pychromVAR is a python package for inferring transcription factor binding variability from scATAC-seq data by implmenting the algorithm proposed in chromVAR. It is built on anndata and mudata therefore can work seamlessly with Scanpy and Muon pipeline.

For more methodological details, please refer to the paper.

The quickest and easiest way to get pychromvar is to to use pip:

pip install pychromvar

pychromVAR is part of scverse ecosystem.

You can find here a tutorial how to use pychromVAR combined with Muon to analysis multimodal single-cell PBMC data.