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.

_images/hicex2.png

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

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.

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

_images/logo_mpi-ie.jpg

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.