DESCRIPTION

Package: MetaProViz
Title: METabolomics pre-PRocessing, functiOnal analysis and VIZualisation
Version: 2.1.2
Authors@R: c(
    person("Christina", "Schmidt", , "christina.schmidt@uni-heidelberg.de", role = c("aut", "cre"),
           comment = c(ORCID = "0000-0002-3867-0881")),
    person("Dimitrios", "Prymidis", role = "aut"),
    person("Denes", "Turei", role = "aut",
           comment = c(ORCID = "0000-0002-7249-9379")),
    person("Macabe", "Daley", 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, missimg value imputation, normalisation and outlier
    detection. It perform 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: Metabolomics, QualityControl, SystemsBiology, Visualization
License: GPL-3 + file LICENSE
Encoding: UTF-8
VignetteBuilder: knitr
Roxygen: list(markdown = TRUE)
Depends:
    R (>= 4.4.1),
    ggplot2 (>= 3.3.5)
Imports:
    clusterProfiler,
    cosmosR,
    dplyr,
    EnhancedVolcano,
    factoextra,
    ggbeeswarm,
    ggfortify,
    ggplot2,
    ggupset,
    ggVennDiagram,
    grid,
    gridExtra,
    gtools,
    hash,
    inflection,
    kableExtra,
    KEGGREST,
    limma,
    logger,
    magrittr,
    OmnipathR,
    patchwork,
    pheatmap,
    purrr,
    qcc,
    readr,
    reshape,
    rlang,
    stringr,
    tibble,
    writexl,
    yaml
Suggests:
    BiocStyle,
    knitr,
    pkgdown,
    svglite,
    testthat (>= 3.0.0)
Remotes: saezlab/OmnipathR, saezlab/cosmosR, git::https://git.bioconductor.org/packages/limma.git
RoxygenNote: 7.3.2
Config/testthat/edition: 3