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cooler

A cool place to store your Hi-C

pairtools

Extract 3D contacts (.pairs) from sequencing alignments

hiclift

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

diffdomain-py3

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

pairliftover

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

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.

firecaller

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