To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicInteractions")

In most cases, you don't need to download the package archive at all.

GenomicInteractions

R package for handling genomic interaction data

Bioconductor version: 3.0

R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics

Author: Harmston, N., Ing-Simmons, E., Perry, M., Baresic A., Lenhard B.

Maintainer: Nathan Harmston <nathan.harmston07 at csc.mrc.ac.uk>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicInteractions")

Documentation

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

browseVignettes("GenomicInteractions")

 

HTML R Script GenomicInteractions-ChIAPET
HTML R Script GenomicInteractions-HiC
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DataRepresentation, Infrastructure, Software
Version 1.0.3
In Bioconductor since BioC 3.0 (R-3.1)
License GPL-3
Depends R (>= 2.10)
Imports Rsamtools, GenomicRanges, IRanges, data.table, stringr, rtracklayer, ggplot2, gridExtra, methods, igraph, plotrix
LinkingTo
Suggests knitr, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm9
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source GenomicInteractions_1.0.3.tar.gz
Windows Binary GenomicInteractions_1.0.3.zip
Mac OS X 10.6 (Snow Leopard) GenomicInteractions_1.0.3.tgz
Mac OS X 10.9 (Mavericks) GenomicInteractions_1.0.3.tgz
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