{
  "_id": "6a1ac9a21d7bb097a09dcddb",
  "Package": "iSEEu",
  "Type": "Package",
  "Title": "iSEE Universe",
  "Version": "1.25.0",
  "Date": "2024-10-01",
  "Authors@R": "c(\nperson(\"Kevin\",\n\"Rue-Albrecht\",\nrole=c(\"aut\", \"cre\"),\nemail=\"kevinrue67@gmail.com\",\ncomment=c(ORCID = \"0000-0003-3899-3872\")),\nperson(\"Charlotte\",\n\"Soneson\",\nrole=\"aut\",\nemail=\"charlottesoneson@gmail.com\",\ncomment=c(ORCID = '0000-0003-3833-2169')),\nperson(\"Federico\",\n\"Marini\",\nrole=\"aut\",\nemail=\"marinif@uni-mainz.de\",\ncomment=c(ORCID = '0000-0003-3252-7758')),\nperson(\"Aaron\",\n\"Lun\",\nrole=\"aut\",\nemail=\"infinite.monkeys.with.keyboards@gmail.com\",\ncomment=c(ORCID = '0000-0002-3564-4813')),\nperson(\"Michael\",\n\"Stadler\",\nrole=\"ctb\",\nemail=\"michael.stadler@fmi.ch\"))",
  "Description": "iSEEu (the iSEE universe) contains diverse functionality\nto extend the usage of the iSEE package, including additional\nclasses for the panels, or modes allowing easy configuration of\niSEE applications.",
  "License": "MIT + file LICENSE",
  "Encoding": "UTF-8",
  "URL": "https://github.com/iSEE/iSEEu",
  "BugReports": "https://github.com/iSEE/iSEEu/issues",
  "biocViews": "ImmunoOncology, Visualization, GUI, DimensionReduction,\nFeatureExtraction, Clustering, Transcription, GeneExpression,\nTranscriptomics, SingleCell, CellBasedAssays",
  "RoxygenNote": "7.3.1",
  "Roxygen": "list(markdown = TRUE)",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "cmake libglpk-dev make libpng-dev libuv1-dev\nlibxml2-dev perl zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:52:26 UTC",
  "RemoteUrl": "https://github.com/bioc/iSEEu",
  "RemoteRef": "HEAD",
  "RemoteSha": "95c260ca9276c6c554153967b79fa1eaf33b19c9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 07:49:12 UTC",
    "User": "root"
  },
  "Author": "Kevin Rue-Albrecht [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-3899-3872>),\nCharlotte Soneson [aut] (ORCID:\n<https://orcid.org/0000-0003-3833-2169>),\nFederico Marini [aut] (ORCID: <https://orcid.org/0000-0003-3252-7758>),\nAaron Lun [aut] (ORCID: <https://orcid.org/0000-0002-3564-4813>),\nMichael Stadler [ctb]",
  "Maintainer": "Kevin Rue-Albrecht <kevinrue67@gmail.com>",
  "MD5sum": "c1336073f92dd7a63e4926c0d83c0cde",
  "_user": "bioc",
  "_type": "src",
  "_file": "iSEEu_1.25.0.tar.gz",
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  "_filesize": 1703601,
  "_sha256": "2eff151f3ab9a916c407c4aa80f28d239a4e2b5644e534d86d64730f60be2288",
  "_created": "2026-05-30T07:49:12.000Z",
  "_published": "2026-05-30T11:27:30.033Z",
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    "warning": 2,
    "note": 8
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  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26678348464",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/iSEEu",
  "_commit": {
    "id": "95c260ca9276c6c554153967b79fa1eaf33b19c9",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380746
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  "_maintainer": {
    "name": "Kevin Rue-Albrecht",
    "email": "kevinrue67@gmail.com",
    "login": "kevinrue",
    "mastodon": "@kevinrue@fosstodon.org",
    "orcid": "0000-0003-3899-3872",
    "description": "Ingénieur diplômé;\nComputational Biologist; \nSoftware engineer;\nBioconductor contributor",
    "uuid": 5769108
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "iSEE",
      "role": "Depends"
    },
    {
      "package": "iSEEhex",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "S4Vectors",
      "role": "Imports"
    },
    {
      "package": "IRanges",
      "role": "Imports"
    },
    {
      "package": "shiny",
      "role": "Imports"
    },
    {
      "package": "SummarizedExperiment",
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    {
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      "role": "Imports"
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      "version": ">= 3.4.0",
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    {
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    {
      "package": "stats",
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    {
      "package": "colourpicker",
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    {
      "package": "shinyAce",
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    },
    {
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    },
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      "version": ">= 2.1.0",
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    {
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    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 1,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 2
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.25.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.24.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "immunooncology",
    "visualization",
    "gui",
    "dimensionreduction",
    "featureextraction",
    "clustering",
    "transcription",
    "geneexpression",
    "transcriptomics",
    "singlecell",
    "cellbasedassays",
    "hacktoberfest"
  ],
  "_stars": 9,
  "_contributors": [
    {
      "user": "ltla",
      "count": 89,
      "uuid": 8166669
    },
    {
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      "count": 51,
      "uuid": 5628952
    },
    {
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      "count": 38,
      "uuid": 5769108
    },
    {
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      "uuid": 7447478
    },
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      "uuid": 1744257
    },
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      "uuid": 2746443
    },
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      "uuid": 13657342
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 445,
    "source": "https://www.bioconductor.org/packages/stats/bioc/iSEEu"
  },
  "_devurl": "https://github.com/isee/iseeu",
  "_searchresults": 38,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/iSEEu.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/isee/iseeu",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    ".allowableXAxisChoices",
    ".allowableYAxisChoices",
    ".cacheCommonInfo",
    ".colorByNoneDotPlotField",
    ".colorByNoneDotPlotScale",
    ".createObservers",
    ".defineDataInterface",
    ".defineInterface",
    ".defineOutput",
    ".definePanelTour",
    ".exportOutput",
    ".fullName",
    ".generateDotPlot",
    ".generateDotPlotData",
    ".generateOutput",
    ".generateTable",
    ".getAcceptableAveAbFields",
    ".getAcceptableLogFCFields",
    ".getAcceptablePValueFields",
    ".getDotPlotColorHelp",
    ".getGeneSetCommands",
    ".getIdentifierType",
    ".getOrganism",
    ".hideInterface",
    ".multiSelectionActive",
    ".multiSelectionAvailable",
    ".multiSelectionClear",
    ".multiSelectionCommands",
    ".multiSelectionDimension",
    ".multiSelectionInvalidated",
    ".panelColor",
    ".prioritizeDotPlotData",
    ".refineParameters",
    ".renderOutput",
    ".setAcceptableAveAbFields",
    ".setAcceptableLogFCFields",
    ".setAcceptablePValueFields",
    ".setGeneSetCommands",
    ".setIdentifierType",
    ".setOrganism",
    "AggregatedDotPlot",
    "createGeneSetCommands",
    "DifferentialStatisticsTable",
    "DynamicMarkerTable",
    "DynamicReducedDimensionPlot",
    "FeatureSetTable",
    "GeneSetTable",
    "getAveAbFields",
    "getAveAbPattern",
    "getAveAbPatterns",
    "getFeatureSetCollections",
    "getFeatureSetCommands",
    "getLogFCFields",
    "getLogFCPattern",
    "getLogFCPatterns",
    "getPValueFields",
    "getPValuePattern",
    "getPValuePatterns",
    "getTableExtraFields",
    "initialize",
    "LogFCLogFCPlot",
    "MAPlot",
    "MarkdownBoard",
    "modeEmpty",
    "modeGating",
    "modeReducedDim",
    "registerAveAbFields",
    "registerAveAbPatterns",
    "registerFeatureSetCollections",
    "registerFeatureSetCommands",
    "registerLogFCFields",
    "registerLogFCPatterns",
    "registerPValueFields",
    "registerPValuePatterns",
    "setAveAbPattern",
    "setFeatureSetCommands",
    "setLogFCPattern",
    "setPValuePattern",
    "setTableExtraFields",
    "VolcanoPlot"
  ],
  "_help": [
    {
      "page": "AggregatedDotPlot",
      "title": "The AggregatedDotPlot class",
      "topics": [
        ".cacheCommonInfo,AggregatedDotPlot-method",
        ".createObservers,AggregatedDotPlot-method",
        ".defineDataInterface,AggregatedDotPlot-method",
        ".defineInterface,AggregatedDotPlot-method",
        ".defineOutput,AggregatedDotPlot-method",
        ".definePanelTour,AggregatedDotPlot-method",
        ".exportOutput,AggregatedDotPlot-method",
        ".fullName,AggregatedDotPlot-method",
        ".generateOutput,AggregatedDotPlot-method",
        ".hideInterface,AggregatedDotPlot-method",
        ".panelColor,AggregatedDotPlot-method",
        ".refineParameters,AggregatedDotPlot-method",
        ".refineParameters,AggregatedDotplot-method",
        ".renderOutput,AggregatedDotPlot-method",
        "AggregatedDotPlot",
        "AggregatedDotPlot-class",
        "initialize,AggregatedDotPlot-method"
      ]
    },
    {
      "page": "createGeneSetCommands",
      "title": "Create gene set commands",
      "topics": [
        "createGeneSetCommands"
      ]
    },
    {
      "page": "defunct",
      "title": "Defunct functions",
      "topics": [
        ".getAcceptableAveAbFields",
        ".getAcceptableLogFCFields",
        ".getAcceptablePValueFields",
        ".setAcceptableAveAbFields",
        ".setAcceptableLogFCFields",
        ".setAcceptablePValueFields",
        "defunct"
      ]
    },
    {
      "page": "DynamicMarkerTable-class",
      "title": "Dynamic marker table",
      "topics": [
        ".cacheCommonInfo,DynamicMarkerTable-method",
        ".createObservers,DynamicMarkerTable-method",
        ".defineDataInterface,DynamicMarkerTable-method",
        ".definePanelTour,DynamicMarkerTable-method",
        ".fullName,DynamicMarkerTable-method",
        ".generateTable,DynamicMarkerTable-method",
        ".hideInterface,DynamicMarkerTable-method",
        ".multiSelectionInvalidated,DynamicMarkerTable-method",
        ".panelColor,DynamicMarkerTable-method",
        ".refineParameters,DynamicMarkerTable-method",
        "DifferentialStatisticsTable",
        "DynamicMarkerTable",
        "DynamicMarkerTable-class",
        "initialize,DynamicMarkerTable-method"
      ]
    },
    {
      "page": "DynamicReducedDimensionPlot-class",
      "title": "Dynamic reduced dimension plot",
      "topics": [
        ".cacheCommonInfo,DynamicReducedDimensionPlot-method",
        ".createObservers,DynamicReducedDimensionPlot-method",
        ".defineDataInterface,DynamicReducedDimensionPlot-method",
        ".definePanelTour,DynamicReducedDimensionPlot-method",
        ".fullName,DynamicReducedDimensionPlot-method",
        ".generateDotPlotData,DynamicReducedDimensionPlot-method",
        ".multiSelectionInvalidated,DynamicReducedDimensionPlot-method",
        ".panelColor,DynamicReducedDimensionPlot-method",
        ".refineParameters,DynamicReducedDimensionPlot-method",
        "DynamicReducedDimensionPlot",
        "DynamicReducedDimensionPlot-class",
        "initialize,DynamicReducedDimensionPlot-method"
      ]
    },
    {
      "page": "FeatureSetTable-class",
      "title": "Feature set table",
      "topics": [
        ".cacheCommonInfo,FeatureSetTable-method",
        ".createObservers,FeatureSetTable-method",
        ".defineDataInterface,FeatureSetTable-method",
        ".defineOutput,FeatureSetTable-method",
        ".definePanelTour,FeatureSetTable-method",
        ".fullName,FeatureSetTable-method",
        ".generateOutput,FeatureSetTable-method",
        ".hideInterface,FeatureSetTable-method",
        ".multiSelectionActive,FeatureSetTable-method",
        ".multiSelectionAvailable,FeatureSetTable-method",
        ".multiSelectionClear,FeatureSetTable-method",
        ".multiSelectionCommands,FeatureSetTable-method",
        ".multiSelectionDimension,FeatureSetTable-method",
        ".panelColor,FeatureSetTable-method",
        ".refineParameters,FeatureSetTable-method",
        ".renderOutput,FeatureSetTable-method",
        "FeatureSetTable",
        "FeatureSetTable-class",
        "initialize,FeatureSetTable-method"
      ]
    },
    {
      "page": "GeneSetTable-class",
      "title": "Gene set table",
      "topics": [
        ".createObservers,GeneSetTable-method",
        ".defineDataInterface,GeneSetTable-method",
        ".defineOutput,GeneSetTable-method",
        ".fullName,GeneSetTable-method",
        ".generateOutput,GeneSetTable-method",
        ".hideInterface,GeneSetTable-method",
        ".multiSelectionActive,GeneSetTable-method",
        ".multiSelectionAvailable,GeneSetTable-method",
        ".multiSelectionClear,GeneSetTable-method",
        ".multiSelectionCommands,GeneSetTable-method",
        ".multiSelectionDimension,GeneSetTable-method",
        ".panelColor,GeneSetTable-method",
        ".renderOutput,GeneSetTable-method",
        "GeneSetTable",
        "GeneSetTable-class",
        "initialize,GeneSetTable-method"
      ]
    },
    {
      "page": "globals-PValuePattern",
      "title": "Global DE prefixes",
      "topics": [
        "getAveAbPattern",
        "getLogFCPattern",
        "getPValuePattern",
        "setAveAbPattern",
        "setLogFCPattern",
        "setPValuePattern"
      ]
    },
    {
      "page": "global-TableExtraFields",
      "title": "Global extra table fields",
      "topics": [
        "getTableExtraFields",
        "setTableExtraFields"
      ]
    },
    {
      "page": "LogFCLogFCPlot-class",
      "title": "The LogFCLogFCPlot class",
      "topics": [
        ".allowableXAxisChoices,LogFCLogFCPlot-method",
        ".allowableYAxisChoices,LogFCLogFCPlot-method",
        ".cacheCommonInfo,LogFCLogFCPlot-method",
        ".colorByNoneDotPlotField,LogFCLogFCPlot-method",
        ".colorByNoneDotPlotScale,LogFCLogFCPlot-method",
        ".createObservers,LogFCLogFCPlot-method",
        ".defineDataInterface,LogFCLogFCPlot-method",
        ".definePanelTour,LogFCLogFCPlot-method",
        ".fullName,LogFCLogFCPlot-method",
        ".generateDotPlot,LogFCLogFCPlot-method",
        ".generateDotPlotData,LogFCLogFCPlot-method",
        ".getDotPlotColorHelp,LogFCLogFCPlot-method",
        ".hideInterface,LogFCLogFCPlot-method",
        ".panelColor,LogFCLogFCPlot-method",
        ".prioritizeDotPlotData,LogFCLogFCPlot-method",
        ".refineParameters,LogFCLogFCPlot-method",
        "initialize,LogFCLogFCPlot-method",
        "LogFCLogFCPlot",
        "LogFCLogFCPlot-class"
      ]
    },
    {
      "page": "MAPlot-class",
      "title": "The MAPlot class",
      "topics": [
        ".allowableXAxisChoices,MAPlot-method",
        ".allowableYAxisChoices,MAPlot-method",
        ".cacheCommonInfo,MAPlot-method",
        ".colorByNoneDotPlotField,MAPlot-method",
        ".colorByNoneDotPlotScale,MAPlot-method",
        ".createObservers,MAPlot-method",
        ".defineDataInterface,MAPlot-method",
        ".definePanelTour,MAPlot-method",
        ".fullName,MAPlot-method",
        ".generateDotPlot,MAPlot-method",
        ".generateDotPlotData,MAPlot-method",
        ".getDotPlotColorHelp,MAPlot-method",
        ".hideInterface,MAPlot-method",
        ".panelColor,MAPlot-method",
