HiContacts

This is the released version of HiContacts; for the devel version, see HiContacts.

All versions

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: Release (3.23)

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

Author: Jacques Serizay [aut, cre] ORCID: 0000-0002-4295-0624

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.

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	PDF
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNA3DStructure, HiC, Software
Version	1.14.0
In Bioconductor since	BioC 3.16 (R-4.2) (4 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

Suggests	HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me	OHCA
Suggests Me	HiCExperiment, HiCool, HiSpaR
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow 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 (64-bit only)
macOS Binary (big-sur-x86_64)	HiContacts_1.14.0.tgz
macOS Binary (sonoma-arm64)	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 Short Url	https://bioconductor.org/packages/HiContacts/
Package Downloads Report	Download Stats