csoneson/SEE
Interactive SummarizedExperiment Explorer

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API

API for csoneson/SEE
Interactive SummarizedExperiment Explorer

Global functions
.activateAppOptionRegistry Man page Source code
.activeColormap Source code
.addCustomLabelsCommands Man page Source code
.addFacets Man page Source code
.addLabelCentersCommands Man page Source code
.addMultiSelectionPlotCommands Man page Source code
.addSpecificTour Man page Source code
.addTourStep Man page Source code
.add_extra_aesthetic_columns Source code
.add_interpanel_link Source code
.add_panel_to_dynamic_sources Source code
.add_selectby_column Source code
.allDigits Source code
.allowableChoiceError Man page Source code
.allowableColorByDataChoices Man page
.allowableColorByDataChoices,DotPlot-method Man page
.allowableXAxisChoices Man page
.allowableXAxisChoices,ColumnDataPlot-method Man page
.allowableXAxisChoices,RowDataPlot-method Man page
.allowableYAxisChoices Man page
.allowableYAxisChoices,ColumnDataPlot-method Man page
.allowableYAxisChoices,RowDataPlot-method Man page
.any_saved_selection Source code
.assayAllColorMap Source code
.assayColorMap Source code
.assemble_tour Source code
.assign_and_check Source code
.buildAes Man page Source code
.buildLabs Man page Source code
.build_heatmap_assay_legend_title Source code
.cacheCommonInfo Man page
.cacheCommonInfo,ColumnDataTable-method Man page
.cacheCommonInfo,ColumnDotPlot-method Man page
.cacheCommonInfo,ComplexHeatmapPlot-method Man page
.cacheCommonInfo,DotPlot-method Man page
.cacheCommonInfo,Panel-method Man page
.cacheCommonInfo,ReducedDimensionPlot-method Man page
.cacheCommonInfo,RowDataTable-method Man page
.cacheCommonInfo,RowDotPlot-method Man page
.checkboxGroupInput.iSEE Man page Source code
.checkboxInput.iSEE Man page Source code
.checkboxInputHidden Source code
.choose_link Source code
.choose_new_parent Source code
.choose_plot_type Source code
.clearSpecificTours Man page Source code
.coerce_box_status Source code
.coerce_dataframe_columns Source code
.coerce_type Source code
.colDataAllColorMap Source code
.colDataColorMap Source code
.collapseBoxHidden Source code
.colorByChoices Source code
.colorByNoneDotPlotField Man page
.colorByNoneDotPlotField,DotPlot-method Man page
.colorByNoneDotPlotScale Man page
.colorByNoneDotPlotScale,DotPlot-method Man page
.conditionalOnCheckGroup Man page Source code
.conditionalOnCheckSolo Man page Source code
.conditionalOnRadio Man page Source code
.convert_text_to_names Source code
.createCustomDimnamesModalObservers Man page Source code
.createObservers Man page
.createObservers,ColumnDataPlot-method Man page
.createObservers,ColumnDotPlot-method Man page
.createObservers,ColumnTable-method Man page
.createObservers,ComplexHeatmapPlot-method Man page
.createObservers,DotPlot-method Man page
.createObservers,FeatureAssayPlot-method Man page
.createObservers,Panel-method Man page
.createObservers,ReducedDimensionPlot-method Man page
.createObservers,RowDataPlot-method Man page
.createObservers,RowDotPlot-method Man page
.createObservers,RowTable-method Man page
.createObservers,SampleAssayPlot-method Man page
.createObservers,Table-method Man page
.createProtectedParameterObservers Man page Source code
.createUnprotectedParameterObservers Man page Source code
.create_box_observers Source code
.create_brush_observer Source code
.create_child_propagation_observer Source code
.create_color_scale Source code
.create_dimname_observers Source code
.create_dimname_propagation_observer Source code
.create_dynamic_multi_selection_source_observer Source code
.create_dynamic_selection_source_observer Source code
.create_dynamic_single_selection_source_observer Source code
.create_export_observers Source code
.create_general_observers Source code
.create_general_output Source code
.create_guides_command Source code
.create_heatmap_extra_observers Source code
.create_hover_observer Source code
.create_lasso_observer Source code
.create_link_info_output Source code
.create_multi_selection_choice_observer Source code
.create_multi_selection_history_observers Source code
.create_multi_selection_restrict_observer Source code
