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Bioconductor - InteractionSet (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews DataRepresentation, HiC, Infrastructure, Software Version 1.37.0 In Bioconductor since BioC 3.3 (R-3.3) (9 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, DuplexDiscovereR, GenomicInteractions, HiCDOC, sevenC, nullrangesData Imports Me CAGEfightR, ChIPpeakAnno, DegCre, EDIRquery, extraChIPs, geomeTriD, HicAggR, HiCcompare, HiCExperiment, HiContacts, HiCool, HiCParser, 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.

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