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).
RELEASE HISTORY OF GeneNet PACKAGE ======================================== CHANGES IN GeneNet VERSION 1.2.13
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
CHANGES IN GeneNet VERSION 1.2.7
ggm.simulate.data() 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.
CHANGES IN GeneNet VERSION 1.2.5
NAMESPACE file added.
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 dev.new() to open a new graphics device.
CHANGES IN GeneNet VERSION 1.2.2
a small bug in ggm.make.dot() 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
the plot function ggm.make.dot() resp. network.make.dot() 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
examples scripts were changed to include examples for A.thaliana and for plotting using ggm.make.dot()
the function ggm.test.edges() was changed internally to use fdrtool() rather than cor.fit.mixture() 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 cor.fit.mixture() 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).