Package: MetNet
Type: Package
Title: Inferring metabolic networks from untargeted high-resolution
        mass spectrometry data
Version: 1.29.0
Date: 2025-10-24
Authors@R: c(person(given = "Thomas", family = "Naake", 
		email = "thomasnaake@googlemail.com", role = c("aut","cre")),
	person(given = "Liesa", family = "Salzer",
		email = "liesa.salzer@helmholtz-muenchen.de", role = "ctb"),
	person(given = "Elva Maria", family = "Novoa-del-Toro",
		email = "elva-maria.novoa-del-toro@inrae.fr", role = "ctb",
		comment = c(ORCID = "0000-0002-6135-5839")
		))
VignetteBuilder: knitr
Depends: R (>= 4.1), S4Vectors (>= 0.28.1), SummarizedExperiment (>=
        1.20.0)
Imports: bnlearn (>= 4.3), BiocParallel (>= 1.12.0), corpcor (>=
        1.6.10), dplyr (>= 1.0.3), ggplot2 (>= 3.3.3), GeneNet (>=
        1.2.15), GENIE3 (>= 1.7.0), methods (>= 4.1), parmigene (>=
        1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6),
        stats (>= 4.1), tibble (>= 3.0.5), tidyr (>= 1.1.2)
Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), glmnet (>=
        4.1-1), igraph (>= 1.1.2), knitr (>= 1.11), rmarkdown (>=
        1.15), testthat (>= 2.2.1), Spectra (>= 1.4.1), MsCoreUtils (>=
        1.6.0)
biocViews: ImmunoOncology, Metabolomics, MassSpectrometry, Network,
        Regression
Description: MetNet contains functionality to infer metabolic network
        topologies from quantitative data and high-resolution
        mass/charge information. Using statistical models (including
        correlation, mutual information, regression and Bayes
        statistics) and quantitative data (intensity values of
        features) adjacency matrices are inferred that can be combined
        to a consensus matrix. Mass differences calculated between
        mass/charge values of features will be matched against a data
        frame of supplied mass/charge differences referring to
        transformations of enzymatic activities. In a third step, the
        two levels of information are combined to form a adjacency
        matrix inferred from both quantitative and structure
        information.
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
Config/pak/sysreqs: libicu-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:47:00 UTC
RemoteUrl: https://github.com/bioc/MetNet
RemoteRef: HEAD
RemoteSha: e4fd4aceea5afee766a2c1f81c4fa51d26502016
NeedsCompilation: no
Packaged: 2025-10-30 07:26:48 UTC; root
Author: Thomas Naake [aut, cre],
  Liesa Salzer [ctb],
  Elva Maria Novoa-del-Toro [ctb] (ORCID:
    <https://orcid.org/0000-0002-6135-5839>)
Maintainer: Thomas Naake <thomasnaake@googlemail.com>
Built: R 4.6.0; ; 2025-10-30 07:29:12 UTC; windows
