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CellOracle

CellOracle is a python library for the in silico gene perturbation analysis 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 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"]

Changelog

Please go to this page.

About

This is the alpha version of the CellOracle package

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  • Python 97.6%
  • R 1.9%
  • Other 0.5%