{
  "_id": "6a1aea581d7bb097a09f322c",
  "Package": "omXplore",
  "Type": "Package",
  "Title": "Vizualization tools for 'omics' datasets with R",
  "Version": "1.7.0",
  "Authors@R": "c(person(given = \"Samuel\", \nfamily = \"Wieczorek\",\nemail = \"samuel.wieczorek@cea.fr\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID=\"0000-0002-5016-1203\")),\nperson(given = \"Thomas\",\nfamily =\"Burger\",\nemail = \"thomas.burger@cea.fr\",\nrole = c(\"aut\")),\nperson(given = \"Enora\",\nfamily = \"Fremy\",\nemail = \"enora.fremy@cea.fr\",\nrole = c(\"ctb\")),\nperson(given = \"Cyril\",\nfamily = \"Ariztegui\",\nemail = \"cyril.ariztegui@cea.fr\",\nrole = c(\"ctb\")),\nperson(given = \"Manon\",\nfamily = \"Gaudin\",\nemail = \"manon.gaudin@cea.fr\",\nrole = c(\"ctb\"))\n)",
  "Description": "This package contains a collection of functions (written\nas shiny modules) for the visualisation and the statistical\nanalysis of omics data. These plots can be displayed\nindividually or embedded in a global Shiny module. Additionaly,\nit is possible to integrate third party modules to the main\ninterface of the package omXplore.",
  "License": "Artistic-2.0",
  "biocViews": "Software, ShinyApps, MassSpectrometry, DataRepresentation,\nGUI, QualityControl",
  "NeedsCompilation": "no",
  "Collate": "'mod_explore_graphs.R' 'Infos_adjacencyMatrix.R'\n'Prostar_1x.R' 'convert_to_mae.R' 'doc-data.R'\n'external_apps_examples.R' 'get_pep_prot_CC.R'\n'mae_accessors.R' 'metacell_utils.R' 'mod_colorLegend.R'\n'modules.R' 'omXplore_cc.R' 'omXplore_corrmatrix.R'\n'omXplore_density.R' 'omXplore_format_DT.R'\n'omXplore_heatmap.R' 'omXplore_intensity.R'\n'omXplore_PCA_nipals.R' 'omXplore_pca.R'\n'omXplore_plots_tracking.R' 'omXplore_tabExplorer.R'\n'omXplore_variance.R' 'omXplore_view_dataset.R' 'palette.R'\n'plot_boxplot.R' 'plot_heatmap.R' 'plot_pca.R' 'plot_violin.R'\n'utils.R' 'zzz.R'",
  "RoxygenNote": "7.3.3",
  "Packaged": {
    "Date": "2026-05-30 09:38:19 UTC",
    "User": "root"
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  "Encoding": "UTF-8",
  "LazyData": "false",
  "URL": "https://github.com/edyp-lab/omXplore,\nhttps://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\nlibxml2-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:\n<https://orcid.org/0000-0002-5016-1203>),\nThomas Burger [aut],\nEnora Fremy [ctb],\nCyril Ariztegui [ctb],\nManon Gaudin [ctb]",
  "Maintainer": "Samuel Wieczorek <samuel.wieczorek@cea.fr>",
  "MD5sum": "a1cb6f4d5ce231dc436c4459b5cd58e2",
  "_user": "bioc",
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  "_created": "2026-05-30T09:38:19.000Z",
  "_published": "2026-05-30T13:47:04.169Z",
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    "source": "https://www.bioconductor.org/packages/stats/bioc/omXplore"
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    "manual.pdf"
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  "_homeurl": "https://github.com/edyp-lab/omxplore",
  "_realowner": "bioc",
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  "_exports": [
    ".initComplete",
    "addModules",
    "boxPlot",
    "Build_enriched_qdata",
    "Build_X_CC",
    "BuildColorStyles",
    "buildGraph",
    "Check_MSnSet_Consistency",
    "Check_se_Consistency",
    "Children",
    "colorLegend",
    "colorLegend_server",
    "colorLegend_ui",
    "convert_to_mae",
    "corrMatrix",
    "custom_metacell_colors",
    "CVDist",
    "densityPlot",
    "df_to_mae",
    "df_to_se",
    "display.CC.visNet",
    "ExtendPalette",
    "extFoo1",
    "extFoo1_server",
    "extFoo1_ui",
    "extFoo2",
    "extFoo2_server",
    "extFoo2_ui",
    "FormatDataForDT",
    "formatDT",
    "formatDT_server",
    "formatDT_ui",
    "get_adjacencyMatrix",
    "get_cc",
    "get_colID",
    "get_design",
    "get_group",
    "get_metacell",
    "get_parentProtId",
    "get_pkg_version",
    "get_type",
    "GetCCInfos",
    "GetColorsForConditions",
    "GetMetacellTags",
    "GetPkgVersion",
    "globals",
    "heatmapD",
    "heatmapForMissingValues",
    "is.listOf",
    "list_to_se",
    "listOfdf_to_mae",
    "listOfLists_to_mae",
    "listOfmatrix_to_mae",
    "listOfMSnSet_to_mae",
    "listOfSE_to_mae",
    "listPlotModules",
    "listShinyApps",
    "MAE_Compatibility_with_Prostar_1x",
    "MAE_to_mae",
    "matrix_to_mae",
    "matrix_to_se",
    "metacell.def",
    "MSnSet_to_mae",
    "MSnSet_to_se",
    "mv.heatmap",
    "my_PCA",
    "omXplore_cc",
    "omXplore_cc_server",
    "omXplore_cc_ui",
    "omXplore_corrmatrix",
    "omXplore_corrmatrix_server",
    "omXplore_corrmatrix_ui",
    "omXplore_density",
    "omXplore_density_server",
    "omXplore_density_ui",
    "omXplore_heatmap",
    "omXplore_heatmap_server",
    "omXplore_heatmap_ui",
    "omXplore_intensity",
    "omXplore_intensity_server",
    "omXplore_intensity_ui",
    "omXplore_pca",
    "omXplore_pca_server",
    "omXplore_pca_ui",
    "omXplore_tabExplorer",
    "omXplore_tabExplorer_server",
    "omXplore_tabExplorer_ui",
    "omXplore_variance",
    "omXplore_variance_server",
    "omXplore_variance_ui",
    "Parent",
    "pkgs.require2",
    "plotCCJitter",
    "plotPCA_Eigen",
    "plotPCA_Eigen_hc",
    "plotPCA_Ind",
    "plotPCA_Var",
    "plots_tracking",
    "plots_tracking_server",
    "plots_tracking_ui",
    "QFeatures_to_mae",
    "SampleColors",
    "SE_Compatibility_with_Prostar_1.x",
    "SE_to_mae",
    "view_dataset",
    "view_dataset_server",
    "view_dataset_ui",
    "violinPlot",
    "wrapper_pca"
  ],
  "_datasets": [
    {
      "name": "sub_R25",
      "title": "Feature example data",
      "object": "sub_R25",
      "file": "sub_R25.rda",
      "class": [
        "MultiAssayExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "vdata",
      "title": "Feature example data",
      "object": "vdata",
      "file": "vdata.rda",
      "class": [
        "MultiAssayExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "accessors",
      "title": "Accessors functions",
      "topics": [
        "accessors",
        "get_adjacencyMatrix",
        "get_adjacencyMatrix,SummarizedExperiment-method",
        "get_cc",
        "get_cc,SummarizedExperiment-method",
        "get_colID",
        "get_colID,SummarizedExperiment-method",
        "get_design",
        "get_design,MultiAssayExperiment-method",
        "get_group",
        "get_group,MultiAssayExperiment-method",
        "get_metacell",
        "get_metacell,SummarizedExperiment-method",
        "get_parentProtId",
        "get_parentProtId,SummarizedExperiment-method",
        "get_pkg_version",
        "get_pkg_version,SummarizedExperiment-method",
        "get_type",
        "get_type,SummarizedExperiment-method"
      ]
    },
    {
      "page": "Build_enriched_qdata",
      "title": "Builds enriched assay with cell metadata info",
      "topics": [
        "Build_enriched_qdata"
      ]
    },
    {
      "page": "BuildColorStyles",
      "title": "Build color style for DT tables",
      "topics": [
        "BuildColorStyles"
      ]
    },
    {
      "page": "color-legend",
      "title": "Color legend for DaparToolshed",
      "topics": [
        "color-legend",
        "colorLegend",
        "colorLegend_server",
        "colorLegend_ui",
        "custom_metacell_colors"
      ]
    },
    {
      "page": "converters",
      "title": "Convert to enriched MultiAssayExperiment",
      "topics": [
        "Build_X_CC",
        "Check_List_consistency",
        "Check_MSnSet_Consistency",
        "Check_se_Consistency",
        "Compute_CC",
        "converters",
        "convert_to_mae",
        "df_to_mae",
        "df_to_se",
        "listOfdf_to_mae",
        "listOfLists_to_mae",
        "listOfmatrix_to_mae",
        "listOfMSnSet_to_mae",
        "listOfSE_to_mae",
        "list_to_se",
        "MAE_to_mae",
        "matrix_to_mae",
        "matrix_to_se",
        "MSnSet_to_mae",
        "MSnSet_to_se",
        "QFeatures_to_mae",
        "SE_to_mae"
