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Base Classes for Storing Genomic Interaction Data

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Genomic interaction classes HTML R Script
Reference Manual PDF


biocViews DataRepresentation, HiC, Infrastructure, Software
Version 1.32.0
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
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Suggests testthat, knitr, rmarkdown, BiocStyle
Linking To Rcpp
Depends On Me diffHic, GenomicInteractions, HiCDOC, sevenC, nullrangesData
Imports Me CAGEfightR, ChIPpeakAnno, DegCre, EDIRquery, extraChIPs, HicAggR, HiCcompare, HiCExperiment, HiContacts, HiCool, hicVennDiagram, mariner, nullranges, plyinteractions, trackViewer, treediff
Suggests Me plotgardener, transmogR, updateObject, CAGEWorkflow
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package InteractionSet_1.32.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) InteractionSet_1.32.0.tgz
macOS Binary (arm64) InteractionSet_1.32.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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