Welcome to CellOracle’s documentation!

CellOracle is a python library for the in silico gene perturbation analysis using single-cell omics data and gene regulatory network models.

Source code is available at CellOracle GitHub repository and PyPI.

For more information, please read our paper: Dissecting cell identity via network inference and in silico gene perturbation

News

Please look Changelog page for all updates history of CellOracle package.

• 02/08/2023: CellOracle paper has been published in Nature article ! It is also highlighted in News and Views . Thank you very much to all contributors and users for your help!!!

• 02/02/2023: We released celloracle version 0.10.15. We fixed a bug in Motif data loading function.

• 01/03/2023: We released celloracle version 0.10.14. We added a Xenopus Laevis data.

• 10/10/2022: We released celloracle version 0.10.12. We added a new function to check distribution range of simulated value. Tutorial is also updated.

Contents

• Installation
  • Docker image
  • Install CellOracle

• Tutorial
  • What the tutorial covers
  • Prerequisites
  • Code and data availability
  • Getting started
  • Index

• API
  • Custom class in celloracle
  • Modules for ATAC-seq analysis
  • Modules for Network analysis
  • Other modules

• Changelog

• License

• Authors and citations
  • Cite celloracle
  • celloracle software development

• Contact
  • CellOracle code issues
  • Inquiry for collabolation or discussion

Indices and tables

• Index

• Module Index

• Search Page