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
Package: iSEEu 1.25.0
Kevin Rue-Albrecht
iSEEu: iSEE Universe
iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.
Authors:
iSEEu_1.25.0.tar.gz
iSEEu_1.25.0.zip(r-4.7)iSEEu_1.25.0.zip(r-4.6)iSEEu_1.25.0.zip(r-4.5)
iSEEu_1.25.0.tgz(r-4.6-any)iSEEu_1.25.0.tgz(r-4.5-any)
iSEEu_1.25.0.tar.gz(r-4.7-any)iSEEu_1.25.0.tar.gz(r-4.6-any)
iSEEu_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iSEEu/json (API)
| # Install 'iSEEu' in R: |
| install.packages('iSEEu', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/isee/iseeu/issues
On BioConductor:iSEEu-1.25.0(bioc 3.24)iSEEu-1.24.0(bioc 3.23)
immunooncologyvisualizationguidimensionreductionfeatureextractionclusteringtranscriptiongeneexpressiontranscriptomicssinglecellcellbasedassayshacktoberfest
Last updated from:95c260ca92. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 341 | ||
| linux-devel-x86_64 | WARNING | 598 | ||
| source / vignettes | OK | 453 | ||
| linux-release-x86_64 | WARNING | 946 | ||
| macos-release-arm64 | WARNING | 375 | ||
| macos-oldrel-arm64 | WARNING | 285 | ||
| windows-devel | WARNING | 1906 | ||
| windows-release | WARNING | 1651 | ||
| windows-oldrel | WARNING | 1584 | ||
| wasm-release | OK | 249 |
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.setOrganismAggregatedDotPlotcreateGeneSetCommandsDifferentialStatisticsTableDynamicMarkerTableDynamicReducedDimensionPlotFeatureSetTableGeneSetTablegetAveAbFieldsgetAveAbPatterngetAveAbPatternsgetFeatureSetCollectionsgetFeatureSetCommandsgetLogFCFieldsgetLogFCPatterngetLogFCPatternsgetPValueFieldsgetPValuePatterngetPValuePatternsgetTableExtraFieldsinitializeLogFCLogFCPlotMAPlotMarkdownBoardmodeEmptymodeGatingmodeReducedDimregisterAveAbFieldsregisterAveAbPatternsregisterFeatureSetCollectionsregisterFeatureSetCommandsregisterLogFCFieldsregisterLogFCPatternsregisterPValueFieldsregisterPValuePatternssetAveAbPatternsetFeatureSetCommandssetLogFCPatternsetPValuePatternsetTableExtraFieldsVolcanoPlot
Dependencies:abindbase64encBiobaseBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkDelayedArraydigestdoParallelDTevaluatefarverfastmapfontawesomeforeachfsgenericsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehexbinhighrhtmltoolshtmlwidgetshttpuvigraphIRangesiSEEiSEEhexisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelistviewermagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUInlmeotelpkgconfigpngpromisesR6rappdirsRColorBrewerRcpprintrojsrjsonrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsourcetoolsSparseArraySummarizedExperimenttinytexvctrsviporviridisLitewithrxfunxtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| The AggregatedDotPlot class | .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 |
| Create gene set commands | createGeneSetCommands |
| Defunct functions | .getAcceptableAveAbFields .getAcceptableLogFCFields .getAcceptablePValueFields .setAcceptableAveAbFields .setAcceptableLogFCFields .setAcceptablePValueFields defunct |
| Dynamic marker table | .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 |
| Dynamic reduced dimension plot | .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 |
| Feature set table | .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 |
| Gene set table | .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 |
| Global DE prefixes | getAveAbPattern getLogFCPattern getPValuePattern setAveAbPattern setLogFCPattern setPValuePattern |
| Global extra table fields | getTableExtraFields setTableExtraFields |
| The LogFCLogFCPlot class | .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 |
| The MAPlot class | .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 |
| The MarkdownBoard class | .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 |
| App pre-configured to launch with no visible panel | modeEmpty |
| App pre-configured to link multiple feature assay plots | modeGating |
| App pre-configured to compare multiple reduced dimension plots | modeReducedDim |
| Register DE-related fields | getAveAbFields getAveAbPatterns getLogFCFields getLogFCPatterns getPValueFields getPValuePatterns registerAveAbFields registerAveAbPatterns registerDEFields registerLogFCFields registerLogFCPatterns registerPValueFields registerPValuePatterns |
| Register feature set collections | getFeatureSetCollections getFeatureSetCommands registerFeatureSetCollections registerFeatureSetCommands |
| Global feature set commands | setFeatureSetCommands |
| Gene set utilities | .getGeneSetCommands .getIdentifierType .getOrganism .setGeneSetCommands .setIdentifierType .setOrganism utils-geneset |
| The VolcanoPlot class | .allowableXAxisChoices,VolcanoPlot-method .allowableYAxisChoices,VolcanoPlot-method .cacheCommonInfo,VolcanoPlot-method .colorByNoneDotPlotField,VolcanoPlot-method .colorByNoneDotPlotScale,VolcanoPlot-method .createObservers,VolcanoPlot-method .defineDataInterface,VolcanoPlot-method .definePanelTour,VolcanoPlot-method .fullName,VolcanoPlot-method .generateDotPlot,VolcanoPlot-method .generateDotPlotData,VolcanoPlot-method .getDotPlotColorHelp,VolcanoPlot-method .hideInterface,VolcanoPlot-method .panelColor,VolcanoPlot-method .prioritizeDotPlotData,VolcanoPlot-method .refineParameters,VolcanoPlot-method initialize,VolcanoPlot-method VolcanoPlot VolcanoPlot-class |
