To install this package, start R and enter:

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

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

GenomicInteractions

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see GenomicInteractions.

R package for handling genomic interaction data

Bioconductor version: 3.2

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:// URLs are not supported
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")
PDF chiapet_vignette.pdf
HTML GenomicInteractions-HiC
PDF Reference Manual
Text NEWS

Details

biocViews DataImport, DataRepresentation, HiC, Infrastructure, Software
Version 1.4.2
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-3
Depends R (>= 2.10)
Imports Rsamtools, GenomicRanges, IRanges, BiocGenerics(>= 0.15.3), data.table, stringr, GenomeInfoDb, ggplot2, grid, gridExtra, methods, igraph, S4Vectors, dplyr, Gviz
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_1.4.2.tar.gz
Windows Binary GenomicInteractions_1.4.2.zip
Mac OS X 10.6 (Snow Leopard) GenomicInteractions_1.4.0.tgz
Mac OS X 10.9 (Mavericks) GenomicInteractions_1.4.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/GenomicInteractions/tree/release-3.2
Package Short Url http://bioconductor.org/packages/GenomicInteractions/
Package Downloads Report Download Stats

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