3d Genome Python Packages

cooler

A cool place to store your Hi-C

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

hiclift

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

diffdomain-py3

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

particlechromo3d

3D chromosome structure reconstruction using ParticleChromo3D+

cloops2

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

pairliftover

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