Welcome to CellOracle’s documentation!

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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 and PyPI.

For more information, please read our paper: Dissecting cell identity via network inference and in silico gene perturbation


Please look at Changelog page 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 ! It is also highlighted in News and Views . 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.


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