nem

DOI: 10.18129/B9.bioc.nem    

This is the development version of nem; for the stable release version, see nem.

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

Bioconductor version: Development (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>

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

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.61.0
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 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
Windows Binary
Mac OS X 10.11 (El Capitan)
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

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