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Routines for the functional analysis of biological networks

Bioconductor version: Release (3.1)

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>

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


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PDF R Script BioNet Tutorial
PDF   Reference Manual


biocViews DataImport, DifferentialExpression, GeneExpression, GraphAndNetwork, Microarray, Network, NetworkEnrichment, Software
Version 1.29.1
In Bioconductor since BioC 2.7 (R-2.12) (5 years)
License GPL (>= 2)
Depends R (>= 2.10.0), graph, RBGL
Imports igraph (>= 1.0.1), AnnotationDbi, Biobase
Suggests rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML
Depends On Me
Imports Me HTSanalyzeR
Suggests Me SANTA
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