CellOracle-lite

Lightweight fork of CellOracle for ReCoN / HuMMuS

⚠️ Important notice
This repository is a lightweight fork of the original CellOracle project
(https://github.com/morris-lab/CellOracle).

It is not affiliated with, endorsed by, or maintained by the original CellOracle authors.

What is CellOracle-lite?

CellOracle-lite is a reduced version of CellOracle designed to support Gene Regulatory Network (GRN) workflows used in ReCoN and HuMMuS, while avoiding heavy dependencies required by the full CellOracle stack.

Version: 0.21.0 (lite fork)
Import as: import celloracle
Maintained by: cantinilab

This fork was created because some dependency combinations required by the full CellOracle package could not be resolved in the environments used by ReCoN and HuMMuS.

This fork:

• keeps the core GRN-related functionality needed by ReCoN
• removes optional or heavyweight components not required for these workflows
• aims to be faster and easier to install in lightweight environments

If you need the full CellOracle feature set, please use the official CellOracle package instead.

Original project

CellOracle is a Python library for in silico gene perturbation analyses using single-cell omics data and Gene Regulatory Network models.

Original repository:
https://github.com/morris-lab/CellOracle

Original publication:
Dissecting cell identity via network inference and in silico gene perturbation
https://www.nature.com/articles/s41586-022-05688-9

Original documentation:
https://morris-lab.github.io/CellOracle.documentation/

License

This fork is distributed under the same license terms as the original CellOracle project.

⚠️ Non-commercial restriction applies
CellOracle (and therefore this fork) may be used for non-commercial academic research purposes only.
Commercial use requires permission from the original CellOracle authors.

See the LICENSE file for full details.

Questions, issues, and support

• For this fork: https://github.com/cantinilab/celloracle/issues
• For the original CellOracle: https://github.com/morris-lab/CellOracle/issues

Please do not contact the original CellOracle maintainers about issues specific to this fork.

Supported species and reference genomes

(Same as upstream; unchanged)

• 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

For upstream changes, see:
https://morris-lab.github.io/CellOracle.documentation/changelog/index.html