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>

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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
Suggests knitr, BiocGenerics
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