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## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("nem")

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nem

   

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see nem.

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

Bioconductor version: 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:

## try http:// if https:// URLs are not supported
source("https://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) (9.5 years)
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
LinkingTo
Suggests Biobase(>= 1.10)
SystemRequirements
Enhances doMC, Rglpk
URL http://www.bioconductor.org
Depends On Me lpNet
Imports Me
Suggests Me rBiopaxParser
Build Report  

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
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/nem/tree/release-3.0
Package Short Url http://bioconductor.org/packages/nem/
Package Downloads Report Download Stats

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