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nem

Nested Effects Models

An R/Bioconductor package to reconstruct phenotypic hierarchies from high-dimensional phenotying screens.

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

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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.


  1. Department of Medicine
  2. Institute of Functional Genomics