.create_organization_observers Source code
.create_persistent_objects Source code
.create_points Source code
.create_selection_info_output Source code
.create_selection_param_box Source code
.create_table_observers Source code
.create_table_output Source code
.create_tour_drafter Source code
.create_tour_observer Source code
.create_visual_box Source code
.create_visual_box_for_complexheatmap Source code
.create_visual_parameter_choice_observer Source code
.create_voice_observers Source code
.create_width_height_observers Source code
.create_zoom_observer Source code
.dataParamBoxOpen Man page
.deactivateAppOptionRegistry Man page Source code
.defaultColorMap Source code
.defaultDiscreteColorMap Source code
.defineDataInterface Man page
.defineDataInterface,ColumnDataPlot-method Man page
.defineDataInterface,ComplexHeatmapPlot-method Man page
.defineDataInterface,FeatureAssayPlot-method Man page
.defineDataInterface,Panel-method Man page
.defineDataInterface,ReducedDimensionPlot-method Man page
.defineDataInterface,RowDataPlot-method Man page
.defineDataInterface,SampleAssayPlot-method Man page
.defineDataInterface,Table-method Man page
.defineInterface Man page
.defineInterface,ColumnDotPlot-method Man page
.defineInterface,ColumnTable-method Man page
.defineInterface,ComplexHeatmapPlot-method Man page
.defineInterface,DotPlot-method Man page
.defineInterface,Panel-method Man page
.defineInterface,RowDotPlot-method Man page
.defineInterface,RowTable-method Man page
.defineOutput Man page
.defineOutput,ComplexHeatmapPlot-method Man page
.defineOutput,DotPlot-method Man page
.defineOutput,Table-method Man page
.definePanelTour Man page
.definePanelTour,ColumnDataPlot-method Man page
.definePanelTour,ColumnDataTable-method Man page
.definePanelTour,ColumnDotPlot-method Man page
.definePanelTour,ComplexHeatmapPlot-method Man page
.definePanelTour,DotPlot-method Man page
.definePanelTour,FeatureAssayPlot-method Man page
.definePanelTour,Panel-method Man page
.definePanelTour,ReducedDimensionPlot-method Man page
.definePanelTour,RowDataPlot-method Man page
.definePanelTour,RowDataTable-method Man page
.definePanelTour,RowDotPlot-method Man page
.definePanelTour,SampleAssayPlot-method Man page
.definePanelTour,Table-method Man page
.defineVisualColorInterface Man page
.defineVisualColorInterface,DotPlot-method Man page
.defineVisualFacetInterface Man page
.defineVisualFacetInterface,DotPlot-method Man page
.defineVisualOtherInterface Man page
.defineVisualOtherInterface,DotPlot-method Man page
.defineVisualPointInterface Man page
.defineVisualPointInterface,DotPlot-method Man page
.defineVisualShapeInterface Man page
.defineVisualShapeInterface,DotPlot-method Man page
.defineVisualSizeInterface Man page
.defineVisualSizeInterface,DotPlot-method Man page
.defineVisualTextInterface Man page
.defineVisualTextInterface,DotPlot-method Man page
.define_box_statuses Source code
.define_color_options_for_column_plots Source code
.define_color_options_for_row_plots Source code
.define_continuous_annotation_colorscale Source code
.define_export_choices Source code
.define_groups Source code
.define_memory_panel_choices Source code
.define_plot_ui Source code
.define_reservoir Source code
.define_selection_choices Source code
.define_table_commands Source code
.delete_interpanel_link Source code
.delete_panel_from_dynamic_sources Source code
.deparse_for_viewing Source code
.digitalizeText Source code
.disableButtonIf Source code
.downsample_points Source code
.draw_brush Source code
.draw_lasso Source code
.emptyDefault Man page Source code
.encodedName Source code
.establish_eval_order Source code
.execute_custom_function Source code
.expand_named_colsearch Source code
.exportOutput Man page
.exportOutput,ComplexHeatmapPlot-method Man page
.exportOutput,DotPlot-method Man page
.exportOutput,Panel-method Man page
.exportOutput,Table-method Man page
.extractAssaySubmatrix Man page Source code
.findAtomicFields Man page Source code
.fullName Man page
.fullName,ColumnDataPlot-method Man page
.fullName,ColumnDataTable-method Man page
.fullName,ComplexHeatmapPlot-method Man page
.fullName,FeatureAssayPlot-method Man page
.fullName,ReducedDimensionPlot-method Man page
