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.
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("nem")
| Source | nem_2.2.1.tar.gz |
|---|---|
| Windows binary | nem_2.2.1.zip |
| OS X binary | nem_2.2.1.tgz |
| biocViews | |
|---|---|
| Depends | R, e1071, graph, Rgraphviz, RBGL, time |
| Suggests | Biobase |
| Imports | |
| SystemRequirements | |
| License | GPL version 2.0 or newer |
| URL | http://www.bioconductor.org |
| dependsOnMe | |
| suggestsMe |