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 paper: Dissecting cell identity via network inference and in silico gene perturbation.

Documentation, Codes, and Tutorials

CellOracle documentation is available through the link 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: ['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.