{ "_id": "6a1acac61d7bb097a09dd87b", "Package": "iSEE", "Title": "Interactive SummarizedExperiment Explorer", "Version": "2.25.0", "Date": "2025-11-16", "Authors@R": "c(\nperson(\"Kevin\", \"Rue-Albrecht\", role = c(\"aut\", \"cre\"), email = \"kevinrue67@gmail.com\", comment = c(ORCID = \"0000-0003-3899-3872\")),\nperson(\"Federico\", \"Marini\", role=\"aut\", email=\"marinif@uni-mainz.de\", comment = c(ORCID = '0000-0003-3252-7758')),\nperson(\"Charlotte\", \"Soneson\", role=\"aut\", email=\"charlottesoneson@gmail.com\", comment = c(ORCID = '0000-0003-3833-2169')),\nperson(\"Aaron\", \"Lun\", role=\"aut\", email=\"infinite.monkeys.with.keyboards@gmail.com\", comment = c(ORCID = '0000-0002-3564-4813')))", "Description": "Create an interactive Shiny-based graphical user interface\nfor exploring data stored in SummarizedExperiment objects,\nincluding row- and column-level metadata. The interface\nsupports transmission of selections between plots and tables,\ncode tracking, interactive tours, interactive or programmatic\ninitialization, preservation of app state, and extensibility to\nnew panel types via S4 classes. Special attention is given to\nsingle-cell data in a SingleCellExperiment object with\nvisualization of dimensionality reduction results.", "URL": "https://isee.github.io/iSEE/", "BugReports": "https://github.com/iSEE/iSEE/issues", "biocViews": "CellBasedAssays, Clustering, DimensionReduction,\nFeatureExtraction, GeneExpression, GUI, ImmunoOncology,\nShinyApps, SingleCell, Transcription, Transcriptomics,\nVisualization", "License": "MIT + file LICENSE", "VignetteBuilder": "knitr", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "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 12:47:29 UTC", "RemoteUrl": "https://github.com/bioc/iSEE", "RemoteRef": "HEAD", "RemoteSha": "f43c73682015f51e0cdd576ff749c8fcb5d15b53", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:53:47 UTC", "User": "root" }, "Author": "Kevin Rue-Albrecht [aut, cre] (ORCID:\n),\nFederico Marini [aut] (ORCID: ),\nCharlotte Soneson [aut] (ORCID:\n),\nAaron Lun [aut] (ORCID: )", "Maintainer": "Kevin Rue-Albrecht ", "MD5sum": "325afd87de05b03183f18d73b014c078", "_user": "bioc", "_type": "src", "_file": "iSEE_2.25.0.tar.gz", "_fileid": "919480e2ce4c7dc17a37f3850b320b6b2488ea0ad163cd8f95dfe9aa60620f14", "_filesize": 10049135, "_sha256": "919480e2ce4c7dc17a37f3850b320b6b2488ea0ad163cd8f95dfe9aa60620f14", "_created": "2026-05-30T07:53:47.000Z", "_published": "2026-05-30T11:32:22.046Z", "_jobs": [ { "job": 78634853382, "time": 360, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306665967" }, { "job": 78634853390, "time": 459, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306676248" }, { "job": 78634853391, "time": 534, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306683313" }, { "job": 78634853394, "time": 415, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", 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{ "page": "setCachedCommonInfo", "title": "Set and get cached commons", "topics": [ ".getCachedCommonInfo", ".setCachedCommonInfo" ] }, { "page": "aes-utils", "title": "Generate ggplot aesthetic instructions", "topics": [ ".buildAes", "aes-utils" ] }, { "page": "cache-utils", "title": "Caching utilities", "topics": [ ".findAtomicFields", ".isAssayNumeric", ".whichGroupable", ".whichNumeric", "cache-utils" ] }, { "page": "checkColormapCompatibility", "title": "Check compatibility between ExperimentColorMap and SummarizedExperiment objects", "topics": [ "checkColormapCompatibility" ] }, { "page": "class-utils", "title": "Set default slot values", "topics": [ ".emptyDefault", "class-utils" ] }, { "page": "cleanDataset", "title": "Clean the dataset", "topics": [ "cleanDataset", "cleanDataset,SingleCellExperiment-method", "cleanDataset,SummarizedExperiment-method" ] }, { "page": "collapseBox", "title": "A collapsible box", "topics": [ "collapseBox" ] }, { "page": "ColumnDataPlot-class", 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"rowSelectionColorMap" ] }, { "page": "ColumnTable-class", "title": "The