A collection of tools for Hi-C data analysis

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

Customizable workflows based on snakemake and python for the analysis of NGS data

Fast, flexible and extensible genome browser.

A cool place to store your Hi-C

Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.

A (continuously updated) collection of references to Hi-C data. Predominantly human/mouse Hi-C data, with replicates.

HapHiC: a fast, reference-independent, allele-aware scaffolding tool based on Hi-C data

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

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

Extract 3D contacts (.pairs) from sequencing alignments

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models f…

Analysis of Chromosome Conformation Capture data (Hi-C)

A modular Hi-C mapping pipeline

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

GENome Organisation Visual Analytics

C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.

Lightweight converter between hic and cool contact matrices.

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