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

nem

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

Bioconductor version: 2.13

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.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.

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

Maintainer: Holger Froehlich <frohlich at bit.uni-bonn.de>

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("nem")

 

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

Details

biocViews	Bioinformatics, GraphsAndNetworks, Microarray, Pathways, Software
Version	2.36.0
In Bioconductor since	BioC 1.9 (R-2.4)
License	GPL (>= 2)
Depends	R (>= 2.0), e1071 (>= 1.5), graph(>= 1.24), plotrix, limma, cluster (>= 1.11), statmod, Hmisc, Rgraphviz
Imports	boot, e1071, graph, graphics, grDevices, methods, RBGL(>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz
Suggests	Biobase(>= 1.10)
System Requirements
URL	http://www.bioconductor.org
Depends On Me	lpNet
Imports Me
Suggests Me

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source	nem_2.36.0.tar.gz
Windows Binary	nem_2.36.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	nem_2.36.0.tgz
Browse/checkout source	(username/password: readonly)
Package Downloads Report	Download Stats