        ".prioritizeDotPlotData,MAPlot-method",
        ".refineParameters,MAPlot-method",
        "initialize,MAPlot-method",
        "MAPlot",
        "MAPlot-class"
      ]
    },
    {
      "page": "MarkdownBoard-class",
      "title": "The MarkdownBoard class",
      "topics": [
        ".createObservers,MarkdownBoard-method",
        ".defineDataInterface,MarkdownBoard-method",
        ".defineOutput,MarkdownBoard-method",
        ".definePanelTour,MarkdownBoard-method",
        ".exportOutput,MarkdownBoard-method",
        ".fullName,MarkdownBoard-method",
        ".generateOutput,MarkdownBoard-method",
        ".hideInterface,MarkdownBoard-method",
        ".panelColor,MarkdownBoard-method",
        ".renderOutput,MarkdownBoard-method",
        "initialize,MarkdownBoard-method",
        "MarkdownBoard",
        "MarkdownBoard-class"
      ]
    },
    {
      "page": "modeEmpty",
      "title": "App pre-configured to launch with no visible panel",
      "topics": [
        "modeEmpty"
      ]
    },
    {
      "page": "modeGating",
      "title": "App pre-configured to link multiple feature assay plots",
      "topics": [
        "modeGating"
      ]
    },
    {
      "page": "modeReducedDim",
      "title": "App pre-configured to compare multiple reduced dimension plots",
      "topics": [
        "modeReducedDim"
      ]
    },
    {
      "page": "registerDEFields",
      "title": "Register DE-related fields",
      "topics": [
        "getAveAbFields",
        "getAveAbPatterns",
        "getLogFCFields",
        "getLogFCPatterns",
        "getPValueFields",
        "getPValuePatterns",
        "registerAveAbFields",
        "registerAveAbPatterns",
        "registerDEFields",
        "registerLogFCFields",
        "registerLogFCPatterns",
        "registerPValueFields",
        "registerPValuePatterns"
      ]
    },
    {
      "page": "registerFeatureSetCollections",
      "title": "Register feature set collections",
      "topics": [
        "getFeatureSetCollections",
        "getFeatureSetCommands",
        "registerFeatureSetCollections",
        "registerFeatureSetCommands"
      ]
    },
    {
      "page": "global-FeatureSetCommands",
      "title": "Global feature set commands",
      "topics": [
        "setFeatureSetCommands"
      ]
    },
    {
      "page": "utils-geneset",
      "title": "Gene set utilities",
      "topics": [
        ".getGeneSetCommands",
        ".getIdentifierType",
        ".getOrganism",
        ".setGeneSetCommands",
        ".setIdentifierType",
        ".setOrganism",
        "utils-geneset"
      ]
    },
    {
      "page": "VolcanoPlot-class",
      "title": "The VolcanoPlot class",
      "topics": [
        ".allowableXAxisChoices,VolcanoPlot-method",
        ".allowableYAxisChoices,VolcanoPlot-method",
        ".cacheCommonInfo,VolcanoPlot-method",
        ".colorByNoneDotPlotField,VolcanoPlot-method",
        ".colorByNoneDotPlotScale,VolcanoPlot-method",
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  "_vignettes": [
    {
      "source": "iSEEu.Rmd",
      "filename": "iSEEu.html",
      "title": "Universe of iSEE panels",
      "author": "Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Differential expression plots",
        "Dynamically recalculated panels",
        "Feature set table",
        "App modes",
        "Miscellaneous panels",
        "Contributing to r Biocpkg(\"iSEEu\")",
        "Using example data sets",
        "Documenting, testing, coding style and conventions",
        "Looking for constants within r Biocpkg(\"iSEE\")",
        "What if I need a custom panel type?",
        "Where can I find a comprehensive introduction to r Biocpkg(\"iSEE\")?",
        "Session information",
        "References"
      ],
      "created": "2022-09-02 10:50:20",
      "modified": "2024-03-26 14:11:47",
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