Epigenomics Python Packages

allcools

Toolkit for single-cell DNA methylation analysis.

finaletoolkit

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

rocco

Robust Open Chromatin Detection via Convex Optimization: Multisample Consensus Peak Calling

broad-genepy

A useful module for any CompBio

cpgtools

Tools to analyze and visualize DNA methylation data

segway

Segway is a tool for easy pattern discovery and identification in functional genomics data.

pyxfr

The Transferase Python API

deepaccess

A package for training and interpreting an ensemble of neural networks for chromatin accessibility

chromoformer

Chromoformer - Pytorch

sincei

A command-line and python toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data

epilogos

Methods for summarizing and visualizing multi-biosample functional genomic annotations

bap-atac

Bead-based scATAC-seq data Processing.

prooverlap

Assessing feature proximity/overlap and testing statistical significance from genomic intervals

mmspao

Multi-modal spatial omics integration with views and combinations.