Juliane Schaefer, Rainer Opgen-Rhein, and Korbinian Strimmer.
GeneNet is a package for analyzing 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).

GeneNet is a package for analyzing 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).

The goal of time delay linear model is to fit a linear
regression model using a set of putative regulators to estimate
the transcription pattern of a specific target gene.

Construct time delay gene regulatory network
pkg{GeneReg} is an R package for inferring time delay gene
regulatory network using time course gene expression profiles.
The main idea of time delay linear model is to fit a linear
regression model using a set of putative regulators to estimate
the transcription pattern of a specific target gene.

GeneReg is an R package for inferring time delay gene
regulatory network using time course gene expression profiles.
The main idea of time delay linear model is to fit a linear
regression model using a set of putative regulators to estimate
the transcription pattern of a specific target gene.

Tao Huang, Lei Liu, Ziliang Qian, Kang Tu, Yixue Li, Lu Xie:
Using GeneReg to construct time delay gene regulatory networks.
BMC Res Notes 2010, 3(1):142.

Clustering Genes using Self-Organizing Map

Konstantinos Fokianos <fokianos@ucy.ac.cy>,
Juliane Schaefer <schaefer@stat.uni-muenchen.de>, and
Korbinian Strimmer <strimmer@stat.uni-muenchen.de>.
GeneTS is a package for analysing multiple gene expression
time series data. Currently, GeneTS implements methods for cell cycle
analysis and for inferring large sparse graphical Gaussian models.
For plotting the inferred genetic networks GeneTS requires the "graph"
and "Rgraphviz" packages (optional, available from www.bioconductor.org).