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 bioRxiv preprint: CellOracle: Dissecting cell identity via network inference and in silico gene perturbation

Warning

CellOracle is still under development. It is currently a beta version. Functions in this package may change in a future release.

News

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

• 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.

• 09/27/2022: We released celloracle version 0.10.11. We added a new function to change cluster color.

• 09/09/2022: We released celloracle version 0.10.10. We updated some functions in the network score calculation and visualization.

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