Package: MetaProViz
Type: Package
Title: METabolomics pre-PRocessing, functiOnal analysis and
        VIZualisation
Version: 4.1.0
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 libjpeg-dev libpng-dev libuv1-dev
        libxml2-dev libssl-dev libx11-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:06:33 UTC
RemoteUrl: https://github.com/bioc/MetaProViz
RemoteRef: HEAD
RemoteSha: 02799d0d5ac3648b123862d0baf76f31f72b2441
NeedsCompilation: no
Packaged: 2026-07-09 06:08:22 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>