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Contributing to SnapATAC2 | ||
========================= | ||
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## A brief guide to adding new features to SnapATAC2 | ||
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The SnapATAC2 Github repository contains three libraries: | ||
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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. | ||
|
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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. |
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SnapATAC2: A Python/Rust package for single-cell epigenomics analysis | ||
===================================================================== | ||
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SnapATAC2 is a flexible, versatile, and scalable single-cell omics analysis framework, featuring: | ||
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- 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. | ||
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How to cite | ||
----------- | ||
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The SnapATAC2 manuscript has not been published yet. The key algorithms used in | ||
SnapATAC2 have been described in the following papers: | ||
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- 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). | ||
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.. toctree:: | ||
:maxdepth: 3 | ||
:hidden: | ||
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install | ||
tutorials/index | ||
reference/index | ||
Development<develop> |
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Installation | ||
============ | ||
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Stable version | ||
-------------- | ||
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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: | ||
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``` | ||
pip install snapatac2 | ||
``` | ||
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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: | ||
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``` | ||
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh | ||
rustup default nightly | ||
``` | ||
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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. | ||
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Nightly build | ||
------------- | ||
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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. | ||
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You can download the wheel files of the latest Nightly build from this | ||
[link](https://nightly.link/kaizhang/SnapATAC2/workflows/wheels/main/artifact.zip). | ||
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After downloading the file, unzip it and then select the appropriate wheel file | ||
for your platform and use `pip install` to install it. | ||
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Build from the latest source code | ||
--------------------------------- | ||
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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 | ||
``` | ||
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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. | ||
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``` | ||
git clone https://github.com/kaizhang/SnapATAC2.git | ||
cd SnapATAC2/snapatac2-python | ||
pip install . | ||
``` | ||
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Optional dependencies | ||
--------------------- | ||
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Here is a list of optional dependencies used by SnapATAC2: | ||
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- `macs2`: Peak calling. | ||
- `harmonypy`: Batch correction using the Harmony. | ||
- `xgboost`: Regulatory network analysis. | ||
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Optional dependencies are not installed by SnapATAC2. Please install them | ||
manually if necessary. |
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snapatac2.AnnData.X | ||
=================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.X |
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_sources/reference/_autosummary/snapatac2.AnnData.backend.rst.txt
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snapatac2.AnnData.backend | ||
========================= | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.backend |
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_sources/reference/_autosummary/snapatac2.AnnData.chunked_X.rst.txt
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snapatac2.AnnData.chunked\_X | ||
============================ | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.chunked_X |
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_sources/reference/_autosummary/snapatac2.AnnData.close.rst.txt
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snapatac2.AnnData.close | ||
======================= | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.close |
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_sources/reference/_autosummary/snapatac2.AnnData.copy.rst.txt
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snapatac2.AnnData.copy | ||
====================== | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.copy |
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_sources/reference/_autosummary/snapatac2.AnnData.filename.rst.txt
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snapatac2.AnnData.filename | ||
========================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.filename |
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_sources/reference/_autosummary/snapatac2.AnnData.is_closed.rst.txt
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snapatac2.AnnData.is\_closed | ||
============================ | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.is_closed |
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_sources/reference/_autosummary/snapatac2.AnnData.isbacked.rst.txt
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snapatac2.AnnData.isbacked | ||
========================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.isbacked |
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_sources/reference/_autosummary/snapatac2.AnnData.layers.rst.txt
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snapatac2.AnnData.layers | ||
======================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.layers |
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_sources/reference/_autosummary/snapatac2.AnnData.n_obs.rst.txt
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snapatac2.AnnData.n\_obs | ||
======================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.n_obs |
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_sources/reference/_autosummary/snapatac2.AnnData.n_vars.rst.txt
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snapatac2.AnnData.n\_vars | ||
========================= | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.n_vars |
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_sources/reference/_autosummary/snapatac2.AnnData.obs.rst.txt
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snapatac2.AnnData.obs | ||
===================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.obs |
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snapatac2.AnnData.obs\_ix | ||
========================= | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.obs_ix |
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snapatac2.AnnData.obs\_names | ||
============================ | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.obs_names |
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snapatac2.AnnData.obsm | ||
====================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.obsm |
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snapatac2.AnnData.obsp | ||
====================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.obsp |
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_sources/reference/_autosummary/snapatac2.AnnData.open.rst.txt
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snapatac2.AnnData.open | ||
====================== | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.open |
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snapatac2.AnnData | ||
================= | ||
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.. currentmodule:: snapatac2 | ||
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.. autoclass:: AnnData | ||
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.. rubric:: Attributes | ||
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.. autosummary:: | ||
:toctree: . | ||
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~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 | ||
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.. rubric:: Methods | ||
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.. autosummary:: | ||
:toctree: . | ||
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~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 | ||
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_sources/reference/_autosummary/snapatac2.AnnData.shape.rst.txt
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snapatac2.AnnData.shape | ||
======================= | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.shape |
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_sources/reference/_autosummary/snapatac2.AnnData.subset.rst.txt
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snapatac2.AnnData.subset | ||
======================== | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.subset |
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_sources/reference/_autosummary/snapatac2.AnnData.to_memory.rst.txt
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snapatac2.AnnData.to\_memory | ||
============================ | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.to_memory |
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_sources/reference/_autosummary/snapatac2.AnnData.uns.rst.txt
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snapatac2.AnnData.uns | ||
===================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.uns |
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_sources/reference/_autosummary/snapatac2.AnnData.var.rst.txt
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snapatac2.AnnData.var | ||
===================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.var |
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_sources/reference/_autosummary/snapatac2.AnnData.var_ix.rst.txt
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snapatac2.AnnData.var\_ix | ||
========================= | ||
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.. currentmodule:: snapatac2 | ||
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.. automethod:: AnnData.var_ix |
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_sources/reference/_autosummary/snapatac2.AnnData.var_names.rst.txt
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snapatac2.AnnData.var\_names | ||
============================ | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.var_names |
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_sources/reference/_autosummary/snapatac2.AnnData.varm.rst.txt
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snapatac2.AnnData.varm | ||
====================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.varm |
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_sources/reference/_autosummary/snapatac2.AnnData.varp.rst.txt
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snapatac2.AnnData.varp | ||
====================== | ||
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.. currentmodule:: snapatac2 | ||
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.. autoattribute:: AnnData.varp |
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