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HiContacts

This is the development version of HiContacts; for the stable release version, see HiContacts.

Analysing cool files in R with HiContacts

Bioconductor version: Development (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")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews DNA3DStructure, HiC, Software
Version 1.3.0
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
Linking To
Suggests HiContactsData, rtracklayer, GenomicFeatures, Biostrings, BSgenome.Scerevisiae.UCSC.sacCer3, WGCNA, Rfast, terra, patchwork, testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown
System Requirements
Enhances
URL https://github.com/js2264/HiContacts
Bug Reports https://github.com/js2264/HiContacts/issues
See More
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_1.3.0.tar.gz
Windows Binary HiContacts_1.3.0.zip
macOS Binary (x86_64) HiContacts_1.3.0.tgz
macOS Binary (arm64) HiContacts_1.3.0.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