HiContacts
This is the released version of HiContacts; for the devel version, see HiContacts.
All Bioconductor versions of HiContacts
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16
Analysing cool files in R with HiContacts
Bioconductor version: 3.23 · Package version: 1.14.0
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"):
Jacques Serizay. HiContacts: Analysing cool files in R with HiContacts. doi:10.18129/B9.bioc.HiContacts, R package version 1.14.0, https://bioconductor.org/packages/HiContacts.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiContacts")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.14.0 |
| License | MIT + file LICENSE |
| URL | https://github.com/js2264/HiContacts |
| Bug Reports | https://github.com/js2264/HiContacts/issues |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 years) |
| Downloads rank | 950 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNA3DStructure, HiC, Software |
| Package Short Url | https://bioconductor.org/packages/HiContacts/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HiContacts")| Introduction to HiContacts | HTML | R Script |
| Reference Manual |
Download
Follow the installation instructions to use this package in your R session.
| Source package | HiContacts_1.14.0.tar.gz |
| Windows binary (x86_64) | HiContacts_1.14.0.zip |
| macOS binary (arm64) | HiContacts_1.14.0.tgz |
| macOS binary (x86_64) | HiContacts_1.14.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HiContacts |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HiContacts |
| Package Downloads Report | Download Stats |
Dependencies
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
Suggests: HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
Reverse dependencies
Suggests Me (3): HiCExperiment, HiCool, HiSpaR