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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scell_hicpipe
Desktop

scell_hicpipe Single cell Hi-C Pipeline

Allows users to identify thousands of simultaneous chromatin contacts in a…

Allows users to identify thousands of simultaneous chromatin contacts in a single cell. The Single cell Hi-C Pipeline consists in a set of scripts that process single cell Hi-C libraries. It is able…

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cancer-hic-norm
Desktop

cancer-hic-norm

Explores the impact of copy number variants (CNVs) on Hi-C data.…

Explores the impact of copy number variants (CNVs) on Hi-C data. cancer-hic-norm provides a solution to deal with its effect on cancer data normalization. This tool proposes a model simulating large…

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gcMapExplorer
Desktop

gcMapExplorer genome contact map explorer

Enables user to browse and analyze genome contact maps with reference to…

Enables user to browse and analyze genome contact maps with reference to genomic datasets. gcMapExplorer includes an interactive visualizer that facilitates the browsing of several contact maps…

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3DGenome_FruitF…
Desktop

3DGenome_FruitFly

Integrates experimental data obtained from different technologies to map the 3D…

Integrates experimental data obtained from different technologies to map the 3D structures of entire genomes. 3DGenome_FruitFly generates a large number of genome structures whose chromatin contacts…

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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