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

segway

Application for semi-automated genomic annotation.

broad-genepy

Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python

cpgtools

Python package to analyze DNA methylation data

mmspao

Multi-modal spatial omics integration with views and combinations.

pyxfr

The Transferase Python API

epilogos

Methods for summarizing and visualizing multi-biosample functional genomic annotations

deepaccess

Methods for training and interpretation of an ensemble of neural networks for multi-task functional prediction of accessibility or histone modifications from DNA sequence.

bap-atac

Bead-based single-cell atac processing

sincei

A user-friendly toolkit for QC, counting, clustering and plotting of single-cell (epi)genomics data

chromoformer

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

prooverlap

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