Package: bnem
Type: Package
Title: Training of logical models from indirect measurements of
        perturbation experiments
Version: 1.21.0
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
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libjpeg-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:54:34 UTC
RemoteUrl: https://github.com/bioc/bnem
RemoteRef: HEAD
RemoteSha: 8c4f4c2c40dd8749864442dab4a99f80d2e7c9d8
NeedsCompilation: no
Packaged: 2026-05-18 10:20:53 UTC; root
Author: Martin Pirkl [aut, cre]
Maintainer: Martin Pirkl <martinpirkl@yahoo.de>
Built: R 4.6.0; ; 2026-05-18 10:23:07 UTC; windows
