nem

DOI: 10.18129/B9.bioc.nem    

This package is for version 3.9 of Bioconductor; for the 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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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")

 

PDF		markowetz-thesis-2006.pdf
PDF	R Script	Nested Effects Models - An example in Drosophila immune response
PDF		Reference Manual

Details

biocViews	Bioinformatics, GraphsAndNetworks, Microarray, NetworkInference, Pathways, Software, SystemsBiology
Version	2.58.0
In Bioconductor since	BioC 1.9 (R-2.4) (13 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
LinkingTo
Suggests	Biobase(>= 1.10)
SystemRequirements
Enhances	doMC, snow, parallel
URL	http://www.bioconductor.org
Depends On Me	lpNet
Imports Me	birte, epiNEM, mnem, OncoSimulR
Suggests Me	rBiopaxParser
Links To Me
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
Package Short Url	https://bioconductor.org/packages/nem/
Package Downloads Report	Download Stats