InteractionSet

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see InteractionSet.

Base Classes for Storing Genomic Interaction Data

Bioconductor version: 3.19

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")):

Installation

To install this package, start R (version "4.4") 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")

Genomic interaction classes	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, HiC, Infrastructure, Software
Version	1.32.0
In Bioconductor since	BioC 3.3 (R-3.3) (8.5 years)
License	GPL-3
Depends	GenomicRanges, SummarizedExperiment
Imports	methods, Matrix, Rcpp, BiocGenerics, S4Vectors(>= 0.27.12), IRanges, GenomeInfoDb
System Requirements	C++11
URL

Suggests	testthat, knitr, rmarkdown, BiocStyle
Linking To	Rcpp
Enhances
Depends On Me	GenomicInteractions, HiCDOC, diffHic, sevenC, nullrangesData
Imports Me	CAGEfightR, ChIPpeakAnno, DegCre, EDIRquery, HiCExperiment, HiCcompare, HiContacts, HiCool, HicAggR, extraChIPs, hicVennDiagram, mariner, nullranges, plyinteractions, trackViewer, treediff
Suggests Me	plotgardener, transmogR, updateObject, CAGEWorkflow
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	InteractionSet_1.32.0.tar.gz
Windows Binary (x86_64)	InteractionSet_1.32.0.zip
macOS Binary (x86_64)	InteractionSet_1.32.0.tgz
macOS Binary (arm64)	InteractionSet_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/InteractionSet
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/InteractionSet
Bioc Package Browser	https://code.bioconductor.org/browse/InteractionSet/
Package Short Url	https://bioconductor.org/packages/InteractionSet/
Package Downloads Report	Download Stats