3d-genome topic
cLoops
Accurate and flexible loops calling tool for 3D genomic data.
cooler
A cool place to store your Hi-C
HiC_tools
A collection of tools for Hi-C data analysis
juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Higashi
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
MATCHA
multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning
SNIPER
nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder
HiCLift
A fast and efficient tool for converting chromatin interaction data between genome assemblies
genomedisco
Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
cLoops2
Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.