      ]
    },
    {
      "page": "corrmatrix",
      "title": "Displays a correlation matrix of the quantitative data of a numeric matrix.",
      "topics": [
        "corrMatrix",
        "corrmatrix",
        "omXplore_corrmatrix",
        "omXplore_corrmatrix_server",
        "omXplore_corrmatrix_ui"
      ]
    },
    {
      "page": "density-plot",
      "title": "Displays a correlation matrix of the quantitative data of a numeric matrix.",
      "topics": [
        "density-plot",
        "densityPlot",
        "omXplore_density",
        "omXplore_density_server",
        "omXplore_density_ui"
      ]
    },
    {
      "page": "ds-pca",
      "title": "my_PCA",
      "topics": [
        "ds-pca",
        "my_PCA",
        "omXplore_pca",
        "omXplore_pca_server",
        "omXplore_pca_ui",
        "plotPCA_Eigen",
        "plotPCA_Eigen_hc",
        "plotPCA_Ind",
        "plotPCA_Var",
        "wrapper_pca"
      ]
    },
    {
      "page": "ds-view",
      "title": "Bar plot of missing values per lines using 'plotly'.",
      "topics": [
        "ds-view",
        "view_dataset",
        "view_dataset_server",
        "view_dataset_ui"
      ]
    },
    {
      "page": "external_app",
      "title": "External module example",
      "topics": [
        "external_app",
        "extFoo1",
        "extFoo1_server",
        "extFoo1_ui",
        "extFoo2",
        "extFoo2_server",
        "extFoo2_ui"
      ]
    },
    {
      "page": "format_DT",
      "title": "formatDT_ui and formatDT_server",
      "topics": [
        "formatDT",
        "formatDT_server",
        "formatDT_ui",
        "format_DT"
      ]
    },
    {
      "page": "FormatDataForDT",
      "title": "Constructs a dataset suitable to use with the module format_DT.",
      "topics": [
        "FormatDataForDT"
      ]
    },
    {
      "page": "GetPkgVersion",
      "title": "Package version",
      "topics": [
        "GetPkgVersion"
      ]
    },
    {
      "page": "globals",
      "title": "Global variables",
      "topics": [
        "globals"
      ]
    },
    {
      "page": "intensity-plots",
      "title": "Displays different intensity plots.",
      "topics": [
        "boxPlot",
        "intensity-plots",
        "omXplore_intensity",
        "omXplore_intensity_server",
        "omXplore_intensity_ui",
        "violinPlot"
      ]
    },
    {
      "page": "is.listOf",
      "title": "Checks the class of a list's slots",
      "topics": [
        "is.listOf"
      ]
    },
    {
      "page": "omXplore_heatmap",
      "title": "Displays a correlation matrix of the quantitative data of a numeric matrix.",
      "topics": [
        "heatmapD",
        "heatmapForMissingValues",
        "mv.heatmap",
        "omXplore_heatmap",
        "omXplore_heatmap_server",
        "omXplore_heatmap_ui"
      ]
    },
    {
      "page": "omXplore_tabExplorer",
      "title": "Explore 'MultiAssayExperiment' objects.",
      "topics": [
        "omXplore_tabExplorer",
        "omXplore_tabExplorer_server",
        "omXplore_tabExplorer_ui"
      ]
    },
    {
      "page": "omXplore-modules",
      "title": "Shiny modules used by 'omXplore'",
      "topics": [
        "addModules",
        "listPlotModules",
        "listShinyApps",
        "omXplore-modules"
      ]
    },
    {
      "page": "palette",
      "title": "Palette for samples.",
      "topics": [
        "ExtendPalette",
        "GetColorsForConditions",
        "palette",
        "SampleColors"
      ]
    },
    {
      "page": "pep_prot_CC",
      "title": "Display a CC",
      "topics": [
        "buildGraph",
        "display.CC.visNet",
        "GetCCInfos",
        "pep_prot_CC",
        "plotCCJitter"
      ]
    },
    {
      "page": "pkgs.require2",
      "title": "Loads packages",
      "topics": [
        "pkgs.require2"
      ]
    },
    {
      "page": "plot-variance",
      "title": "Variance plot",
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