nem

Nested Effects Models to reconstruct phenotypic hierarchies

Bioconductor version: 2.5

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 <c.bender at dkfz-heidelberg.de>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("nem")

Documentation

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

Details

biocViews	Microarray, Bioinformatics, GraphsAndNetworks, Pathways
Depends	R (>= 2.0), e1071 (>= 1.5), graph(>= 1.10), Rgraphviz(>= 1.10), plotrix
Imports	boot, e1071, graph, graphics, grDevices, methods, RBGL(>= 1.8.1), RColorBrewer, Rgraphviz, stats, utils
Suggests	Biobase(>= 1.10)
System Requirements
License	GPL (>= 2)
URL	http://www.bioconductor.org
Depends On Me
Imports Me
Suggests Me
Version	2.10.0
Since	Bioconductor 1.9 (R-2.4)

Package Downloads

Package Source	nem_2.10.0.tar.gz
Windows Binary	nem_2.10.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	nem_2.10.0.tgz
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Hosting provided by Fred Hutchinson Cancer Research Center