To install this package, start R and enter:

## try http if https is not available
source("https://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: 3.1

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

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

Installation

To install this package, start R and enter:

## try http if https is not available
source("https://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, HiC, Infrastructure, Software
Version 1.2.3
In Bioconductor since BioC 3.0 (R-3.1) (1 year)
License GPL-3
Depends R (>= 2.10)
Imports Rsamtools, GenomicRanges, IRanges, BiocGenerics, data.table, stringr, rtracklayer, GenomeInfoDb, ggplot2, gridExtra, methods, igraph, plotrix, S4Vectors, dplyr
LinkingTo
Suggests knitr, BiocStyle, testthat
SystemRequirements
Enhances
URL https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
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_1.2.3.tar.gz
Windows Binary GenomicInteractions_1.2.3.zip
Mac OS X 10.6 (Snow Leopard) GenomicInteractions_1.2.3.tgz
Mac OS X 10.9 (Mavericks) GenomicInteractions_1.2.3.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GenomicInteractions/tree/release-3.1
Package Short Url http://bioconductor.org/packages/GenomicInteractions/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center