Inference for predictive networks designed for (but not limited to) genomic data

Bioconductor version: Release (2.11)

This package contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases. The main function is able to generate networks using Bayesian or regression-based inference methods; while the former is limited to < 100 of variables, the latter may infer networks with hundreds of variables. Several statistics at the edge and node levels have been implemented (edge stability, predictive ability of each node, ...) in order to help the user to focus on high quality subnetworks. Ultimately, this package is used in the 'Predictive Networks' web application developed by the Dana-Farber Cancer Institute in collaboration with Entagen.

Author: Benjamin Haibe-Kains, Catharina Olsen, Gianluca Bontempi, John Quackenbush

Maintainer: Benjamin Haibe-Kains <bhaibeka at>, Catharina Olsen <colsen at>

To install this package, start R and enter:


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



PDF R Script predictionet
PDF predictionet-boxplotr2pwcvfig2.pdf
PDF predictionet-boxplotstabpwcvfig2.pdf
PDF predictionet-cytoscape.pdf
PDF predictionet-edgecoldiffig.pdf
PDF predictionet-edgestabfig.pdf
PDF predictionet-genepredabmccfig.pdf
PDF predictionet-genepredabmcctestfig.pdf
PDF predictionet-genepredabr2fig.pdf
PDF predictionet-genepredabr2testfig.pdf
PDF predictionet-pn_webapp_ras.pdf
PDF predictionet-regnetcvpriorsweightfig2.pdf
PDF predictionet-regnetcvtopo1topo2fig2.pdf
PDF predictionet-regnetcvtopo1topo2predfig2.pdf
PDF predictionet-regnetcvtopo1topo2stabfig2.pdf
PDF predictionet-regrnet_design.pdf
PDF predictionet-regrnetopofig.pdf
PDF   Reference Manual


biocViews GraphsAndNetworks, NetworkInference, Software
Version 1.4.0
In Bioconductor since BioC 2.9 (R-2.14)
License Artistic-2.0
Depends igraph0, catnet
Imports penalized, RBGL, MASS
Suggests network, minet, knitr
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source predictionet_1.4.0.tar.gz
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MacOS 10.5 (Leopard) predictionet_1.4.0.tgz
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