Nested Effects Models to reconstruct phenotypic hierarchies
Bioconductor version: 2.5
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.
Author: Holger Froehlich, Florian Markowetz, Achim Tresch, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth
Maintainer: Christian Bender <c.bender at dkfz-heidelberg.de>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("nem")
To cite this package in a publication, start R and enter:
citation("nem")
Documentation
| markowetz-thesis-2006.pdf | ||
| Nested Effects Models – An example in Drosophila immune response | ||
| Reference Manual |
Details
| biocViews | Microarray, Bioinformatics, GraphsAndNetworks, Pathways |
| Depends | R (>= 2.0), e1071 (>= 1.5), graph(>= 1.10), Rgraphviz(>= 1.10), plotrix |
| Imports | boot, e1071, graph, graphics, grDevices, methods, RBGL(>= 1.8.1), RColorBrewer, Rgraphviz, stats, utils |
| Suggests | Biobase(>= 1.10) |
| System Requirements | |
| License | GPL (>= 2) |
| URL | www.bioconductor.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Version | 2.10.0 |
| Since | Bioconductor 1.9 (R-2.4) |
Package Downloads
Read more here: Source link