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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 (3.18)

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 "4.3") and enter: 

if (!require("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

Reference Manual PDF

Details

biocViews GeneExpression, GeneRegulation, Network, NetworkInference, Pathways, Preprocessing, Software, SystemsBiology
Version 1.9.0
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
Linking To
Suggests knitr, BiocGenerics, MatrixGenerics, BiocStyle
System Requirements
Enhances
URL https://github.com/MartinFXP/bnem/
Bug Reports https://github.com/MartinFXP/bnem/issues
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Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64) bnem_1.9.0.tgz
macOS Binary (arm64) bnem_1.9.0.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/
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