InteractionSet
Base Classes for Storing Genomic Interaction Data
Bioconductor version: 3.23 · Package version: 1.40.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("InteractionSet")Details
| Maintainer | Aaron Lun <infinite.monkeys.with.keyboards@gmail.com> |
| Author | Aaron Lun [aut, cre], Malcolm Perry [aut], Elizabeth Ing-Simmons [aut] |
| License | GPL-3 |
| System Requirements | C++11 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DataRepresentation, HiC, Infrastructure, Software |
| Package Short Url | https://bioconductor.org/packages/InteractionSet/ |
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 1.40.0, https://bioconductor.org/packages/InteractionSet.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | InteractionSet_1.40.0.tar.gz |
| Windows binary (x86_64) | InteractionSet_1.40.0.zip |
| macOS binary (arm64) | InteractionSet_1.40.0.tgz |
| macOS binary (x86_64) | InteractionSet_1.40.0.tgz |
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 (24): annoLinker, CAGEfightR, ChIPpeakAnno, DegCre, DMRcaller, EDIRquery, extraChIPs, GenomicCoordinates, geomeTriD, HicAggR, HiCaptuRe, HiCcompare, HiCDCPlus, HiCExperiment, HiContacts, HiCool, HiCParser, hicream, hicVennDiagram, linkSet, mariner, nullranges, trackViewer, treediff
Suggests Me (5): CAGEWorkflow, CNVScope, plotgardener, transmogR, updateObject