Package: omXplore
Type: Package
Title: Vizualization tools for 'omics' datasets with R
Version: 1.7.0
Authors@R: c(person(given = "Samuel", 
      family = "Wieczorek",
      email = "samuel.wieczorek@cea.fr", 
      role = c("aut", "cre"),
      comment = c(ORCID="0000-0002-5016-1203")),
  person(given = "Thomas", 
      family ="Burger",
      email = "thomas.burger@cea.fr",
      role = c("aut")),
  person(given = "Enora", 
    family = "Fremy",
    email = "enora.fremy@cea.fr", 
    role = c("ctb")),
  person(given = "Cyril", 
    family = "Ariztegui",
    email = "cyril.ariztegui@cea.fr", 
    role = c("ctb")),
  person(given = "Manon", 
    family = "Gaudin",
    email = "manon.gaudin@cea.fr", 
    role = c("ctb"))
    )
Description: This package contains a collection of functions (written
        as shiny modules) for the visualisation and the statistical
        analysis of omics data. These plots can be displayed
        individually or embedded in a global Shiny module. Additionaly,
        it is possible to integrate third party modules to the main
        interface of the package omXplore.
License: Artistic-2.0
Depends: R (>= 4.5.0), methods
Imports: DT, shiny, MSnbase, PSMatch, SummarizedExperiment,
        MultiAssayExperiment, shinyBS, shinyjs, shinyjqui,
        RColorBrewer, gplots, plotly, visNetwork, tibble, grDevices,
        stats, utils, htmlwidgets, vioplot, graphics, FactoMineR,
        dendextend, dplyr, factoextra, tidyr, nipals, Biobase
Suggests: knitr, rmarkdown, BiocStyle, testthat, Matrix, graph
biocViews: Software, ShinyApps, MassSpectrometry, DataRepresentation,
        GUI, QualityControl
NeedsCompilation: no
Collate: 'mod_explore_graphs.R' 'Infos_adjacencyMatrix.R'
        'Prostar_1x.R' 'convert_to_mae.R' 'doc-data.R'
        'external_apps_examples.R' 'get_pep_prot_CC.R'
        'mae_accessors.R' 'metacell_utils.R' 'mod_colorLegend.R'
        'modules.R' 'omXplore_cc.R' 'omXplore_corrmatrix.R'
        'omXplore_density.R' 'omXplore_format_DT.R'
        'omXplore_heatmap.R' 'omXplore_intensity.R'
        'omXplore_PCA_nipals.R' 'omXplore_pca.R'
        'omXplore_plots_tracking.R' 'omXplore_tabExplorer.R'
        'omXplore_variance.R' 'omXplore_view_dataset.R' 'palette.R'
        'plot_boxplot.R' 'plot_heatmap.R' 'plot_pca.R' 'plot_violin.R'
        'utils.R' 'zzz.R'
RoxygenNote: 7.3.3
Packaged: 2026-06-21 11:00:08 UTC; root
Encoding: UTF-8
LazyData: false
URL: https://github.com/edyp-lab/omXplore,
        https://edyp-lab.github.io/omXplore/
BugReports: https://github.com/edyp-lab/omXplore/issues
Roxygen: list(markdown = TRUE)
VignetteBuilder: knitr
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libnetcdf-dev libssl-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:03:44 UTC
RemoteUrl: https://github.com/bioc/omXplore
RemoteRef: HEAD
RemoteSha: 2b3acd9f97105f5d80a95c9c38b3fdc1bc589a7f
Author: Samuel Wieczorek [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5016-1203>),
  Thomas Burger [aut],
  Enora Fremy [ctb],
  Cyril Ariztegui [ctb],
  Manon Gaudin [ctb]
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>