bnem

DOI: 10.18129/B9.bioc.bnem  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see bnem.

Training of logical models from indirect measurements of perturbation experiments

Bioconductor version: 3.16

bnem combines the use of indirect measurements of Nested Effects Models (package mnem) with the Boolean networks of CellNOptR. Perturbation experiments of signalling nodes in cells are analysed for their effect on the global gene expression profile. Those profiles give evidence for the Boolean regulation of down-stream nodes in the network, e.g., whether two parents activate their child independently (OR-gate) or jointly (AND-gate).

Author: Martin Pirkl [aut, cre]

Maintainer: Martin Pirkl <martinpirkl at yahoo.de>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("bnem")

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("bnem")

 

HTML	R Script	bnem.html
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, GeneRegulation, Network, NetworkInference, Pathways, Preprocessing, Software, SystemsBiology
Version	1.6.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	GPL-3
Depends	R (>= 4.1)
Imports	CellNOptR, matrixStats, snowfall, Rgraphviz, cluster, flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods, utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
LinkingTo
Suggests	knitr, BiocGenerics
SystemRequirements
Enhances
URL	https://github.com/MartinFXP/bnem/
BugReports	https://github.com/MartinFXP/bnem/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	bnem_1.6.0.tar.gz
Windows Binary	bnem_1.6.0.zip
macOS Binary (x86_64)	bnem_1.6.0.tgz
macOS Binary (arm64)	bnem_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bnem
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bnem
Bioc Package Browser	https://code.bioconductor.org/browse/bnem/
Package Short Url	https://bioconductor.org/packages/bnem/
Package Downloads Report	Download Stats