InteractionSet

DOI: 10.18129/B9.bioc.InteractionSet    

Base Classes for Storing Genomic Interaction Data

Bioconductor version: Release (3.7)

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>

Citation (from within R, enter citation("InteractionSet")):

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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("InteractionSet")

 

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

Details

biocViews DataRepresentation, HiC, Infrastructure, Software
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (2 years)
License GPL-3
Depends R (>= 3.5), GenomicRanges, SummarizedExperiment
Imports IRanges, S4Vectors(>= 0.17.21), GenomeInfoDb, BiocGenerics, methods, Matrix, Rcpp
LinkingTo Rcpp
Suggests testthat, knitr, rmarkdown, BiocStyle
SystemRequirements C++11
Enhances
URL
Depends On Me diffHic, GenomicInteractions, MACPET, sevenC
Imports Me HiCcompare, trackViewer
Suggests Me
Build Report  

Package Archives

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

Source Package InteractionSet_1.8.0.tar.gz
Windows Binary InteractionSet_1.8.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) InteractionSet_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/InteractionSet
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/InteractionSet
Package Short Url http://bioconductor.org/packages/InteractionSet/
Package Downloads Report Download Stats

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