Hi-C data analysis bioinformatics software tools

Hi-C allows unbiased identification of chromatin interactions across an entire genome. Briefly: cells are crosslinked with formaldehyde; DNA is digested with a restriction enzyme that leaves a 5′-overhang; the 5′-overhang is filled, including a biotinylated residue;…

Hi-C analysis steps

Most recent bioinformatics tools

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GenomeDISCO
Desktop

GenomeDISCO Genome DIfferences between Smoothed COntact maps

Assesses the similarity of a pair of contact maps obtained from chromosome…

Assesses the similarity of a pair of contact maps obtained from chromosome capture experiments. GenomeDISCO is designed for evaluating concordance and reproducibility of chromatin contact maps…

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CscoreTool
Desktop

CscoreTool

Allows user to infer A/B compartments from Hi-C data. CscoreTool is a…

Allows user to infer A/B compartments from Hi-C data. CscoreTool is a prediction method for A/B compartments that can work on high resolution for dataset. It carries out high-resolution, precise high…

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TADkit
Web
Desktop

TADkit

Produces interactive 3D representations of modelled chromatin conformations.…

Produces interactive 3D representations of modelled chromatin conformations. TADkit allows users to study the relationship between 3D structure of the genome and its biological function. This tool is…

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HiC-3DViewer
Web

HiC-3DViewer

Simplifies the 3D exploratory analysis of High Chromosome Contact map (Hi-C)…

Simplifies the 3D exploratory analysis of High Chromosome Contact map (Hi-C) data. HiC-3DViewer is an interactive chromatin visualization tool that maps genome-scale interactions to identify…

Most popular analytical software

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HOMER
Desktop

HOMER Hypergeometric Optimization of Motif EnRichment

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER…

A suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of…

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HiTC
Desktop

HiTC

Facilitates the exploration of high-throughput 3C-based data. HiTC allows users…

Facilitates the exploration of high-throughput 3C-based data. HiTC allows users to import and export ‘C’ data, to transform, normalize, annotate and visualize interaction maps. It proposes a…

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WashU…
Web

WashU Epigenome Browser

A genome browser focusing on the human epigenome. The Browser is web-based and…

A genome browser focusing on the human epigenome. The Browser is web-based and it extends the seminal concept invented by the UCSC Cancer Genomics Browser to support large, sequencing-based datasets.…

Curators for Hi-C analysis

  • Nicolas Servant's avatar image
    Nicolas Servant
    Institut Curie, Paris, France
  • Muhammad Shamim's avatar image Muhammad Shamim's country flag
    Muhammad Shamim
    Baylor College of Medicine

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