Package: omXplore
Type: Package
Title: Vizualization tools for 'omics' datasets with R
Version: 1.5.0
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"))
    )
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,
    highcharter,
    visNetwork,
    tibble,
    grDevices,
    stats,
    utils,
    htmlwidgets,
    vioplot,
    graphics,
    FactoMineR,
    dendextend,
    dplyr,
    factoextra,
    tidyr,
    nipals
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: 2017-10-13 11:13:04 UTC; sw175264
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
git_url: https://git.bioconductor.org/packages/omXplore
git_branch: devel
git_last_commit: dd3714f
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
