Added project proposal as deliverable

mkempenaar · Sep 9, 2024 · 29e800f · 29e800f
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diff --git a/docs/404.html b/docs/404.html
@@ -101,7 +101,7 @@ <h1>Page not found<a class="anchor" aria-label="anchor" href="#page-not-found"><
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
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diff --git a/docs/EDA.html b/docs/EDA.html
@@ -716,7 +716,7 @@ <h2>
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   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
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diff --git a/docs/a2-annotation.html b/docs/a2-annotation.html
@@ -899,7 +899,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
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diff --git a/docs/a2-data_loading.html b/docs/a2-data_loading.html
@@ -474,7 +474,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
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diff --git a/docs/chapter-4.html b/docs/chapter-4.html
@@ -489,7 +489,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/chapter-5.html b/docs/chapter-5.html
@@ -318,7 +318,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/datasets.html b/docs/datasets.html
@@ -192,7 +192,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
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diff --git a/docs/from-reads-to-counts.html b/docs/from-reads-to-counts.html
@@ -483,7 +483,7 @@ <h3>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
   </div>
 
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diff --git a/docs/index.html b/docs/index.html
@@ -98,6 +98,8 @@ <h3>
 </h3>
 <ul>
 <li>
+<strong>Project Proposal</strong>: A short written proposal of the project clearly describing the data set, the research question and the methods + tools to be used.</li>
+<li>
 <strong>Genomics pipeline</strong>: The genomics analysis pipeline is well documented in one or more <em>lab journals</em> and contains the correct tools based on the research question and data set.</li>
 <li>
 <strong>Presentation</strong>: The research results will be presented in an attractive method and proper level given the target audience.</li>
@@ -141,7 +143,7 @@ <h3>
 </li>
 </ul>
 <p>Data is available from the NCBI <a href="https://www.ncbi.nlm.nih.gov/sra">Sequence Read Archive</a> and Gene Expression Omnibus.</p>
-<p>The proper way to search for a data set suitable for both Genomics and Transcriptomics projects is by creating a query that searches for both: <a href="https://www.ncbi.nlm.nih.gov/gds/?term=(%22expression+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D)+AND+%22genome+variation+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D">(“expression profiling by high throughput sequencing”[DataSet Type]) AND “genome variation profiling by high throughput sequencing”[DataSet Type]</a>.</p>
+<p>The proper way to search for a data set suitable for both Genomics and Transcriptomics projects is by creating a query that searches for both: <a href="https://www.ncbi.nlm.nih.gov/gds/?term=(%22expression+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D)+AND+%22genome+variation+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D">(“expression profiling by high throughput sequencing”[DataSet Type]) AND “genome variation profiling by high throughput sequencing”[DataSet Type]</a>. If this selection actually contains anything of interest is up to you; if you cannot find something interesting please use a different search strategy. One could be to search for RNA-Seq experiments in the GEO where one of the groups is preferably a mutant.</p>
 <p>Note that for the genomics part, not all available samples have to be processed. Other than for transcriptomics, it is not common that there is a case/control experimental setup but rather a single condition of group with possibly a few replicates. If the data set does include many samples, it is recommended to select a subset of samples to process (do discuss the reasoning behind this selection).</p>
 </div>
 </div>
@@ -157,6 +159,8 @@ <h3>
 </h3>
 <ul>
 <li>
+<strong>Project Proposal</strong>: A short written proposal of the project clearly describing the data set, the research question and the methods + libraries to be used.</li>
+<li>
 <strong>Lab Journal</strong>: The lab journal is readable, complete and aimed at the reproducability of the research. Relevant visualisations are include and statistical methods performed to support the biological interpretation of the results.</li>
 </ul>
 </div>
@@ -574,7 +578,7 @@ <h2>
 <footer class="bg-primary text-light mt-5"><div class="container"><div class="row">
 
   <div class="col-12 col-md-6 mt-3">
-    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-08.</p>
+    <p>"<strong>2.1.2 Genomics &amp; Transcriptomics</strong>" was written by Marcel Kempenaar. It was last built on 2024-09-09.</p>
   </div>
 
   <div class="col-12 col-md-6 mt-3">

diff --git a/docs/search.json b/docs/search.json
diff --git a/index.Rmd b/index.Rmd
@@ -23,6 +23,7 @@ For this Genomics analysis we are going to look at variants between the chosen d
 
 ### Project Deliverables
 
+* **Project Proposal**: A short written proposal of the project clearly describing the data set, the research question and the methods + tools to be used.
 * **Genomics pipeline**: The genomics analysis pipeline is well documented in one or more *lab journals* and contains the correct tools based on the research question and data set.
 * **Presentation**: The research results will be presented in an attractive method and proper level given the target audience.
 
@@ -61,7 +62,7 @@ Finding a suitable data set can be challenging as there are a few requirements s
 
 Data is available from the NCBI [Sequence Read Archive](https://www.ncbi.nlm.nih.gov/sra) and Gene Expression Omnibus.
 
-The proper way to search for a data set suitable for both Genomics and Transcriptomics projects is by creating a query that searches for both: [("expression profiling by high throughput sequencing"[DataSet Type]) AND "genome variation profiling by high throughput sequencing"[DataSet Type]](https://www.ncbi.nlm.nih.gov/gds/?term=(%22expression+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D)+AND+%22genome+variation+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D).
+The proper way to search for a data set suitable for both Genomics and Transcriptomics projects is by creating a query that searches for both: [("expression profiling by high throughput sequencing"[DataSet Type]) AND "genome variation profiling by high throughput sequencing"[DataSet Type]](https://www.ncbi.nlm.nih.gov/gds/?term=(%22expression+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D)+AND+%22genome+variation+profiling+by+high+throughput+sequencing%22%5BDataSet+Type%5D). If this selection actually contains anything of interest is up to you; if you cannot find something interesting please use a different search strategy. One could be to search for RNA-Seq experiments in the GEO where one of the groups is preferably a mutant. 
 
 Note that for the genomics part, not all available samples have to be processed. Other than for transcriptomics, it is not common that there is a case/control experimental setup but rather a single condition of group with possibly a few replicates. If the data set does include many samples, it is recommended to select a subset of samples to process (do discuss the reasoning behind this selection).
 
@@ -73,6 +74,7 @@ While there is no golden standard for analyzing RNA-sequencing data sets as ther
 
 ### Project Deliverables
 
+* **Project Proposal**: A short written proposal of the project clearly describing the data set, the research question and the methods + libraries to be used.
 * **Lab Journal**: The lab journal is readable, complete and aimed at the reproducability of the research. Relevant visualisations are include and statistical methods performed to support the biological interpretation of the results.
 
 ## *Lab Journal*