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epiNEM

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

epiNEM


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

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

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")
epiNEM HTML R Script
Reference Manual PDF

Details

biocViews Network, NetworkInference, Pathways, Software, SystemsBiology
Version 1.27.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL-3
Depends R (>= 4.1)
Imports BoolNet, e1071, gtools, stats, igraph, utils, lattice, latticeExtra, RColorBrewer, pcalg, minet, grDevices, graph, mnem, latex2exp
System Requirements
URL https://github.com/cbg-ethz/epiNEM/
Bug Reports https://github.com/cbg-ethz/epiNEM/issues
See More
Suggests knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me bnem, dce, nempi
Suggests Me mnem
Links To Me
Build Report Build Report

Package Archives

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

Source Package epiNEM_1.27.0.tar.gz
Windows Binary epiNEM_1.27.0.zip (64-bit only)
macOS Binary (x86_64) epiNEM_1.27.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/epiNEM
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/epiNEM
Bioc Package Browser https://code.bioconductor.org/browse/epiNEM/
Package Short Url https://bioconductor.org/packages/epiNEM/
Package Downloads Report Download Stats