Search Packages

rocco

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

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

segway

Application for semi-automated genomic annotation.

cpgtools

Python package to analyze DNA methylation data

pyxfr

The Transferase Python API

deepaccess

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

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

chromoformer

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

bap-atac

Bead-based single-cell atac processing

prooverlap

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

mmspao

Multi-modal spatial omics integration with views and combinations.