HiCExplorer tools

tool type input files main output file(s) application
findRestSites preprocessing 1 genome FASTA file bed file with restriction site coordinates Identifies the genomic locations of restriction sites
hicBuildMatrix preprocessing 2 BAM/SAM files hicMatrix object Creates a Hi-C matrix using the aligned BAM files of the Hi-C sequencing reads
hicCorrectMatrix preprocessing hicMatrix object normalized hicMatrix object Uses iterative correction to remove biases from a Hi-C matrix
hicMergeMatrixBins preprocessing hicMatrix object hicMatrix object Merges consecutives bins on a Hi-C matrix to reduce resolution
hicSumMatrices preprocessing 2 or more hicMatrix objects hicMatrix object Adds Hi-C matrices of the same size
hicFindEnrichedContacts analysis hicMatrix object hicMatrix object Identifies enriched Hi-C contacts
hicCorrelate analysis 2 or more hicMatrix objects a heatmap/scatterplot Computes and visualises the correlation of Hi-C matrices
hicFindTADs analysis hicMatrix object bedGraph file (TAD score), a boundaries.bed file, a domains.bed file (TADs) Identifies Topologically Associating Domains (TADs)
hicPlotMatrix visualization hicMatrix object a heatmap of Hi-C contacts Plots a Hi-C matrix as a heatmap
hicPlotTADs visualization hicMatrix object, a config file Hi-C contacts on a given region, along with other provided signal (bigWig) or regions (bed) file Plots TADs as a track that can be combined with other tracks (genes, signal, interactions)
hicPlotDistVsCounts visualization hicMatrix object log log plot of Hi-C contacts per distance Quality control
hicExport data integration multiple Hi-C file formats Hi-C matrices/outputs in several formats Export matrix to different formats
hicInfo information one or more hicMatrix objects Screen info Prints information about matrices, like size, maximum, minimux, bin size, etc.
hicPCA analysis one Hi-C matrix bedgraph or bigwig file(s) for each eigenvector Computes for A / B compartments the eigenvectors
hicTransform analysis one Hi-C matrix Hi-C matrix 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.
hicPlotViewpoint visualization one Hi-C matrix A viewpoint plot A plot with the interactions around a reference point or region.
hicQC information log files from hicBuildMatrix A quality control report Quality control of the created contact matrix.
hicCorrectMatrix analysis two Hi-C matrices one Hi-C matrix Applies diff, ratio or log2ratio on matrices to compare them.
hicLog2Ratio analysis two Hi-C matrices one Hi-C matrix Computes the log2 ratio between two matrices.
hicMergeTADbins preprocessing one Hi-C matrix, one BED file one Hi-C matrix Uses a BED file of domains or TAD boundaries to merge the bin counts of a Hi-C matrix.