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 can test the significant difference of TADs on chromatin.

particlechromo3d

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

cloops2

Loop-calling and peak-calling for sequencing-based interaction data, including related analysis utilities.

pairliftover

Convert genomic coordinates of contact pairs from one assembly to another.

firecaller

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