CellOracle
==========
|GitHub Workflow Status| |PyPI| |PyPI - Python Version| |PyPI - Wheel|
|Downloads| |Docker Pulls|
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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