InteractionSet

DOI: 10.18129/B9.bioc.InteractionSet    

Base Classes for Storing Genomic Interaction Data

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	Genomic interaction classes
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, HiC, Infrastructure, Software
Version	1.24.0
In Bioconductor since	BioC 3.3 (R-3.3) (6.5 years)
License	GPL-3
Depends	GenomicRanges, SummarizedExperiment
Imports	methods, Matrix, Rcpp, BiocGenerics, S4Vectors(>= 0.27.12), IRanges, GenomeInfoDb
LinkingTo	Rcpp
Suggests	testthat, knitr, rmarkdown, BiocStyle
SystemRequirements	C++11
Enhances
URL
Depends On Me	diffHic, GenomicInteractions, MACPET, nullrangesData, sevenC
Imports Me	CAGEfightR, ChIPpeakAnno, extraChIPs, HiCcompare, HiCDCPlus, nullranges, trackViewer
Suggests Me	CAGEWorkflow, plotgardener, updateObject
Links To Me
Build Report

Package Archives

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

Source Package	InteractionSet_1.24.0.tar.gz
Windows Binary	InteractionSet_1.24.0.zip
macOS Binary (x86_64)	InteractionSet_1.24.0.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