nem

Nested Effects Models to reconstruct phenotypic hierarchies

Bioconductor version: Release (2.7)

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 2.14.0

Package Downloads

Package Source nem_2.14.0.tar.gz
Windows Binary nem_2.14.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary nem_2.14.0.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!

Fred Hutchinson Cancer Research Center