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Analysing cool files in R with HiContacts

Bioconductor version: Release (3.19)

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

Author: Jacques Serizay [aut, cre]

Maintainer: Jacques Serizay <jacquesserizay at>

Citation (from within R, enter citation("HiContacts")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to HiContacts HTML R Script
Reference Manual PDF


biocViews DNA3DStructure, HiC, Software
Version 1.6.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License MIT + file LICENSE
Depends R (>= 4.2), HiCExperiment
Imports InteractionSet, SummarizedExperiment, GenomicRanges, IRanges, GenomeInfoDb, S4Vectors, methods, BiocGenerics, BiocIO, BiocParallel, RSpectra, Matrix, tibble, tidyr, dplyr, readr, stringr, ggplot2, ggrastr, scales, stats, utils
System Requirements
Bug Reports
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Suggests HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
Linking To
Depends On Me
Imports Me OHCA
Suggests Me HiCExperiment, HiCool
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package HiContacts_1.6.0.tar.gz
Windows Binary
macOS Binary (x86_64) HiContacts_1.6.0.tgz
macOS Binary (arm64) HiContacts_1.6.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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