nem
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see nem.
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
Bioconductor version: 3.9
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.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.
Author: Holger Froehlich, Florian Markowetz, Achim Tresch, Theresa Niederberger, Christian Bender, Matthias Maneck, Claudio Lottaz, Tim Beissbarth
Maintainer: Holger Froehlich <frohlich at bit.uni-bonn.de>
citation("nem")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("nem")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("nem")| markowetz-thesis-2006.pdf | ||
| Nested Effects Models - An example in Drosophila immune response | R Script | |
| Reference Manual |
Details
| biocViews | Bioinformatics, GraphsAndNetworks, Microarray, NetworkInference, Pathways, Software, SystemsBiology |
| Version | 2.58.0 |
| In Bioconductor since | BioC 1.9 (R-2.4) (17.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0) |
| Imports | boot, e1071, graph, graphics, grDevices, methods, RBGL(>= 1.8.1), RColorBrewer, stats, utils, Rgraphviz, statmod, plotrix, limma |
| System Requirements | |
| URL | http://www.bioconductor.org |
See More
| Suggests | Biobase(>= 1.10) |
| Linking To | |
| Enhances | doMC, snow, parallel |
| Depends On Me | lpNet |
| Imports Me | birte, epiNEM, mnem, OncoSimulR |
| Suggests Me | rBiopaxParser |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | nem_2.58.0.tar.gz |
| Windows Binary | nem_2.58.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | nem_2.58.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/nem |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/nem |
| Bioc Package Browser | https://code.bioconductor.org/browse/nem/ |
| Package Short Url | https://bioconductor.org/packages/nem/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |