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 and Spang R
  Bioinformatics, 2005 21: 4026-4032.
  [ PMID: 16159925 | doi:10.1093/bioinformatics/bti662 ]
• Nested Effects Models for High-Dimensional Phenotyping
  Markowetz F, Kostka D, Trojanskaja O and Spang R
  Bioinformatics ISMB, 2007, 23 (13): 305-312.2005 21: 4026-4032.
  [ PMID: 17646311 | doi:10.1182/blood-2006-10-049783 ]

Download

Download the tared and gzipped source file, which is compliant to Bioconductor.

→ the released version
→ the development version

To run the package, you need R and at least packages e1071, graph, RBGL and Rgraphviz from Bioconductor.