Welcome to CellOracle’s documentation!¶
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
Warning
CellOracle is still under development. It is currently a beta version. Functions in this package may change in a future release.
News¶
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.