Package: MetNet
Type: Package
Title: Inferring metabolic networks from untargeted high-resolution
        mass spectrometry data
Version: 1.27.0
Date: 2024-10-31
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 (>= 4.1.0), 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 (>= 3.5), parmigene (>=
        1.0.2), psych (>= 2.1.6), rlang (>= 0.4.10), stabs (>= 0.6),
        stats (>= 3.6), 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: 7.1.2
git_url: https://git.bioconductor.org/packages/MetNet
git_branch: devel
git_last_commit: 790be15
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-05 00:17:37 UTC; biocbuild
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 4.5.0; ; 2025-06-05 13:23:41 UTC; windows
