pychromVAR

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.

Installation

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

pip install pychromvar

Ecosystem

pychromVAR is part of scverse ecosystem.

Tutorial

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