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biocLite("nem")

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nem

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

Bioconductor version: Release (3.0)

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>

Citation (from within R, enter citation("nem")):

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 R Script Nested Effects Models - An example in Drosophila immune response
PDF   Reference Manual

Details

biocViews DecisionTree, GraphAndNetwork, Microarray, Pathways, Software
Version 2.40.0
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 rBiopaxParser

Package Archives

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

Package Source nem_2.40.0.tar.gz
Windows Binary nem_2.40.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) nem_2.40.0.tgz
Mac OS X 10.9 (Mavericks) nem_2.40.0.tgz
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