_path: str,\n    approved_biotypes: list[str],\n    interval_sources: dict[str, str],\n    v2g_path: str,\n    max_distance: int = 500_000,\n    liftover_max_length_difference: int = 100,\n) -&gt; None:\n    \"\"\"Run Variant-to-gene (V2G) step.\n\n    Args:\n        session (Session): Session object.\n        variant_index_path (str): Input variant index path.\n        variant_annotation_path (str): Input variant annotation path.\n        gene_index_path (str): Input gene index path.\n        vep_consequences_path (str): Input VEP consequences path.\n        liftover_chain_file_path (str): Path to GRCh37 to GRCh38 chain file.\n        approved_biotypes (list[str]): List of approved biotypes.\n        interval_sources (dict[str, str]): Dictionary of interval sources.\n        v2g_path (str): Output V2G path.\n        max_distance (int): Maximum distance to consider.\n        liftover_max_length_difference (int): Maximum length difference for liftover.\n    \"\"\"\n    # Read\n    gene_index = GeneIndex.from_parquet(session, gene_index_path)\n    vi = VariantIndex.from_parquet(session, variant_index_path).persist()\n    va = VariantAnnotation.from_parquet(session, variant_annotation_path)\n    vep_consequences = session.spark.read.csv(\n        vep_consequences_path, sep=\"\\t\", header=True\n    ).select(\n        f.element_at(f.split(\"Accession\", r\"/\"), -1).alias(\n            \"variantFunctionalConsequenceId\"\n        ),\n        f.col(\"Term\").alias(\"label\"),\n        f.col(\"v2g_score\").cast(\"double\").alias(\"score\"),\n    )\n\n    # Transform\n    lift = LiftOverSpark(\n        # lift over variants to hg38\n        liftover_chain_file_path,\n        liftover_max_length_difference,\n    )\n    gene_index_filtered = gene_index.filter_by_biotypes(\n        # Filter gene index by approved biotypes to define V2G gene universe\n        list(approved_biotypes)\n    )\n    va_slimmed = va.filter_by_variant_df(\n        # Variant annotation reduced to the variant index to define V2G variant universe\n        vi.df\n    ).persist()\n    intervals = Intervals(\n        _df=reduce(\n            lambda x, y: x.unionByName(y, allowMissingColumns=True),\n            # create interval instances by parsing each source\n            [\n                Intervals.from_source(\n                    session.spark, source_name, source_path, gene_index, lift\n                ).df\n                for source_name, source_path in interval_sources.items()\n            ],\n        ),\n        _schema=Intervals.get_schema(),\n    )\n    v2g_datasets = [\n        va_slimmed.get_distance_to_tss(gene_index_filtered, max_distance),\n        va_slimmed.get_most_severe_vep_v2g(vep_consequences, gene_index_filtered),\n        va_slimmed.get_plof_v2g(gene_index_filtered),\n        intervals.v2g(vi),\n    ]\n    v2g = V2G(\n        _df=reduce(\n            lambda x, y: x.unionByName(y, allowMissingColumns=True),\n            [dataset.df for dataset in v2g_datasets],\n        ).repartition(\"chromosome\"),\n        _schema=V2G.get_schema(),\n    )\n\n    # Load\n    (\n        v2g.df.write.partitionBy(\"chromosome\")\n        .mode(session.write_mode)\n        .parquet(v2g_path)\n    )\n</code></pre>"},{"location":"python_api/steps/window_based_clumping/","title":"window_based_clumping","text":""},{"location":"python_api/steps/window_based_clumping/#gentropy.window_based_clumping.WindowBasedClumpingStep","title":"<code>gentropy.window_based_clumping.WindowBasedClumpingStep</code>","text":"<p>Apply window based clumping on summary statistics datasets.</p> Source code in <code>src/gentropy/window_based_clumping.py</code> <pre><code>class WindowBasedClumpingStep:\n    \"\"\"Apply window based clumping on summary statistics datasets.\"\"\"\n\n    def __init__(\n        self,\n        session: Session,\n        summary_statistics_input_path: str,\n        study_locus_output_path: str,\n        inclusion_list_path: str | None = None,\n        locus_collect_distance: int | None = None,\n    ) -&gt; None:\n        \"\"\"Run window-based clumping step.\n\n        Args:\n            session (Session): Session object.\n            summary_statistics_input_path (str): Path to the harmonized summary statistics dataset.