Nested Effects Models to reconstruct phenotypic hierarchies

Bioconductor version: 2.10

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, 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>

To install this package, start R and enter:


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



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


biocViews Bioinformatics, GraphsAndNetworks, Microarray, Pathways, Software
Depends R (>= 2.0), e1071 (>= 1.5), graph(>= 1.24), Rgraphviz(>= 1.22), plotrix, limma, cluster (>= 1.11), statmod, Hmisc
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 2.32.1
Since Bioconductor 1.9 (R-2.4)

Package Downloads

Package Source nem_2.32.1.tar.gz
Windows Binary (32- & 64-bit)
MacOS 10.5 (Leopard) binary nem_2.32.1.tgz
Package Downloads Report Download Stats

Workflows »

Common Bioconductor workflows include:


Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center