bnem

DOI: 10.18129/B9.bioc.bnem    

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

Training of logical models from indirect measurements of perturbation experiments

Bioconductor version: Development (3.14)

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>

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

Installation

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

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

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

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 1.1.3
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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_1.1.3.tar.gz
Windows Binary bnem_1.1.3.zip
macOS 10.13 (High Sierra) bnem_1.1.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/bnem
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bnem
Package Short Url https://bioconductor.org/packages/bnem/
Package Downloads Report Download Stats

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