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 bioRxiv preprint: CellOracle: Dissecting cell identity via network inference and in silico gene perturbation


CellOracle is still under development. It is currently a beta version. Functions in this package may change in a future release.


Please look Changelog page for all updates history of CellOracle package.

  • 09/27/2022: We released celloracle version 0.10.11. We added a new function to change cluster color.

  • 09/09/2022: We released celloracle version 0.10.10. We updated some functions in the network score calculation and visualization.

  • 07/21/2022: We released celloracle version 0.10.8. Simulation tutorial notebook is updated; We added a guidance to find best vm parameter for the simulation result visualization.

  • 07/15/2022: We released celloracle version 0.10.7. Docker image was updated. This version supports mm39 reference genome.

  • 07/08/2022: Docker image was updated. We made quick start page to guide user how to start celloracle analysis with our docker image.

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