BioNet

Routines for the functional analysis of biological networks

Bioconductor version: Development (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

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("BioNet")    

Documentation

PDF	R Script	BioNet Tutorial
PDF		cytoscape.pdf
PDF		prec_recall_large.pdf
PDF		prec_recall_small.pdf
PDF		Tutorial-3dplot.pdf

Reference Manual

Details

biocViews	Microarray, DataImport, GraphsAndNetworks, Visualization, Bioinformatics, GeneExpression, DifferentialExpression
Depends	R, Biobase, graph, RBGL
Imports	igraph, XML, AnnotationDbi
Suggests	rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db
System Requirements
License	GPL (>= 2)
URL	http://bionet.bioapps.biozentrum.uni-wuerzburg.de/
Depends On Me	HTSanalyzeR
Imports Me	HTSanalyzeR
Suggests Me
Version	1.9.0

Package Downloads

Package Source	BioNet_1.9.0.tar.gz
Windows Binary	BioNet_1.9.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	BioNet_1.9.0.tgz
Package Downloads Report	Download Stats