InteractionSet
This is the development version of InteractionSet; for the stable release version, see InteractionSet.
All Bioconductor versions of InteractionSet
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: 3.24 · Package version: 1.41.0
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 1.41.0, 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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("InteractionSet")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.41.0 |
| License | GPL-3 |
| System Requirements | C++11 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.3 (R-3.3) (10 years) |
| Downloads rank | 200 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, HiC, Infrastructure, Software |
| Package Short Url | https://bioconductor.org/packages/InteractionSet/ |
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 | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | InteractionSet_1.41.0.tar.gz |
| Windows binary (x86_64) | InteractionSet_1.41.0.zip |
| macOS binary (arm64) | InteractionSet_1.41.0.tgz |
| macOS binary (x86_64) | InteractionSet_1.41.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/InteractionSet |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/InteractionSet |
| Package Downloads Report | Download Stats |
Dependencies
Depends: GenomicRanges, SummarizedExperiment
Imports: methods, Matrix, Rcpp, BiocGenerics, S4Vectors (>= 0.27.12), IRanges, Seqinfo
LinkingTo: Rcpp
Reverse dependencies
Depends On Me (7): diffHic, DuplexDiscovereR, GenomicInteractions, HiCDOC, nullrangesData, plyinteractions, sevenC
Imports Me (23): annoLinker, CAGEfightR, ChIPpeakAnno, DegCre, DMRcaller, EDIRquery, extraChIPs, GenomicCoordinates, geomeTriD, HicAggR, HiCaptuRe, HiCcompare, HiCDCPlus, HiCExperiment, HiContacts, HiCool, HiCParser, hicream, hicVennDiagram, mariner, nullranges, trackViewer, treediff
Suggests Me (6): CAGEWorkflow, CNVScope, plotgardener, S4Cartographer, transmogR, updateObject