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