InteractionSet

This is the released version of InteractionSet; for the devel version, see InteractionSet.

Base Classes for Storing Genomic Interaction Data

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DOI: 10.18129/B9.bioc.InteractionSet

Bioconductor version: Release (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")
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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, HiC, Infrastructure, Software

Version 1.38.0

In Bioconductor since BioC 3.3 (R-3.3) (9.5 years)

License GPL-3

Depends GenomicRanges, SummarizedExperiment

Imports methods, Matrix, Rcpp, BiocGenerics, S4Vectors(>= 0.27.12), IRanges, Seqinfo

System Requirements C++11

URL

Suggests testthat, knitr, rmarkdown, BiocStyle

Linking To Rcpp

Enhances

Depends On Me diffHic, DuplexDiscovereR, GenomicInteractions, HiCDOC, sevenC, nullrangesData

Imports Me CAGEfightR, ChIPpeakAnno, DegCre, DMRcaller, EDIRquery, extraChIPs, geomeTriD, HicAggR, HiCaptuRe, HiCcompare, HiCExperiment, HiContacts, HiCParser, hicVennDiagram, linkSet, mariner, nullranges, plyinteractions, trackViewer, hicream, 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.

Source Package InteractionSet_1.38.0.tar.gz

Windows Binary (x86_64) InteractionSet_1.37.1.zip (64-bit only)

macOS Binary (x86_64) InteractionSet_1.38.0.tgz

macOS Binary (arm64) InteractionSet_1.38.0.tgz

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/

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