Package: iSEEu 1.19.0

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:Kevin Rue-Albrecht [aut, cre], Charlotte Soneson [aut], Federico Marini [aut], Aaron Lun [aut], Michael Stadler [ctb]

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iSEEu.pdf |iSEEu.html✨
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NEWS

# 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-1.19.0(bioc 3.21)iSEEu-1.18.0(bioc 3.20)

immunooncology visualization gui dimensionreduction featureextraction clustering transcription geneexpression transcriptomics singlecell cellbasedassays hacktoberfest

7.15 score 9 stars 1 packages 35 scripts 265 downloads 80 exports 114 dependencies

Last updated 2 months agofrom:48696424c7. Checks:OK: 1 WARNING: 5 ERROR: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 19 2024
R-4.5-win	WARNING	Dec 19 2024
R-4.5-linux	WARNING	Dec 19 2024
R-4.4-win	WARNING	Dec 19 2024
R-4.4-mac	WARNING	Dec 19 2024
R-4.3-win	WARNING	Dec 19 2024
R-4.3-mac	ERROR	Dec 19 2024

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

Dependencies:abind askpass base64enc Biobase BiocGenerics bslib cachem circlize cli clue cluster codetools colorspace colourpicker commonmark ComplexHeatmap cpp11 crayon crosstalk curl DelayedArray digest doParallel DT evaluate fansi farver fastmap fontawesome foreach fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggplot2 ggrepel GlobalOptions glue gtable hexbin highr htmltools htmlwidgets httpuv httr igraph IRanges iSEE iSEEhex isoband iterators jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle listviewer magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme openssl pillar pkgconfig png promises R6 rappdirs RColorBrewer Rcpp rintrojs rjson rlang rmarkdown S4Arrays S4Vectors sass scales shape shiny shinyAce shinydashboard shinyjs shinyWidgets SingleCellExperiment sourcetools SparseArray SummarizedExperiment sys tibble tinytex UCSC.utils utf8 vctrs vipor viridisLite withr xfun xtable XVector yaml zlibbioc

Universe of iSEE panels

Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron Lun

Rendered fromiSEEu.Rmdusingknitr::rmarkdownon Dec 19 2024.

Last update: 2024-03-26
Started: 2022-09-02

Citation

Development and contributors

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