To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("nem")
In most cases, you don't need to download the package archive at all.
nem
|
This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see nem.
Nested Effects Models to reconstruct phenotypic hierarchies
Bioconductor version: 2.9
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: Holger Froehlich <frohlich at bit.uni-bonn.de>
Citation (from within R,
enter citation("nem")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("nem")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("nem")
| markowetz-thesis-2006.pdf | ||
| nem.pdf | ||
| Reference Manual |
Details
| biocViews | Bioinformatics, GraphsAndNetworks, Microarray, Pathways, Software |
| Version | 2.18.0 |
| In Bioconductor since | BioC 1.9 (R-2.4) (9.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 2.0), e1071 (>= 1.5), graph(>= 1.24), Rgraphviz(>= 1.22), plotrix, limma, time (>= 1.0), cluster (>= 1.11), statmod |
| Imports | boot, e1071, graph, graphics, grDevices, methods, RBGL(>= 1.8.1), RColorBrewer, Rgraphviz, stats, utils |
| LinkingTo | |
| Suggests | Biobase(>= 1.10) |
| SystemRequirements | |
| Enhances | doMC |
| URL | http://www.bioconductor.org |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | nem_2.18.0.tar.gz |
| Windows Binary | nem_2.18.0.zip |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/nem/tree/release-2.9 |
| Package Short Url | http://bioconductor.org/packages/nem/ |
| Package Downloads Report | Download Stats |
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