nem

Nested Effects Models to reconstruct phenotypic hierarchies

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

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("nem")

Documentation

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

Details

biocViews Microarray, Bioinformatics, GraphsAndNetworks, Pathways
Depends R (>= 2.0), e1071 (>= 1.5), graph(>= 1.24), Rgraphviz(>= 1.22), plotrix, limma, time (>= 1.0), cluster (>= 1.11), statmod
Imports boot, e1071, graph, graphics, grDevices, methods, RBGL(>= 1.8.1), RColorBrewer, Rgraphviz, stats, utils
Suggests Biobase(>= 1.10)
System Requirements
License GPL (>= 2)
URL http://www.bioconductor.org
Depends On Me
Imports Me
Suggests Me
Version 2.16.1
Since Bioconductor 1.9 (R-2.4)

Package Downloads

Package Source nem_2.16.1.tar.gz
Windows Binary nem_2.16.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary nem_2.16.1.tgz
Package Downloads Report Download Stats

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Fred Hutchinson Cancer Research Center