nem

This package is for version 3.6 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

DOI: 10.18129/B9.bioc.nem

Bioconductor version: 3.6

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 (from within R, enter citation("nem")):

Installation

To install this package, start R (version "3.4") 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 PDF

Nested Effects Models - An example in Drosophila immune response PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bioinformatics, GraphsAndNetworks, Microarray, NetworkInference, Pathways, Software, SystemsBiology

Version 2.52.0

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

Suggests Biobase(>= 1.10)

Linking To

Enhances doMC, snow, parallel

Depends On Me lpNet

Imports Me birte, epiNEM, 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_2.52.0.tar.gz

Windows Binary nem_2.52.0.zip (32- & 64-bit)

Mac OS X 10.11 (El Capitan) nem_2.52.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/nem

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/nem

Package Short Url https://bioconductor.org/packages/nem/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.6 Source Archive