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 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¶
|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.|
- HiCExplorer tools
- Example usage
- News and Developments
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
This tool suite is developed by the Bioinformatics Unit at the Max Planck Institute for Immunobiology and Epigenetics, Freiburg.