Epigenomics Python Packages

rocco

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

diffbio

End-to-end differentiable bioinformatics for JAX/Flax NNX: soft Smith-Waterman alignment, read mapping and assembly, variant calling, RNA-seq, single-cell, epigenomics, CRISPR, metabolomics, multi-omics, protein and RNA structure, molecular dynamics and drug-discovery operators composed into trainable pipelines on the Avitai stack.

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.

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

sincei

Explore data from single-cell genomics assays on a terminal (QC, counting, clustering, plotting, and more..)

pyxfr

The transferase system for retrieving methylome data from methbase

segway

Application for semi-automated genomic annotation.

chromoformer

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

epilogos

Methods for summarizing and visualizing multi-biosample functional genomic annotations

bap-atac

Bead-based single-cell atac processing

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.

mmspao

Multi-modal spatial omics integration with views and combinations.

prooverlap

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

sincei-rust

Explore data from single-cell genomics assays on a terminal (QC, counting, clustering, plotting, and more..)