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.

Availability¶

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
hicQuickQC	Estimates the quality of Hi-C dataset
hicQC	Plots QC measures from the output of hicBuildMatrix
hicCorrectMatrix	Uses iterative correction to remove biases from a Hi-C matrix
hicDetectLoops	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
hicValidateLocations	Compare the loops with known peak protein locations
hicMergeLoops	Merges loops of different resolutions
hicCompartmentsPolarization	Compute the global compartmentalization signal
chicQualityControl	Quality control for cHi-C data
chicViewpointBackgroundModel	Background model computation for cHi-C analysis
chicViewpoint	Computation of all viewpoints based on background model for cHi-C analysis
chicSignificantInteractions	Detection of significant interactions per viewpoint based on background model
chicAggregateStatistic	Compiling of target regions for two samples as input for differential analysis
chicDifferentialTest	Differential analysis of interactions of two samples
chicPlotViewpoint	Plotting of viewpoint with background model and highlighting of significant and differential regions

Getting Help¶

For all kind of questions, suggesting changes/enhancements and to report bugs, please create an issue on our GitHub repository
In the past we offered to post on Biostars with Tag hicexplorer : Biostars or on the deepTools mailing list. We still check these resources from time to time but the preferred way to communicate are GitHub issues.

Contents:¶

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

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.