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

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


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)
hicMergeMatrixBins Merges consecutive bins on a Hi-C matrix to reduce resolution
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)
hicSumMatrices Adds Hi-C matrices of the same size
hicPlotDistVsCounts Plots distance vs. Hi-C counts of corrected data
hicExport Export matrix to text formats
hicInfo Shows information about a Hi-C matrix file (no. of bins, bin length, sum, max, min, etc)
hicCorrectMatrix Computes difference or ratio between two matrices

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”. bioRxiv 115063 doi: https://doi.org/10.1101/115063


This tool suite is developed by the Bioinformatics Unit at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.