Modeling and Inferring Gene Networks

Analyzes gene expression (time series) data with focus on the inference of gene networks. In particular, GeneNet implements the methods of Schaefer and Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007) for learning large-scale gene association networks (including assignment of putative directions).



  • added import statement as required by R-devel.

  • removed dependency on igraph, as igraph now has too many subsequent mandatory dependencies (>20 packages).

  • instead use we now use again the "graph" and "Rgraphviz" from Bioconductor for graph modeling and plotting.

  • All example scripts and related functions in GeneNet have been updated and modified accordingly.

      CHANGES IN GeneNet VERSION 1.2.12
  • maintainance update to fix bad URL (as requested by R core team).

      CHANGES IN GeneNet VERSION 1.2.11
  • the example files have been converted into R notebook format.

  • change of maintainer email address.

      CHANGES IN GeneNet VERSION 1.2.10
  • change of maintainer email address.

  • corrections to index.html file in inst/doc folder.

      CHANGES IN GeneNet VERSION 1.2.9
  • added import() statement in NAMESPACE file to get rid of warning of R 3.1.0.

      CHANGES IN GeneNet VERSION 1.2.8
  • small changes to get rid of warnings in R-devel

  • updated dependencies

      CHANGES IN GeneNet VERSION 1.2.7
  • now uses eigen() to simulate multinormal data.

  • No dependency on Rgraphviz any more. Instead, igraph is used for plotting.

  • new function ggm.make.igraph() and network.make.igraph() to generate igraph objects have been added.

  • correspondingly, the old functions ggm.make.graph() and show.edge.weights() are removed, and all examples have been adapted to igraph.

      CHANGES IN GeneNet VERSION 1.2.6
  • License file removed.

  • Dependencies updated.

      CHANGES IN GeneNet VERSION 1.2.5
  • NAMESPACE file added.

  • Dependencies updated.

      CHANGES IN GeneNet VERSION 1.2.4
  • small changes to pass the tests of R version 2.10.

  • GeneNet now requires corpcor (>= 1.5.3) and longitudinal (>= 1.1.5).

      CHANGES IN GeneNet VERSION 1.2.3
  • small bug fixed in the plotting routine in ggm.test.edges().
    In current versions of R you need to use to open a new graphics device.

      	CHANGES IN GeneNet VERSION 1.2.2
  • a small bug in was corrected. Now variable names such as "1776837_at" can be plotted properly with graphviz (this bug fix was kindly provided by Colin Gillespie, Newcastle).

      	CHANGES IN GeneNet VERSION 1.2.1
  • a number of small internal changes were needed to adjust GeneNet to the new version of the fdrtool package (version 1.2.0).

  • the licence was changed from "GNU GPL 2 or later" to "GNU GPL 3 or later".

  • some parts of the documentation were updated.

      	CHANGES IN GeneNet VERSION 1.2.0

Newly added:

  • this version implements the approach described in Opgen-Rhein and Strimmer (2007) for estimating partially directed graphs. See the arbidopsis example script for illustration.
  • new utility function to simplify the extraction of significant edges.


  • the plot function resp. now produce dot code for partially directed graphs.

  • the function ggm.plot.graph() was removed.

  • all example scripts were updated accordingly.

  • ggm.test.edges now has option "fdr" to allow to skip fdr computations if necessary.

      CHANGES IN GeneNet VERSION 1.1.0

Newly added:

  • arth800: new example data from A. thaliana Affymetrix time series experiment
  • utility function for network plotting (produces dot files for use with graphviz) Removed:
  • dcor0: the density and distribution function for correlation have been moved into the "fdrtool" package
  • this function is not necessary any more, as a similar function is available in the "fdrtool" package


  • examples scripts were changed to include examples for A.thaliana and for plotting using

  • the function ggm.test.edges() was changed internally to use fdrtool() rather than and locfdr()

  • all fdr/Fdr calculations for edge testing are now done using the "fdrtool" package, so the dependency from "locfdr" was removed

      CHANGES IN GeneNet VERSION 1.0.1
  • function was adapted to API changes in "locfdr" package

  • new dependency requirement: locfdr >= 1.1-1

      CHANGES IN GeneNet VERSION 1.0.0

This is the first standalone release (9 August 2006). Previously, the functions available in this package were part of the GeneTS package (version 2.10.2).

Reference manual

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1.2.16 by Korbinian Strimmer, 16 days ago

Browse source code at

Authors: Juliane Schaefer , Rainer Opgen-Rhein , and Korbinian Strimmer.

Documentation:   PDF Manual  

Task views: gRaphical Models in R

GPL (>= 3) license

Imports stats, grDevices

Depends on corpcor, longitudinal, fdrtool

Suggests graph, Rgraphviz

Imported by ccid.

Suggested by ebdbNet.

See at CRAN