InteractionSet
This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see InteractionSet.
Base Classes for Storing Genomic Interaction Data
Bioconductor version: 3.8
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("InteractionSet")):
Installation
To install this package, start R (version "3.5") 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")| Interacting with InteractionSet classes for genomic interaction data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DataRepresentation, HiC, Infrastructure, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8 years) |
| License | GPL-3 |
| Depends | R (>= 3.5), GenomicRanges, SummarizedExperiment |
| Imports | IRanges, S4Vectors(>= 0.19.4), GenomeInfoDb, BiocGenerics, methods, Matrix, Rcpp |
| System Requirements | C++11 |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, BiocStyle |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | diffHic, GenomicInteractions, MACPET, sevenC |
| Imports Me | CAGEfightR, HiCcompare, trackViewer |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | InteractionSet_1.10.0.tar.gz |
| Windows Binary | InteractionSet_1.10.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | InteractionSet_1.10.0.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 |
| Old Source Packages for BioC 3.8 | Source Archive |