nem

Nested Effects Models to reconstruct phenotypic hierarchies

The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) high-dimensional phenotypic readout of these perturbations (e.g. gene expression or morphological profiles). The output is a directed graph representing the phenotypic hierarchy.

Author	Holger Froehlich, Florian Markowetz, Achim Tresch, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth
Maintainer	Christian Bender

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("nem")

Documentation

Nested Effects Models - An example in Drosophila immune response	PDF	R Script
markowetz-thesis-2006.pdf	PDF
Reference Manual

Details

biocViews	Microarray , Bioinformatics , GraphsAndNetworks , Pathways
Depends	R , e1071 , graph , Rgraphviz , plotrix , limma , time , cluster
Imports	boot , e1071 , graph , graphics , grDevices , methods , RBGL , RColorBrewer , Rgraphviz , stats , utils
Suggests	Biobase
System Requirements
License	GPL (>= 2)
URL	http://www.bioconductor.org
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Package Downloads

Package source	nem_2.12.0.tar.gz
Windows 32-bit binary	nem_2.12.0.zip
Windows 64-bit binary	nem_2.12.0.zip
MacOS X 10.5 (Leopard) binary	nem_2.12.0.tgz
Package Downloads Report	Downloads Stats