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

Bioconductor version: Release (3.1)

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>

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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 Bioinformatics, GraphsAndNetworks, Microarray, NetworkInference, Pathways, Software, SystemsBiology
Version 2.42.0
In Bioconductor since BioC 1.9 (R-2.4) (9 years)
License GPL (>= 2)
Depends R (>= 3.0)
Imports boot, e1071, graph, graphics, grDevices, methods, RBGL(>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod, plotrix, limma
Suggests Biobase(>= 1.10)
Enhances doMC, snow, parallel
Depends On Me lpNet
Imports Me birte
Suggests Me rBiopaxParser
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