in silico gene perturbation analysis and GRN analysis with single cell data
Project description
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.
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: [“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.
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