ColumnTable class", "topics": [ ".createObservers,ColumnTable-method", ".defineInterface,ColumnTable-method", ".hideInterface,ColumnTable-method", ".multiSelectionDimension,ColumnTable-method", ".multiSelectionResponsive,ColumnTable-method", ".refineParameters,ColumnTable-method", ".showSelectionDetails,ColumnTable-method", ".singleSelectionDimension,ColumnTable-method", "ColumnTable-class", "initialize,ColumnTable-method" ] }, { "page": "ComplexHeatmapPlot-class", "title": "The ComplexHeatmapPlot panel", "topics": [ ".cacheCommonInfo,ComplexHeatmapPlot-method", ".createObservers,ComplexHeatmapPlot-method", ".defineDataInterface,ComplexHeatmapPlot-method", ".defineInterface,ComplexHeatmapPlot-method", ".defineOutput,ComplexHeatmapPlot-method", ".definePanelTour,ComplexHeatmapPlot-method", ".exportOutput,ComplexHeatmapPlot-method", ".fullName,ComplexHeatmapPlot-method", ".generateOutput,ComplexHeatmapPlot-method", 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"page": "defaultTour", "title": "Define the default tour", "topics": [ "defaultTour" ] }, { "page": "documentation-generics", "title": "Documentation generics", "topics": [ ".definePanelTour", ".getDotPlotColorHelp", "documentation-generics" ] }, { "page": "DotPlot-class", "title": "The DotPlot virtual class", "topics": [ ".allowableColorByDataChoices,DotPlot-method", ".cacheCommonInfo,DotPlot-method", ".colorByNoneDotPlotField,DotPlot-method", ".colorByNoneDotPlotScale,DotPlot-method", ".createObservers,DotPlot-method", ".defineInterface,DotPlot-method", ".defineOutput,DotPlot-method", ".definePanelTour,DotPlot-method", ".defineVisualColorInterface,DotPlot-method", ".defineVisualFacetInterface,DotPlot-method", ".defineVisualOtherInterface,DotPlot-method", ".defineVisualPointInterface,DotPlot-method", ".defineVisualShapeInterface,DotPlot-method", ".defineVisualSizeInterface,DotPlot-method", ".defineVisualTextInterface,DotPlot-method", ".exportOutput,DotPlot-method", 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"show,ExperimentColorMap-method" ] }, { "page": "FeatureAssayPlot-class", "title": "The FeatureAssayPlot panel", "topics": [ ".createObservers,FeatureAssayPlot-method", ".defineDataInterface,FeatureAssayPlot-method", ".definePanelTour,FeatureAssayPlot-method", ".fullName,FeatureAssayPlot-method", ".generateDotPlotData,FeatureAssayPlot-method", ".multiSelectionInvalidated,FeatureAssayPlot-method", ".panelColor,FeatureAssayPlot-method", ".refineParameters,FeatureAssayPlot-method", ".singleSelectionSlots,FeatureAssayPlot-method", "FeatureAssayPlot", "FeatureAssayPlot-class", "initialize,FeatureAssayPlot-method" ] }, { "page": "filterDTColumn", "title": "Filter 'DT' columns", "topics": [ "filterDT", "filterDTColumn" ] }, { "page": "hidden-inputs", "title": "Hidden interface elements", "topics": [ ".selectInputHidden", "hidden-inputs" ] }, { "page": "interface-generics", "title": "Generics for the panel interface", "topics": [ ".defineDataInterface", ".defineInterface", ".hideInterface", "interface-generics" ] }, { "page": "interface-wrappers", "title": "'iSEE' UI element wrappers", "topics": [ ".checkboxGroupInput.iSEE", ".checkboxInput.iSEE", ".numericInput.iSEE", ".radioButtons.iSEE", ".selectInput.iSEE", ".selectizeInput.iSEE", ".sliderInput.iSEE", "interface-wrappers" ] }, { "page": "iSEE", "title": "iSEE: interactive SummarizedExperiment Explorer", "topics": [ "iSEE" ] }, { "page": "iSEE-pkg", "title": "iSEE: interactive SummarizedExperiment/SingleCellExperiment Explorer", "topics": [ "iSEE-package", "iSEE-pkg" ] }, { "page": "iSEEOptions", "title": "Global 'iSEE' options", "topics": [ "iSEEOptions" ] }, { "page": "jitterPoints", "title": "Jitter points for categorical variables", "topics": [ "jitterSquarePoints", "jitterViolinPoints" ] }, { "page": "lassoPoints", "title": "Find rows of data within a closed lasso", "topics": [ "lassoPoints" ] }, { "page": "manage_commands", "title": "Manage commands to be evaluated", "topics": [ ".textEval", "manage_commands" ] 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