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episcanpy

Episcanpy: Epigenomics Single Cell Analysis in Python

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EpiScanpy – Epigenomics single cell analysis in python

EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq analysis tool Scanpy (Genome Biology <https://doi.org/10.1186/s13059-017-1382-0>, 2018) [Wolf18]. For more information on scanpy, read the following documentation <https://scanpy.readthedocs.io>.

EpiScanpy paper is now accessible on Nature Communications <https://www.nature.com/articles/s41467-021-25131-3>. For more information on how to use the package, more information are available on the website <https://colomemaria.github.io/episcanpy_doc>.

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* - Python versions
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* - Operating System
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* - Document status
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* - Github status
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.. |Docs| image:: https://readthedocs.com/projects/icb-scanpy/badge/?version=latest :target: https://episcanpy.readthedocs.io/en/latest/ .. |PyPI| image:: https://img.shields.io/pypi/v/episcanpy.svg :target: https://pypi.org/project/episcanpy .. |py27| image:: https://github.com/colomemaria/epiScanpy/workflows/py27/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |py36| image:: https://github.com/colomemaria/epiScanpy/workflows/py36/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |py37| image:: https://github.com/colomemaria/epiScanpy/workflows/py37/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |py38| image:: https://github.com/colomemaria/epiScanpy/workflows/py38/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |py39| image:: https://github.com/colomemaria/epiScanpy/workflows/py39/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |ubuntu-20.04| image:: https://github.com/colomemaria/epiScanpy/workflows/ubuntu-20.04/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |macOS Catalina| image:: https://github.com/colomemaria/epiScanpy/workflows/macOS%20Catalina/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |windows-latest| image:: https://github.com/colomemaria/epiScanpy/workflows/windows-latest/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |Conda-Linux| image:: https://github.com/colomemaria/epiScanpy/workflows/Conda-Linux/badge.svg :target: https://github.com/colomemaria/epiScanpy/ .. |GitHub release| image:: https://img.shields.io/github/release/colomemaria/epiScanpy.svg :target: https://GitHub.com/colomemaria/epiScanpy/releases/ .. |GitHub tag| image:: https://img.shields.io/github/tag/colomemaria/epiScanpy.svg :target: https://GitHub.com/colomemaria/epiScanpy/tags/ .. |GitHub forks| image:: https://img.shields.io/github/forks/colomemaria/epiScanpy.svg?style=social&label=Fork&maxAge=2592000 :target: https://GitHub.com/colomemaria/epiScanpy/network/
.. |GitHub stars| image:: https://img.shields.io/github/stars/colomemaria/epiScanpy.svg?style=social&label=Star&maxAge=2592000 :target: https://GitHub.com/colomemaria/epiScanpy/stargazers/ .. |GitHub watchers| image:: https://img.shields.io/github/watchers/colomemaria/epiScanpy.svg?style=social&label=Watch&maxAge=2592000 :target: https://GitHub.com/colomemaria/epiScanpy/watchers/ .. |GitHub followers| image:: https://img.shields.io/github/followers/colomemaria.svg?style=social&label=Follow&maxAge=2592000 :target: https://GitHub.com/colomemaria?tab=followers .. |GitHub contributors| image:: https://img.shields.io/github/contributors/colomemaria/epiScanpy.svg :target: https://GitHub.com/colomemaria/epiScanpy/graphs/contributors/

Documentation

The documentation for epiScanpy is available here <https://colomemaria.github.io/episcanpy_doc/>. If epiScanpy is useful to your research, consider citing epiScanpy <https://www.nature.com/articles/s41467-021-25131-3>.

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