Nested Effects Models to reconstruct phenotypic hierarchies

Bioconductor version: 2.9

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>

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


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)
Depends On Me
Imports Me
Suggests Me
Version 2.18.0
Since Bioconductor 1.9 (R-2.4)

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Package Source nem_2.18.0.tar.gz
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MacOS 10.5 (Leopard) binary nem_2.18.0.tgz
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