.. celloracle documentation master file, created by
   sphinx-quickstart on Thu Sep 19 17:42:52 2019.
   You can adapt this file completely to your liking, but it should at least
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Welcome to CellOracle's documentation!
======================================
|GitHub Workflow Status| |PyPI| |PyPI - Python Version| |PyPI - Wheel|
|Downloads| |Docker Pulls|


CellOracle is a python library for the in silico gene perturbation analysis using single-cell omics data and gene regulatory network models.

Source code is available at `CellOracle  GitHub repository <https://github.com/morris-lab/CellOracle>`_ and `PyPI <https://pypi.org/project/celloracle/>`_.

For more information, please read our paper: `Dissecting cell identity via network inference and in silico gene perturbation <https://www.nature.com/articles/s41586-022-05688-9>`_


.. raw:: html
   :file: test2.html


News
====

Please look at `Changelog page <https://morris-lab.github.io/CellOracle.documentation/changelog/index.html>`_ for all updates history of CellOracle package.

- 03/31/2024: We released celloracle version 0.18.0. Refactoring was done in the motif analysis to improve the stability of the function. Docker image was updated to the latest version of celloracle. From this version, we use python 3.10 in the docker image.

- 03/19/2024: We released celloracle version 0.17.1. This update includes a bug fix, refactoring, and new test functions. Now we support Python 3.10. 

- 02/01/2024: We released celloracle version 0.16.0. Fixed a bug in the Systematic Simulation function to comply with the latest update of pandas.

- 07/25/2023: We released celloracle version 0.15.0. This update includes refactoring in the Markov simulation function. 

- 02/08/2023: CellOracle paper has been published in `Nature article <https://www.nature.com/articles/s41586-022-05688-9>`_ ! It is also highlighted in `News and Views <https://www.nature.com/articles/d41586-023-00251-6>`_ . Thank you very much to all contributors and users for your help!!!

- 02/02/2023: We released celloracle version 0.10.15. We fixed a bug in Motif data loading function.




Contents
========


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   self


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   installation/index

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   tutorials/index


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   modules/index

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   changelog/index

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   license/index

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   citation/index

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   contact/index


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`


.. |GitHub Workflow Status| image:: https://img.shields.io/github/actions/workflow/status/morris-lab/CellOracle/build_check.yml?branch=master
   :target: https://github.com/morris-lab/CellOracle/actions/workflows/build_check.yml
.. |PyPI| image:: https://img.shields.io/pypi/v/celloracle?color=blue
   :target: https://pypi.org/project/celloracle/
.. |PyPI - Python Version| image:: https://img.shields.io/pypi/pyversions/celloracle
   :target: https://pypi.org/project/celloracle/
.. |PyPI - Wheel| image:: https://img.shields.io/pypi/wheel/celloracle
   :target: https://pypi.org/project/celloracle/
.. |Downloads| image:: https://static.pepy.tech/personalized-badge/celloracle?period=total&units=international_system&left_color=grey&right_color=orange&left_text=Downloads
   :target: https://pepy.tech/project/celloracle
.. |Docker Pulls| image:: https://img.shields.io/docker/pulls/kenjikamimoto126/celloracle_ubuntu?color=orange
   :target: https://hub.docker.com/r/kenjikamimoto126/celloracle_ubuntu