nem

Nested Effects Models to reconstruct phenotypic hierarchies

Bioconductor version: Development (2.8)

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:///biocLite.R")
biocLite("nem")    

Documentation

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

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
Depends On Me
Imports Me
Suggests Me
Version	2.15.0

Package Downloads

Package Source	nem_2.15.0.tar.gz
Windows Binary	nem_2.15.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	nem_2.15.0.tgz
Package Downloads Report	Download Stats