3d Genome Python Packages

cooler

A cool place to store your Hi-C

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

particlechromo3d

A Web-Server implementation of ParticleChromo3D for 3D chromosome structure reconstruction

diffdomain-py3

DiffDomain is a statistically sound method for detecting differential TADs between conditions

pairliftover

A fast and efficient tool for converting chromatin interaction data between genome assemblies

hiclift

A fast and efficient tool for converting chromatin interaction data between genome assemblies

firecaller

FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

cloops2

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph