epiNEM

DOI: 10.18129/B9.bioc.epiNEM    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see epiNEM.

epiNEM

Bioconductor version: 3.13

epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways. It is tailored towards large scale double knock-out screens.

Author: Madeline Diekmann & Martin Pirkl

Maintainer: Martin Pirkl <martinpirkl at yahoo.de>

Installation

To install this package, start R (version "4.1") and enter:

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

BiocManager::install("epiNEM")

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("epiNEM")

 

HTML	R Script	epiNEM
PDF		Reference Manual
Text		NEWS

Details

biocViews	Network, NetworkInference, Pathways, Software, SystemsBiology
Version	1.16.0
In Bioconductor since	BioC 3.5 (R-3.4) (4.5 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp
LinkingTo
Suggests	knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db
SystemRequirements
Enhances
URL	https://github.com/cbg-ethz/epiNEM/
BugReports	https://github.com/cbg-ethz/epiNEM/issues
Depends On Me
Imports Me	bnem, dce, nempi
Suggests Me	mnem
Links To Me
Build Report

Package Archives

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

Source Package	epiNEM_1.16.0.tar.gz
Windows Binary	epiNEM_1.16.0.zip
macOS 10.13 (High Sierra)	epiNEM_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/epiNEM
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/epiNEM
Package Short Url	https://bioconductor.org/packages/epiNEM/
Package Downloads Report	Download Stats