celloracle

CellOracle

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CellOracle is a python library for in silico gene perturbation analyses using single-cell omics data and Gene Regulatory Network models.

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>__.

Documentation, Codes, and Tutorials

CellOracle documentation is available through the link below.

`Web
documentation <https://morris-lab.github.io/CellOracle.documentation/>`__

Questions and errors
~~~~~~~~~~~~~~~~~~~~

If you have a question, error, bug, or problem, please use the `Github
issue page <https://github.com/morris-lab/CellOracle/issues>`__.

Supported Species and reference genomes

• Human: [‘hg38’, ‘hg19’]
• Mouse: [‘mm39’, ‘mm10’, ‘mm9’]
• S.cerevisiae: [“sacCer2”, “sacCer3”]
• Zebrafish: [“danRer7”, “danRer10”, “danRer11”]
• Xenopus tropicalis: [“xenTro2”, “xenTro3”]
• Xenopus laevis: [“Xenopus_laevis_v10.1”]
• Rat: [“rn4”, “rn5”, “rn6”]
• Drosophila: [“dm3”, “dm6”]
• C.elegans: [“ce6”, “ce10”]
• Arabidopsis: [“TAIR10”]
• Chicken: [“galGal4”, “galGal5”, “galGal6”]
• Guinea Pig: [“Cavpor3.0”]
• Pig: [“Sscrofa11.1”]

Changelog

Please go to `this
page <https://morris-lab.github.io/CellOracle.documentation/changelog/index.html>`__.

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