To install this package, start R and enter:

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

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

BioNet

This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see BioNet.

Routines for the functional analysis of biological networks

Bioconductor version: 2.8

This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.

Author: Marcus Dittrich and Daniela Beisser

Maintainer: Marcus Dittrich <marcus.dittrich at biozentrum.uni-wuerzburg.de>

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

Installation

To install this package, start R and enter:

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

Documentation

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

browseVignettes("BioNet")

PDF		bum1.pdf
PDF		bum2.pdf
PDF		cytoscape.pdf
PDF		prec_recall_large.pdf
PDF		prec_recall_small.pdf
PDF		Tutorial-3dplot.pdf
PDF		Tutorial.pdf
PDF		Reference Manual

Details

biocViews	Bioinformatics, DataImport, DifferentialExpression, GeneExpression, GraphsAndNetworks, Microarray, Software, Visualization
Version	1.10.1
In Bioconductor since	BioC 2.7 (R-2.12) (5.5 years)
License	GPL (>= 2)
Depends	R (>= 2.10.0), Biobase, graph, RBGL
Imports	igraph, AnnotationDbi
LinkingTo
Suggests	rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML
SystemRequirements
Enhances
URL	http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
Depends On Me	HTSanalyzeR
Imports Me	HTSanalyzeR
Suggests Me
Build Report

Package Archives

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

Package Source	BioNet_1.10.1.tar.gz
Windows Binary	BioNet_1.10.1.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/BioNet/tree/release-2.8
Package Short Url	http://bioconductor.org/packages/BioNet/
Package Downloads Report	Download Stats