InteractionSet

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

Base Classes for Storing Genomic Interaction Data

Bioconductor version: Release (3.23)

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

Author: Aaron Lun [aut, cre], Malcolm Perry [aut], Elizabeth Ing-Simmons [aut]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>

Citation (from within R, enter citation("InteractionSet")):

Aaron Lun, Malcolm Perry, Elizabeth Ing-Simmons. InteractionSet: Base Classes for Storing Genomic Interaction Data. doi:10.18129/B9.bioc.InteractionSet, R package version 1.40.0, https://bioconductor.org/packages/InteractionSet.

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("InteractionSet")

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("InteractionSet")

Classes for genomic interaction data	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, HiC, Infrastructure, Software
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL-3
Depends	GenomicRanges, SummarizedExperiment
Imports	methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12), IRanges, Seqinfo
System Requirements	C++11
URL

Suggests	testthat, knitr, rmarkdown, BiocStyle
Linking To	Rcpp
Enhances
Depends On Me	diffHic, DuplexDiscovereR, GenomicInteractions, HiCDOC, nullrangesData, plyinteractions, sevenC
Imports Me	annoLinker, CAGEfightR, ChIPpeakAnno, DegCre, DMRcaller, EDIRquery, extraChIPs, GenomicCoordinates, geomeTriD, HicAggR, HiCaptuRe, HiCcompare, HiCDCPlus, HiCExperiment, HiContacts, HiCool, HiCParser, hicream, hicVennDiagram, linkSet, mariner, nullranges, trackViewer, treediff
Suggests Me	CAGEWorkflow, CNVScope, plotgardener, transmogR, updateObject
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	InteractionSet_1.40.0.tar.gz
Windows Binary (x86_64)	InteractionSet_1.40.0.zip
macOS Binary (big-sur-x86_64)	InteractionSet_1.40.0.tgz
macOS Binary (sonoma-arm64)	InteractionSet_1.40.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/InteractionSet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/InteractionSet
Package Short Url	https://bioconductor.org/packages/InteractionSet/
Package Downloads Report	Download Stats