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Releases: cantinilab/CellOracle

v0.22.0+lite

14 Jan 13:40
@r-trimbour r-trimbour
v0.22.0+lite
14aa89b

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Update of the default_motifs importation from gimmemotifs, to make CellOracle compatible with gimmemotifs>=0.18.0

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v0.21.0+lite

10 Jan 19:09
@r-trimbour r-trimbour
v0.21.0+lite
9688a29

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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

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

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