A collection of tools for Hi-C data analysis

A One-Click System for Analyzing Loop-Resolution Hi-C Experiments

A cool place to store your Hi-C

Accurate and flexible loops calling tool for 3D genomic data.

Extract 3D contacts (.pairs) from sequencing alignments

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph

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

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

multiway chromatin interaction, 3D genome, single-nucleus, hypergraph representation learning

nuclear compartments, subcompartments, nuclear organization, Hi-C, autoencoder

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition

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

Data and the co-authored network I extracted for lab selection in 3D genome research field

3DGB is a workflow to build 3D models of genomes from HiC data

Visual exploration of large genome interaction matrices with interactive small multiples.

Spectral and reproducibility analysis of Hi-C contact maps

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs