Routines for the functional analysis of biological networks

Bioconductor version: 2.9

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 Microarray, DataImport, GraphsAndNetworks, Visualization, Bioinformatics, GeneExpression, DifferentialExpression
Depends R (>= 2.10.0), Biobase, graph, RBGL
Imports igraph, AnnotationDbi
Suggests rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML
System Requirements
License GPL (>= 2)
Depends On Me HTSanalyzeR
Imports Me HTSanalyzeR
Suggests Me
Version 1.12.0
Since Bioconductor 2.7 (R-2.12)

Package Downloads

Package Source BioNet_1.12.0.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary BioNet_1.12.0.tgz
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