nem

DOI: 10.18129/B9.bioc.nem    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.11 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: 3.11

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 "4.0") 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

PDF		Reference Manual

Details

biocViews	Bioinformatics, GraphsAndNetworks, Microarray, NetworkInference, Pathways, Software, SystemsBiology
Version	2.62.0
In Bioconductor since	BioC 1.9 (R-2.4) (14 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
Suggests Me	rBiopaxParser
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package
Windows Binary
macOS 10.13 (High Sierra)
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