DOI: 10.18129/B9.bioc.HiContacts  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see HiContacts.

Analysing cool files in R with HiContacts

Bioconductor version: 3.17

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.


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HTML R Script Introduction to HiContacts
PDF   Reference Manual


biocViews DNA3DStructure, HiC, Software
Version 1.2.0
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
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
Suggests HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
URL https://github.com/js2264/HiContacts
BugReports https://github.com/js2264/HiContacts/issues
Depends On Me
Imports Me
Suggests Me HiCExperiment, HiCool
Links To Me
Build Report  

Package Archives

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

Source Package HiContacts_1.2.0.tar.gz
Windows Binary HiContacts_1.2.0.zip
macOS Binary (x86_64) HiContacts_1.2.0.tgz
macOS Binary (arm64) HiContacts_1.2.0.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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