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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: d8158e6d80a4e413539252e5d79255e7
+tags: 645f666f9bcd5a90fca523b33c5a78b7
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diff --git a/_sources/develop.md.txt b/_sources/develop.md.txt
@@ -0,0 +1,14 @@
+Contributing to SnapATAC2
+=========================
+
+## A brief guide to adding new features to SnapATAC2
+
+The SnapATAC2 Github repository contains three libraries:
+
+1. `snapatac2-core`: Core functions written in Rust.
+2. `snapatac2-python`: High-level user-facing functions written in mostly Python.
+3. `snapatac2-contrib`: Python package containing additional features from external contributors.
+
+Unless the new feature is essential and highly relevant to functions in the core library, it is recommended to add it to the `snapatac2-contrib` library.
+Otherwise, add the feature to the `snapatac2-python` library under the `snapatac2.experimental` module.
+We will move function from `snapatac2.experimental` to `snapatac2` once they are sufficiently tested and stable.
diff --git a/_sources/index.rst.txt b/_sources/index.rst.txt
@@ -0,0 +1,30 @@
+SnapATAC2: A Python/Rust package for single-cell epigenomics analysis
+=====================================================================
+
+SnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis framework, featuring:
+
+- Scale to more than 10 million cells.
+- Blazingly fast preprocessing tools for BAM to fragment files conversion and count matrix generation.
+- Matrix-free spectral embedding algorithm that is applicable to a wide range of single-cell omics data, including single-cell ATAC-seq, single-cell RNA-seq, single-cell Hi-C, and single-cell methylation.
+- Efficient and scalable co-embedding algorithm for single-cell multi-omics data integration.
+- End-to-end analysis pipeline for single-cell ATAC-seq data, including preprocessing, dimension reduction, clustering, data integration, peak calling, differential analysis, motif analysis, regulatory network analysis.
+- Seamless integration with other single-cell analysis packages such as Scanpy.
+- Implementation of fully backed AnnData.
+
+How to cite
+-----------
+
+The SnapATAC2 manuscript has not been published yet. The key algorithms used in
+SnapATAC2 have been described in the following papers:
+
+- Zhang, K. et al. A single-cell atlas of chromatin accessibility in the human genome. Cell 184, 5985-6001.e19 (2021).
+- Fang, R. et al. Comprehensive analysis of single cell ATAC-seq data with SnapATAC. Nat Commun 12, 1337 (2021).
+
+.. toctree::
+   :maxdepth: 3
+   :hidden:
+
+   install
+   tutorials/index
+   reference/index
+   Development<develop>
diff --git a/_sources/install.md.txt b/_sources/install.md.txt
@@ -0,0 +1,79 @@
+Installation
+============
+
+Stable version
+--------------
+
+Stable versions of SnapATAC2 are published on PyPI.
+Precompiled binaries are available for x86_64 Linux systems and macOS.
+So installing it is as simple as running:
+
+```
+pip install snapatac2
+```
+
+If there are no precompiled binaries published for your system, you will have to
+build the package from source.
+Building the SnapATAC2 library requires `cmake >= 3.5.1` and
+the [Rust](https://www.rust-lang.org/tools/install) compiler. You need to install
+them first if they are not available on your system.
+You can find the instructions for installing cmake [here](https://cmake.org/install/).
+The Rust compiler can be installed using:
+
+```
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+rustup default nightly
+```
+
+Once you have cmake and the Rust compiler properly installed,
+running `pip install snapatac2` will build SnapATAC2 from the source package and
+install it just as it would if there was a prebuilt binary available.
+
+Nightly build
+-------------
+
+The nightly build is the build from the latest source codes, which includes the
+latest features, enhancements, and bug fixes that haven't been released. 
+The nightly build can be unstable and include some untested features.
+
+You can download the wheel files of the latest Nightly build from this
+[link](https://nightly.link/kaizhang/SnapATAC2/workflows/wheels/main/artifact.zip).
+
+After downloading the file, unzip it and then select the appropriate wheel file
+for your platform and use `pip install` to install it.
+
+Build from the latest source code 
+---------------------------------
+
+Building the SnapATAC2 library requires `cmake >= 3.5.1` and
+the [Rust](https://www.rust-lang.org/tools/install) compiler. You need to install
+them first if they are not available on your system.
+You can find the instructions for installing cmake [here](https://cmake.org/install/).
