To install this package, start R and enter:

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

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

RedeR

This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see RedeR.

Bridging the gap between hierarchical network representation and functional analysis.

Bioconductor version: 2.10

RedeR is an R-based package combined with a stand-alone Java application for dynamic network visualization and manipulation. It implements a callback engine by using a low-level R-to-Java interface to build and run common plugins. In this sense, RedeR takes advantage of R to run robust statistics, while the R-to-Java interface bridges the gap between network analysis and visualization: for R Developers, it allows the development of Java plug-ins exclusively using R codes; for Java Users, it runs R methods implemented in a stand-alone application, and for R Users RedeR interactively displays R graphs using a robust Java graphic engine embedded in this package.

Author: Mauro Castro, Xin Wang, Florian Markowetz

Maintainer: Mauro Castro <mauro.a.castro at gmail.com>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("RedeR")

PDF		fig1.pdf
PDF		fig2.pdf
PDF		fig3.pdf
PDF		fig4.pdf
PDF		fig5a.pdf
PDF		fig5b.pdf
PDF		fig5c.pdf
PDF		fig6.pdf
PDF		Main vignette: RedeR Overview
PDF		Reference Manual
Text		NEWS

Details

biocViews	GUI, GraphsAndNetworks, Software, Visualization
Version	1.2.5
In Bioconductor since	BioC 2.9 (R-2.14) (4.5 years)
License	GPL (>= 2)
Depends	R (>= 2.15), igraph0, RCurl, XML, XMLRPC
Imports	rJava, methods
LinkingTo
Suggests	PANR, HTSanalyzeR, pvclust, graph
SystemRequirements
Enhances
URL	http://www.markowetzlab.org/software/networks.html
Depends On Me
Imports Me	Mulder2012
Suggests Me	PANR
Build Report

Package Archives

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

Package Source	RedeR_1.2.5.tar.gz
Windows Binary	RedeR_1.2.5.zip
Mac OS X 10.6 (Snow Leopard)
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/RedeR/tree/release-2.10
Package Short Url	http://bioconductor.org/packages/RedeR/
Package Downloads Report	Download Stats