InteractionSet
Base Classes for Storing Genomic Interaction Data
Bioconductor version: Release (3.20)
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 "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, HiC, Infrastructure, Software |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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, 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.
| Source Package | InteractionSet_1.34.0.tar.gz |
| Windows Binary (x86_64) | InteractionSet_1.34.0.zip |
| macOS Binary (x86_64) | InteractionSet_1.34.0.tgz |
| macOS Binary (arm64) | InteractionSet_1.33.0.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/ |
| Package Downloads Report | Download Stats |