CellOracle

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

Documentation, Codes, and Tutorials

CellOracle documentation is available through the links below.

Web documentation

Questions and errors

If you have a question, error, bug, or problem, please use the Github issue page.

Supported Species and reference genomes

• Human: ['hg38', 'hg19']
• Mouse: ['mm10', 'mm9']
• S.cerevisiae: ["sacCer2", "sacCer3"]
• Zebrafish: ["danRer7", "danRer10", "danRer11"]
• Xenopus: ["xenTro2", "xenTro3"]
• Rat: ["rn4", "rn5", "rn6"]
• Drosophila: ["dm3", "dm6"]
• C.elegans: ["ce6", "ce10"]
• Arabidopsis: ["TAIR10"]
• Chicken: ["galGal4", "galGal5", "galGal6"]
• Guinea Pig: ["Cavpor3.0"]

Please let us know through Github issue page if you have a request for another reference genome.

Changelog

Please go to this page.