Package: bnem
Type: Package
Title: Training of logical models from indirect measurements of
        perturbation experiments
Version: 1.16.0
Authors@R: person("Martin", "Pirkl",
    email = "martinpirkl@yahoo.de",
    role = c("aut", "cre"))
Description: 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).
Depends: R (>= 4.1)
License: GPL-3
Encoding: UTF-8
biocViews: Pathways, SystemsBiology, NetworkInference, Network,
        GeneExpression, GeneRegulation, Preprocessing
Imports: CellNOptR, matrixStats, snowfall, Rgraphviz, cluster,
        flexclust, stats, RColorBrewer, epiNEM, mnem, Biobase, methods,
        utils, graphics, graph, affy, binom, limma, sva, vsn, rmarkdown
VignetteBuilder: knitr
Suggests: knitr, BiocGenerics, MatrixGenerics, BiocStyle, RUnit
BugReports: https://github.com/MartinFXP/bnem/issues
URL: https://github.com/MartinFXP/bnem/
RoxygenNote: 7.1.1
git_url: https://git.bioconductor.org/packages/bnem
git_branch: RELEASE_3_21
git_last_commit: 479b487
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-15 23:25:13 UTC; biocbuild
Author: Martin Pirkl [aut, cre]
Maintainer: Martin Pirkl <martinpirkl@yahoo.de>
Built: R 4.5.0; ; 2025-04-16 14:00:47 UTC; windows
