Routines for the functional analysis of biological networks

Bioconductor version: Release (2.12)

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>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



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


biocViews DataImport, DifferentialExpression, GeneExpression, GraphsAndNetworks, Microarray, NetworkAnalysis, NetworkEnrichment, Software
Version 1.18.0
In Bioconductor since BioC 2.7 (R-2.12)
License GPL (>= 2)
Depends R (>= 2.10.0), Biobase, graph, RBGL
Imports igraph0, AnnotationDbi
Suggests rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML
System Requirements
Depends On Me
Imports Me HTSanalyzeR
Suggests Me

Package Downloads

Package Source BioNet_1.18.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BioNet_1.18.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center