This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see HiContacts.

Analysing cool files in R with HiContacts

Bioconductor version: 3.18

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 gmail.com>

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


To install this package, start R (version "4.3") 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 1.4.0
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
URL https://github.com/js2264/HiContacts
Bug Reports https://github.com/js2264/HiContacts/issues
See More
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
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_1.4.0.tar.gz
Windows Binary HiContacts_1.4.0.zip
macOS Binary (x86_64) HiContacts_1.4.0.tgz
macOS Binary (arm64) HiContacts_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/HiContacts
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HiContacts
Bioc Package Browser https://code.bioconductor.org/browse/HiContacts/
Package Short Url https://bioconductor.org/packages/HiContacts/
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