DESCRIPTION

Package: MetNet
Type: Package
Title: Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Version: 1.25.0
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 (>= 4.0),
    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: 7.3.2