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InteractionSet

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

Base Classes for Storing Genomic Interaction Data


Bioconductor version: Development (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")

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

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

Details

biocViews DataRepresentation, HiC, Infrastructure, Software
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 years)
License GPL-3
Depends GenomicRanges, SummarizedExperiment
Imports methods, Matrix, Rcpp, BiocGenerics, S4Vectors(>= 0.27.12), IRanges, GenomeInfoDb
System Requirements C++11
URL
See More
Suggests testthat, knitr, rmarkdown, BiocStyle
Linking To Rcpp
Enhances
Depends On Me diffHic, GenomicInteractions, HiCDOC, nullrangesData, sevenC
Imports Me CAGEfightR, ChIPpeakAnno, DegCre, EDIRquery, extraChIPs, HiCcompare, HiCDCPlus, HiCExperiment, HiContacts, HiCool, hicVennDiagram, mariner, nullranges, plyinteractions, trackViewer
Suggests Me CAGEWorkflow, plotgardener, transmogR, updateObject
Links To Me
Build Report Build Report

Package Archives

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

Source Package InteractionSet_1.31.0.tar.gz
Windows Binary
macOS Binary (x86_64) InteractionSet_1.31.0.tgz
macOS Binary (arm64)
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