+The Rust compiler can be installed using:
+
+```
+curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
+rustup default nightly
+```
+
+Once you have cmake and the Rust compiler properly installed,
+clone the source code repository and go to the `snapatac2-python` directory,
+use `pip install .` to install the package.
+
+```
+git clone https://github.com/kaizhang/SnapATAC2.git
+cd SnapATAC2/snapatac2-python
+pip install .
+```
+
+Optional dependencies
+---------------------
+
+Here is a list of optional dependencies used by SnapATAC2:
+
+- `macs2`: Peak calling.
+- `harmonypy`: Batch correction using the Harmony.
+- `xgboost`: Regulatory network analysis.
+
+Optional dependencies are not installed by SnapATAC2. Please install them
+manually if necessary.
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.X.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.X.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.X
+===================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.X
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.backend.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.backend.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.backend
+=========================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.backend
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.chunked_X.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.chunked_X.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.chunked\_X
+============================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.chunked_X
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.close.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.close.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.close
+=======================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.close
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.copy.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.copy.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.copy
+======================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.copy
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.filename.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.filename.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.filename
+==========================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.filename
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.is_closed.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.is_closed.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.is\_closed
+============================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.is_closed
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.isbacked.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.isbacked.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.isbacked
+==========================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.isbacked
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.layers.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.layers.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.layers
+========================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.layers
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.n_obs.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.n_obs.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.n\_obs
+========================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.n_obs
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.n_vars.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.n_vars.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.n\_vars
+=========================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.n_vars
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.obs.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.obs.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.obs
+=====================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.obs
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.obs_ix.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.obs_ix.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.obs\_ix
+=========================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.obs_ix
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.obs_names.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.obs_names.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.obs\_names
+============================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.obs_names
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.obsm.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.obsm.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.obsm
+======================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.obsm
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.obsp.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.obsp.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.obsp
+======================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.obsp
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.open.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.open.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.open
+======================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.open
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.rst.txt
@@ -0,0 +1,53 @@
+snapatac2.AnnData
+=================
+
+.. currentmodule:: snapatac2
+
+.. autoclass:: AnnData
+
+
+
+   .. rubric:: Attributes
+
+   .. autosummary::
+      :toctree: .
+
+      ~snapatac2.AnnData.X
+      ~snapatac2.AnnData.backend
+      ~snapatac2.AnnData.filename
+      ~snapatac2.AnnData.isbacked
+      ~snapatac2.AnnData.layers
+      ~snapatac2.AnnData.n_obs
+      ~snapatac2.AnnData.n_vars
+      ~snapatac2.AnnData.obs
+      ~snapatac2.AnnData.obs_names
+      ~snapatac2.AnnData.obsm
+      ~snapatac2.AnnData.obsp
+      ~snapatac2.AnnData.shape
+      ~snapatac2.AnnData.uns
+      ~snapatac2.AnnData.var
+      ~snapatac2.AnnData.var_names
+      ~snapatac2.AnnData.varm
+      ~snapatac2.AnnData.varp
+
+
+
+
+
+   .. rubric:: Methods
+
+   .. autosummary::
+      :toctree: .
+
+      ~snapatac2.AnnData.chunked_X
+      ~snapatac2.AnnData.close
+      ~snapatac2.AnnData.copy
+      ~snapatac2.AnnData.is_closed
+      ~snapatac2.AnnData.obs_ix
+      ~snapatac2.AnnData.open
+      ~snapatac2.AnnData.subset
+      ~snapatac2.AnnData.to_memory
+      ~snapatac2.AnnData.var_ix
+      ~snapatac2.AnnData.write
+
+
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.shape.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.shape.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.shape
+=======================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.shape
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.subset.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.subset.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.subset
+========================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.subset
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.to_memory.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.to_memory.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.to\_memory
+============================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.to_memory
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.uns.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.uns.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.uns
+=====================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.uns
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.var.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.var.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.var
+=====================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.var
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.var_ix.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.var_ix.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.var\_ix
+=========================
+
+.. currentmodule:: snapatac2
+
+.. automethod:: AnnData.var_ix
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.var_names.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.var_names.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.var\_names
+============================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.var_names
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.varm.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.varm.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.varm
+======================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.varm
diff --git a/_sources/reference/_autosummary/snapatac2.AnnData.varp.rst.txt b/_sources/reference/_autosummary/snapatac2.AnnData.varp.rst.txt
@@ -0,0 +1,6 @@
+snapatac2.AnnData.varp
+======================
+
+.. currentmodule:: snapatac2
+
+.. autoattribute:: AnnData.varp