bnem

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

Training of logical models from indirect measurements of perturbation experiments

Bioconductor version: 3.13

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 (!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")

bnem.html HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, GeneRegulation, Network, NetworkInference, Pathways, Preprocessing, Software, SystemsBiology

Version 1.0.0

In Bioconductor since BioC 3.13 (R-4.1) (3 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

System Requirements

URL https://github.com/MartinFXP/bnem/

Bug Reports https://github.com/MartinFXP/bnem/issues

Suggests knitr, BiocGenerics

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