https://github.com/colomemaria/epiScanpy

Episcanpy: Epigenomics Single Cell Analysis in Python
https://github.com/colomemaria/epiScanpy

Last synced: 6 months ago
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Episcanpy: Epigenomics Single Cell Analysis in Python

• Host: GitHub
• URL: https://github.com/colomemaria/epiScanpy
• Owner: colomemaria
• License: bsd-3-clause
• Created: 2019-02-12T09:28:15.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2024-05-01T19:35:39.000Z (about 1 year ago)
• Last Synced: 2024-07-26T02:35:34.438Z (11 months ago)
• Language: Python
• Homepage:
• Size: 45.3 MB
• Stars: 138
• Watchers: 4
• Forks: 33
• Open Issues: 26
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE.txt

Awesome Lists containing this project

• awesome-atac-analysis - epiScanpy
• awesome-single-cell - EpiScanpy - [python] - EpiScanpy is the epigenomic extension of scRNA-seq analysis tool Scanpy. It analyses single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. [EpiScanpy: integrated single-cell epigenomic analysis](https://www.nature.com/articles/s41467-021-25131-3) (Software packages / Epigenomics)

README

        

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 `__, 2018) [Wolf18]. For more information on scanpy, read the following `documentation `__. 

EpiScanpy paper is now accessible on `Nature Communications `__. For more information on how to use the package, more information are available on the `website `__. 

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    * - Releases

      - | |GitHub release| |GitHub tag| |PyPI|

    * - Build status via Conda

      - | |Conda-Linux| 

    * - Python versions

      - | |py39| |py38| |py37| |py36| |py27| 

    * - Operating System

      - | |ubuntu-20.04| |macOS Catalina| |windows-latest|

    * - Document status

      - | |Docs|

    * - Github status

      - | |GitHub contributors| |GitHub stars| |GitHub forks| |GitHub watchers| |GitHub followers| 

.. |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 `__. If epiScanpy is useful to your research, consider citing `epiScanpy `__.