HiCExplorer

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.

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Availability

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

A Galaxy HiCExplorer version is available on the Galaxy Tool Shed and on the corresponding GitHub repository. A Docker image is also available at https://github.com/deeptools/docker-galaxy-hicexplorer. Finally, Galaxy HiCExplorer is directly available to users at http://hicexplorer.usegalaxy.eu. Training material is available at this address, while a Galaxy Tour is available at https://hicexplorer.usegalaxy.eu/tours/hixexplorer for users not familiar with this platform.

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.
hicAggreagteContacts 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
hicExport Export matrix to text formats
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
hicLog2Ratio Computes the log2 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

Citation

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

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