pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.

Installation

To install pycisTopic, install SCENIC+ (which includes pycisTopic):

conda create --name scenicplus python=3.11 -y
conda activate scenicplus
git clone https://github.com/aertslab/scenicplus.git
cd scenicplus
pip install .

Check version

To check your pycisTopic version:

import pycisTopic
pycisTopic.__version__

Tutorials & documentation

Tutorial and documentation are available at https://pycistopic.readthedocs.io/.

Questions?

• If you have technical questions or problems, such as bug reports or ideas for new features, please open an issue under the issues tab.
• If you have questions about the interpretation of results or your analysis, please start a Discussion under the Discussions tab.

Reference

Bravo Gonzalez-Blas, C. & De Winter, S. et al. (2022). SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks