GeneNet: Modeling and Inferring Gene Networks

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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).

Author
Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
Date of publication
2015-08-02 19:17:14
Maintainer
Korbinian Strimmer <strimmerlab@gmail.com>
License
GPL (>= 3)
Version
1.2.13
URLs

View on CRAN

Man pages

arth800
Time Series Expression Data for 800 Arabidopsis Thaliana...
cor0.test
Test of Vanishing (Partial) Correlation
ecoli
Microarray Time Series Data for 102 E. Coli Genes Genes
GeneNet-internal
Internal GeneNet Functions
GeneNet.package
The GeneNet package
ggm.estimate.pcor
Graphical Gaussian Models: Small Sample Estimation of Partial...
ggm.simulate.data
Graphical Gaussian Models: Simulation of Data
ggm.simulate.pcor
Graphical Gaussian Models: Simulation of Networks
kappa2n
Relationship Between Sample Size and the Degree of Freedom of...
network.make.graph
Graphical Gaussian Models: Plotting the Network
network.test.edges
Graphical Gaussian Models: Assess Significance of Edges (and...
z.transform
Variance-Stabilizing Transformations of the Correlation...

Files in this package

GeneNet
GeneNet/inst
GeneNet/inst/doc
GeneNet/inst/doc/index.html
GeneNet/inst/doc/tcell-net.R
GeneNet/inst/doc/ecoli-net.R
GeneNet/inst/doc/arabidopsis-net.R
GeneNet/NAMESPACE
GeneNet/NEWS
GeneNet/data
GeneNet/data/arth800.rda
GeneNet/data/ecoli.rda
GeneNet/R
GeneNet/R/network.make.dot.R
GeneNet/R/network.test.edges.R
GeneNet/R/ggm.simulate.data.R
GeneNet/R/cor0.test.R
GeneNet/R/ggm.estimate.pcor.R
GeneNet/R/network.make.graph.R
GeneNet/R/kappa2n.R
GeneNet/R/extract.network.R
GeneNet/R/ggm.simulate.pcor.R
GeneNet/R/z.transform.R
GeneNet/MD5
GeneNet/DESCRIPTION
GeneNet/man
GeneNet/man/cor0.test.Rd
GeneNet/man/GeneNet.package.Rd
GeneNet/man/ecoli.Rd
GeneNet/man/ggm.estimate.pcor.Rd
GeneNet/man/kappa2n.Rd
GeneNet/man/ggm.simulate.data.Rd
GeneNet/man/z.transform.Rd
GeneNet/man/arth800.Rd
GeneNet/man/network.test.edges.Rd
GeneNet/man/network.make.graph.Rd
GeneNet/man/ggm.simulate.pcor.Rd
GeneNet/man/GeneNet-internal.Rd