Set of programs to process, normalize, analyze and visualize Hi-C data

HiCExplorer addresses the common tasks of Hi-C data analysis from processing to visualization.



HiCExplorer is available as a command line suite of tools on this GitHub repository.

A Galaxy HiCExplorer version is directly available to users at http://hicexplorer.usegalaxy.eu. Training material is available at the Galaxy Training Network, while a Galaxy Tour is available here for users not familiar with this platform. Galaxy HiCExplorer is also available as a Docker image at the Docker Galaxy HiCExplorer GitHub repository. Finally, this Galaxy version is available on the Galaxy Tool Shed and on the corresponding GitHub repository.

The following is the list of tools available in HiCExplorer

tool description
findRestSites Identifies the genomic locations of restriction sites
hicBuildMatrix Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads
hicQC Plots QC measures from the output of hicBuildMatrix
hicCorrectMatrix Uses iterative correction to remove biases from a Hi-C matrix
hicFindEnrichedContacts Identifies enriched Hi-C contacts
hicCorrelate Computes and visualises the correlation of Hi-C matrices
hicFindTADs Identifies Topologically Associating Domains (TADs)
hicPCA Computes for A / B compartments the eigenvectors
hicTransform Computes a obs_exp matrix like Lieberman-Aiden (2009), a pearson correlation matrix and or a covariance matrix. These matrices can be used for plotting.
hicMergeMatrixBins Merges consecutive bins on a Hi-C matrix to reduce resolution
hicMergeTADbins Uses a BED file of domains or TAD boundaries to merge the bin counts of a Hi-C matrix.
hicPlotDistVsCounts Plot the decay in interaction frequency with distance
hicPlotMatrix Plots a Hi-C matrix as a heatmap
hicPlotTADs Plots TADs as a track that can be combined with other tracks (genes, signal, interactions)
hicPlotViewpoint A plot with the interactions around a reference point or region.
hicAggregateContacts A tool that allows plotting of aggregated Hi-C sub-matrices of a specified list of positions.
hicSumMatrices Adds Hi-C matrices of the same size
hicPlotDistVsCounts Plots distance vs. Hi-C counts of corrected data
hicInfo Shows information about a Hi-C matrix file (no. of bins, bin length, sum, max, min, etc)
hicCompareMatrices Computes difference or ratio between two matrices
hicAverageRegions Computes the average of multiple given regions, usually TAD regions
hicPlotAverageRegions visualization of hicAverageRegions
hicNormalize Normalizes the given matrices to 0-1 range or the smallest read coverage
hicConvertFormat Converts between different Hi-C interaction matrices
hicAdjustMatrix Keeps, removes or masks regions in a Hi-C matrix

Getting Help

  • For general questions, please use Biostars with Tag hicexplorer : Biostars
  • For specific questions and feature requests, use the deepTools mailing list
  • For suggesting changes/enhancements and to report bugs, please create an issue on our GitHub repository


Please cite HiCExplorer as follows:

Fidel Ramirez, Vivek Bhardwaj, Jose Villaveces, Laura Arrigoni, Bjoern A Gruening,Kin Chung Lam, Bianca Habermann, Asifa Akhtar, Thomas Manke. “High-resolution TADs reveal DNA sequences underlying genome organization in flies”. Nature Communications, Volume 9, Article number: 189 (2018), doi: https://doi.org/10.1038/s41467-017-02525-w

Joachim Wolff, Vivek Bhardwaj, Stephan Nothjunge, Gautier Richard, Gina Renschler, Ralf Gilsbach, Thomas Manke, Rolf Backofen, Fidel Ramírez, Björn A Grüning. Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W11–W16, doi: https://doi.org/10.1093/nar/gky504


This tool suite is developed by the Bioinformatics Unit at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg and by the Bioinformatics Lab of the Albert-Ludwigs-University Freiburg, Germany.