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 hiC file formats HiC matices/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.