HiContacts

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>

Installation

To install this package, start R (version "4.3") 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.

Documentation

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

browseVignettes("HiContacts")

 

HTML	R Script	Introduction to HiContacts
PDF		Reference Manual
Text		LICENSE

Details

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
LinkingTo
Suggests	HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
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/
Package Downloads Report	Download Stats