Package: MetaProViz
Type: Package
Title: METabolomics pre-PRocessing, functiOnal analysis and
        VIZualisation
Version: 4.0.0
Authors@R: c(
    person("Christina", "Schmidt",
           email = "christina.schmidt.science@gmail.com",
           role = c("aut", "cre", "fnd"),
           comment = c(ORCID = "0000-0002-3867-0881")),
    person("Denes", "Turei", role = "aut",
           comment = c(ORCID = "0000-0002-7249-9379")),
    person("Dimitrios", "Prymidis", role = "aut",
           comment = c(ORCID = "0009-0000-0168-3841")),
    person("Macabe", "Daley", role = "aut",
           comment = c(ORCID = "0000-0002-8026-7068")),
    person("Jannik", "Franken", role = "aut"),
    person("Julio", "Saez-Rodriguez", role = "aut",
           comment = c(ORCID = "0000-0002-8552-8976")),
    person("Christian", "Frezza", role = "aut",
           comment = c(ORCID = "0000-0002-3293-7397"))
  )
Description: MetaProViz can analyse standard metabolomics and
        exometabolomics data (CoRe). It performs pre-processing
        including feature filtering, missing value imputation,
        normalisation and outlier detection. It performs functional
        analysis including differential metabolite analysis (DMA),
        clustering based on regulatory rules (MCA) and contains
        different visualisation methods to extract biological
        interpretable graphs and saves them in a publication ready
        format.
URL: https://saezlab.github.io/MetaProViz
BugReports: https://github.com/saezlab/MetaProViz/issues
biocViews: Clustering, Metabolomics, Pathways, QualityControl,
        Software, SystemsBiology, Visualization
License: BSD_3_clause + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
LazyData: false
Depends: R (>= 4.4)
Imports: broom, ComplexUpset (>= 1.3.3), cosmosR, DBI, dplyr,
        EnhancedVolcano, factoextra, ggbeeswarm, ggfortify, ggplot2 (>=
        3.3.5), ggpubr, ggrepel, grid, gridExtra, gtools, hash, igraph,
        ggraph, inflection, limma, logger, magrittr, methods, OmnipathR
        (>= 3.19.12), patchwork, pheatmap, Polychrome, purrr, qcc,
        qvalue, rappdirs, readr, rlang, rstatix, S4Vectors, stringr,
        SummarizedExperiment, tibble, tidyr, tidyselect, writexl
Suggests: BiocStyle, ggupset, ggVennDiagram, kableExtra, knitr,
        pkgdown, svglite, testthat (>= 3.1.4)
RoxygenNote: 7.3.3
Config/testthat/edition: 3
Config/pak/sysreqs: cmake libfontconfig1-dev libfreetype6-dev
        libglpk-dev make libicu-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev libx11-dev zlib1g-dev
Repository: Bioconductor 3.23
Date/Publication: 2026-04-28 13:06:33 UTC
RemoteUrl: https://github.com/bioc/MetaProViz
RemoteRef: RELEASE_3_23
RemoteSha: 31f4cb3ac3df8f15550dba537fd0b1d2ec140fe1
NeedsCompilation: no
Packaged: 2026-10-10 18:07:37 UTC; root
Author: Christina Schmidt [aut, cre, fnd] (ORCID:
    <https://orcid.org/0000-0002-3867-0881>),
  Denes Turei [aut] (ORCID: <https://orcid.org/0000-0002-7249-9379>),
  Dimitrios Prymidis [aut] (ORCID:
    <https://orcid.org/0009-0000-0168-3841>),
  Macabe Daley [aut] (ORCID: <https://orcid.org/0000-0002-8026-7068>),
  Jannik Franken [aut],
  Julio Saez-Rodriguez [aut] (ORCID:
    <https://orcid.org/0000-0002-8552-8976>),
  Christian Frezza [aut] (ORCID: <https://orcid.org/0000-0002-3293-7397>)
Maintainer: Christina Schmidt <christina.schmidt.science@gmail.com>