nem - Nested Effects Models to Reconstruct Phenotypic Hierarchies

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.

Publications

• Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
  Markowetz F, Bloch J, Spang R
  Bioinformatics 2005 21: 4026-4032.
  [ PMID: 16159925 | doi:10.1093/bioinformatics/bti662 ]

Download

Download the tared and gzipped source file, which is compliant to Bioconductor. To run the package, you need R and at least packages e1071, graph, RBGL and Rgraphviz from Bioconductor.

→ the current source package
→ the current binary package for Windows

Direct installation from the CompDiag R/Bioconductor-repository

Start the R version where you want to install adSplit. Use the following commands on the R prompt to install StAM directly from our repository:

library(reposTools)
z <- getReposEntry("http://compdiag.molgen.mpg.de/software/Rrepos")
install.packages2("nem", z)