\n            study_locus_output_path (str): Output path for the resulting study locus dataset.\n            inclusion_list_path (str | None): Path to the inclusion list (list of white-listed study identifier). Optional.\n            locus_collect_distance (int | None): Distance, within which tagging variants are collected around the semi-index. Optional.\n        \"\"\"\n        # If inclusion list path is provided, only these studies will be read:\n        if inclusion_list_path:\n            study_ids_to_ingest = [\n                f'{summary_statistics_input_path}/{row[\"studyId\"]}.parquet'\n                for row in session.spark.read.parquet(inclusion_list_path).collect()\n            ]\n        else:\n            # If no inclusion list is provided, read all summary stats in folder:\n            study_ids_to_ingest = [summary_statistics_input_path]\n\n        (\n            SummaryStatistics.from_parquet(\n                session,\n                study_ids_to_ingest,\n                recursiveFileLookup=True,\n            )\n            .coalesce(4000)\n            # Applying window based clumping:\n            .window_based_clumping(locus_collect_distance=locus_collect_distance)\n            # Save resulting study locus dataset:\n            .df.write.mode(session.write_mode)\n            .parquet(study_locus_output_path)\n        )\n</code></pre>"},{"location":"python_api/steps/window_based_clumping/#gentropy.window_based_clumping.WindowBasedClumpingStep.__init__","title":"<code>__init__(session: Session, summary_statistics_input_path: str, study_locus_output_path: str, inclusion_list_path: str | None = None, locus_collect_distance: int | None = None) -&gt; None</code>","text":"<p>Run window-based clumping step.</p> <p>Parameters:</p> Name Type Description Default <code>session</code> <code>Session</code> <p>Session object.</p> required <code>summary_statistics_input_path</code> <code>str</code> <p>Path to the harmonized summary statistics dataset.</p> required <code>study_locus_output_path</code> <code>str</code> <p>Output path for the resulting study locus dataset.</p> required <code>inclusion_list_path</code> <code>str | None</code> <p>Path to the inclusion list (list of white-listed study identifier). Optional.</p> <code>None</code> <code>locus_collect_distance</code> <code>int | None</code> <p>Distance, within which tagging variants are collected around the semi-index. Optional.</p> <code>None</code> Source code in <code>src/gentropy/window_based_clumping.py</code> <pre><code>def __init__(\n    self,\n    session: Session,\n    summary_statistics_input_path: str,\n    study_locus_output_path: str,\n    inclusion_list_path: str | None = None,\n    locus_collect_distance: int | None = None,\n) -&gt; None:\n    \"\"\"Run window-based clumping step.\n\n    Args:\n        session (Session): Session object.\n        summary_statistics_input_path (str): Path to the harmonized summary statistics dataset.\n        study_locus_output_path (str): Output path for the resulting study locus dataset.\n        inclusion_list_path (str | None): Path to the inclusion list (list of white-listed study identifier). Optional.\n        locus_collect_distance (int | None): Distance, within which tagging variants are collected around the semi-index. Optional.\n    \"\"\"\n    # If inclusion list path is provided, only these studies will be read:\n    if inclusion_list_path:\n        study_ids_to_ingest = [\n            f'{summary_statistics_input_path}/{row[\"studyId\"]}.parquet'\n            for row in session.spark.read.parquet(inclusion_list_path).collect()\n        ]\n    else:\n        # If no inclusion list is provided, read all summary stats in folder:\n        study_ids_to_ingest = [summary_statistics_input_path]\n\n    (\n        SummaryStatistics.from_parquet(\n            session,\n            study_ids_to_ingest,\n            recursiveFileLookup=True,\n        )\n        .coalesce(4000)\n        # Applying window based clumping:\n        .window_based_clumping(locus_collect_distance=locus_collect_distance)\n        # Save resulting study locus dataset:\n        .df.write.mode(session.write_mode)\n        .parquet(study_locus_output_path)\n    )\n</code></pre>"}]}
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