hi-c topic
HiCLift
A fast and efficient tool for converting chromatin interaction data between genome assemblies
TADLib
A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains
genomedisco
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
3d-genome-processing-tutorial
A 3D genome data processing tutorial for ISMB/ECCB 2017
ChromeGCN
Bioinformatics 2020: Graph Neural Networks for DNA Sequence Classification
cLoops2
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.
coolpuppy
A versatile tool to perform pile-up analysis on Hi-C data in .cool format.
polychrom
Chromosome polymer simulations and in silico capture experiments
hic
Analysis of Chromosome Conformation Capture data (Hi-C)
clodius
Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.