https://github.com/pinellolab/pychromvar

A python package for chromVAR
https://github.com/pinellolab/pychromvar

chromatin-accessibiity chromvar scatac-seq

Last synced: 11 months ago
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A python package for chromVAR

• Host: GitHub
• URL: https://github.com/pinellolab/pychromvar
• Owner: pinellolab
• License: mit
• Created: 2022-05-17T21:07:15.000Z (about 4 years ago)
• Default Branch: main
• Last Pushed: 2023-05-01T23:20:59.000Z (about 3 years ago)
• Last Synced: 2025-06-07T04:07:38.272Z (about 1 year ago)
• Topics: chromatin-accessibiity, chromvar, scatac-seq
• Language: Python
• Homepage: https://pychromvar.readthedocs.io/
• Size: 2.57 MB
• Stars: 28
• Watchers: 1
• Forks: 4
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# pychromVAR 

pychromVAR is a python package for inferring transcription factor binding variability from scATAC-seq data by implmenting the algorithm proposed in [chromVAR](https://github.com/GreenleafLab/chromVAR). It is built on [anndata](https://anndata.readthedocs.io/en/latest/) and [mudata](https://mudata.readthedocs.io/en/latest/) therefore can work seamlessly with [Scanpy](https://scanpy.readthedocs.io/en/stable/index.html) and [Muon](https://gtca.github.io/muon/) pipeline. 

For more methodological details, please refer to the [paper](https://www.nature.com/articles/nmeth.4401). 

# Installation

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

```shell

pip install pychromvar

```

# Ecosystem

pychromVAR is part of [scverse](https://scverse.org/packages/#ecosystem) ecosystem.

# Tutorial

You can find [here](https://pychromvar.readthedocs.io/en/latest/notebooks/multimodal_pbmc_3k.html) a tutorial how to use pychromVAR combined with Muon to analysis multimodal single-cell PBMC data.