InteractionSet

DOI: 10.18129/B9.bioc.InteractionSet    

Base Classes for Storing Genomic Interaction Data

Bioconductor version: Release (3.6)

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 <alun at wehi.edu.au>, Malcolm Perry <mgperry32 at gmail.com>, Liz Ing-Simmons <liz.ing-simmons12 at csc.mrc.ac.uk>

Maintainer: Aaron Lun <alun at wehi.edu.au>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("InteractionSet")

Documentation

HTML	R Script	Interacting with InteractionSet classes for genomic interaction data
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, HiC, Infrastructure, Software
Version	1.6.0
In Bioconductor since	BioC 3.3 (R-3.3) (2 years)
License	GPL-3
Depends	R (>= 3.4), GenomicRanges(>= 1.29.6), SummarizedExperiment(>= 1.1.6)
Imports	IRanges, S4Vectors(>= 0.13.13), GenomeInfoDb, BiocGenerics, methods, Matrix, Rcpp
LinkingTo	Rcpp
Suggests	testthat, knitr, rmarkdown, BiocStyle
SystemRequirements	C++11
Enhances
URL
Depends On Me	diffHic, GenomicInteractions
Imports Me	HiCcompare
Suggests Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	InteractionSet_1.6.0.tar.gz
Windows Binary	InteractionSet_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	InteractionSet_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/InteractionSet
Package Short Url	http://bioconductor.org/packages/InteractionSet/
Package Downloads Report	Download Stats