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 2.9 of Bioconductor; for the stable, up-to-date release version, see RedeR.

Bridging the gap between hierarchical network representation and functional analysis.

Bioconductor version: 2.9

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		RedeR.pdf
PDF		Reference Manual

Details

biocViews	GUI, GraphsAndNetworks, Software, Visualization
Version	1.0.14
In Bioconductor since	BioC 2.9 (R-2.14) (4.5 years)
License	GPL (>= 2)
Depends	R (>= 2.12.0), igraph (>= 0.5.5), RCurl (>= 1.6-0), XML (>= 3.4-0), XMLRPC (>= 0.2.2)
Imports	rJava, methods
LinkingTo
Suggests	PANR, HTSanalyzeR, pvclust, graph
SystemRequirements
Enhances
URL	http://www.markowetzlab.org/software/networks.html
Depends On Me
Imports Me
Suggests Me	PANR
Build Report

Package Archives

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

Package Source	RedeR_1.0.14.tar.gz
Windows Binary	RedeR_1.0.14.zip
Mac OS X 10.6 (Snow Leopard)
Mac OS X 10.9 (Mavericks)
Subversion source	(username/password: readonly)
Git source	https://github.com/Bioconductor-mirror/RedeR/tree/release-2.9
Package Short Url	http://bioconductor.org/packages/RedeR/
Package Downloads Report	Download Stats