/CellOracle

This is the alpha version of the CellOracle package

Primary LanguagePythonApache License 2.0Apache-2.0

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

  • 0.6.5 <2021-3-25>

    • Minor bug fix in the installation process.

  • 0.6.4 <2021-2-18>

    • Minor change for oracle object. Metadata will be shown if you print oracle object.
    • Add new function to oracle class.

  • 0.6.3 <2021-1-26>

    • Big fix to solve this issue.
    • Bug fix. Anndata>=0.7.5 is required.

  • 0.6.2 <2020-12-16>

    • Big fix. h5py>=3.1.0 is required.

  • 0.6.0 <2020-12-14>

    • Add new modules: dev_modules and analysis_helper.

  • 0.5.1 <2020-08-4>

    • Add new promoter-TSS reference data for several reference genomes; (1)"Xenopus": ["xenTro2", "xenTro3"], (2)"Rat": ["rn4", "rn5", "rn6"], (3)"Drosophila": ["dm3", "dm6"], (4)"C.elegans": ["ce6", "ce10"], (5)"Arabidopsis": ["tair10"].
    • Add new motif data for several species: "Xenopus", "Rat", "Drosophila", "C.elegans" and "Arabidopsis".

  • 0.5.0 <2020-08-3>

    • Add new functions for custom motifs. You can select motifs from several options. Also, we updated our web tutorial to introduce how to load / make different motif data.
    • Change default motifs for S.cerevisiae and zebrafish.
    • Change requirements for dependent package: gimmemotifs and geomepy. Celloracle codes were updated to support new version of gimmemotifs (0.14.4) and genomepy (0.8.4).

  • 0.4.2 <2020-07-14>

    • Add promoter-TSS information for zebrafish reference genome (danRer7, danRer10 and danRer11).

  • 0.4.1 <2020-07-02>

    • Add promoter-TSS information for S.cerevisiae reference genome (sacCer2 and sacCer3).

  • 0.4.0 <2020-06-28>

    • Change requirements.
    • From this version, pandas version 1.0.3 or later is required.
    • From this version, scanpy version 1.5.3 or later is required.

  • 0.3.7 <2020-06-12>

    • Delete GO function from r-script
    • Update some functions for network visualization

  • 0.3.6 <2020-06-08>

    • Fix a bug on the transition probability calculation in Markov simulation
    • Add new function "count_cells_in_mc_results" to oracle class

  • 0.3.5 <2020-05-09>

    • Fix a bug on the function for gene cortography visualization
    • Change some settings for installation
    • Update data conversion module

  • 0.3.4 <2020-04-29>

    • Change pandas version restriction
    • Fix a bug on the function for gene cortography visualization
    • Add new functions for R-path configuration

  • 0.3.3 <2020-04-24>

    • Add promoter-TSS information for hg19 and hg38 reference genome

  • 0.3.1 <2020-03-23>

    • Fix an error when try to save file larger than 4GB file

  • 0.3.0 <2020-2-17>

    • Release beta version