Package: omXplore
Type: Package
Title: Vizualization tools for 'omics' datasets with R
Version: 1.2.2
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: 7.3.2
Packaged: 2025-08-08 00:43:52 UTC; biocbuild
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: RELEASE_3_21
git_last_commit: 5d446d1
git_last_commit_date: 2025-08-07
Repository: Bioconductor 3.21
Date/Publication: 2025-08-07
Author: Samuel Wieczorek [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5016-1203>),
  Thomas Burger [aut],
  Enora Fremy [ctb],
  Cyril Ariztegui [ctb]
Maintainer: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Built: R 4.5.1; ; 2025-08-08 13:29:27 UTC; windows