.fullName,RowDataPlot-method Man page
.fullName,RowDataTable-method Man page
.fullName,SampleAssayPlot-method Man page
.gather_current_memory Source code
.generateDotPlot Man page
.generateDotPlot,DotPlot-method Man page
.generateDotPlotData Man page
.generateDotPlotData,ColumnDataPlot-method Man page
.generateDotPlotData,FeatureAssayPlot-method Man page
.generateDotPlotData,ReducedDimensionPlot-method Man page
.generateDotPlotData,RowDataPlot-method Man page
.generateDotPlotData,SampleAssayPlot-method Man page
.generateOutput Man page
.generateOutput,ComplexHeatmapPlot-method Man page
.generateOutput,DotPlot-method Man page
.generateOutput,Table-method Man page
.generateTable Man page
.generateTable,ColumnDataTable-method Man page
.generateTable,RowDataTable-method Man page
.generate_tooltip_html Source code
.getCachedCommonInfo Man page Source code
.getDotPlotColorHelp Man page
.getDotPlotColorHelp,ColumnDotPlot-method Man page
.getDotPlotColorHelp,RowDotPlot-method Man page
.getEncodedName Man page Source code
.getFullName Man page Source code
.getPanelColor Man page Source code
.getSpecificTours Man page Source code
.getTooltipUI Man page
.getTooltipUI,ColumnDotPlot-method Man page
.getTooltipUI,RowDotPlot-method Man page
.get_brushed_points Source code
.get_color_maxlevels Source code
.get_colormap Source code
.get_direct_children Source code
.get_factor_maxlevels Source code
.get_selection_sources Source code
.globalColorMap Source code
.grab_all_args Source code
.has_child Source code
.hideInterface Man page
.hideInterface,ColumnDotPlot-method Man page
.hideInterface,ColumnTable-method Man page
.hideInterface,ComplexHeatmapPlot-method Man page
.hideInterface,DotPlot-method Man page
.hideInterface,Panel-method Man page
.hideInterface,RowDotPlot-method Man page
.hideInterface,RowTable-method Man page
.hideInterface,Table-method Man page
.hide_this_thing Source code
.hide_this_thing2 Source code
.identical_brushes Source code
.increment_counter Source code
.initialize_server Source code
.insert_help_icon Source code
.isAssayNumeric Man page Source code
.isBrushable Man page
.isBrushable,DotPlot-method Man page
.isBrushable,Panel-method Man page
.is_brush Source code
.is_closed_lasso Source code
.is_groupable Source code
.is_heatmap_continuous Source code
.is_latest_version Source code
.is_numeric Source code
.is_options_list Source code
.label_with_help Source code
.lighten_color_for_fill Source code
.make_single_aes Source code
.make_single_lab Source code
.mark_panel_as_modified Source code
.multiSelectHistory Man page
.multiSelectionActive Man page
.multiSelectionActive,DotPlot-method Man page
.multiSelectionActive,Panel-method Man page
.multiSelectionActive,Table-method Man page
.multiSelectionAvailable Man page
.multiSelectionAvailable,Panel-method Man page
.multiSelectionClear Man page
.multiSelectionClear,DotPlot-method Man page
.multiSelectionClear,Panel-method Man page
.multiSelectionCommands Man page
.multiSelectionCommands,DotPlot-method Man page
.multiSelectionCommands,Table-method Man page
.multiSelectionDimension Man page
.multiSelectionDimension,ColumnDotPlot-method Man page
.multiSelectionDimension,ColumnTable-method Man page
.multiSelectionDimension,DotPlot-method Man page
.multiSelectionDimension,Panel-method Man page
.multiSelectionDimension,RowDotPlot-method Man page
.multiSelectionDimension,RowTable-method Man page
.multiSelectionHasActive Source code
.multiSelectionInvalidated Man page
.multiSelectionInvalidated,ColumnDataPlot-method Man page
.multiSelectionInvalidated,ColumnDotPlot-method Man page
.multiSelectionInvalidated,FeatureAssayPlot-method Man page
.multiSelectionInvalidated,Panel-method Man page
.multiSelectionInvalidated,RowDataPlot-method Man page
.multiSelectionInvalidated,RowDotPlot-method Man page
.multiSelectionInvalidated,SampleAssayPlot-method Man page
.multiSelectionResponsive Man page
.multiSelectionResponsive,ColumnDotPlot-method Man page
.multiSelectionResponsive,ColumnTable-method Man page
.multiSelectionResponsive,ComplexHeatmapPlot-method Man page
.multiSelectionResponsive,Panel-method Man page
.multiSelectionResponsive,RowDotPlot-method Man page
.multiSelectionResponsive,RowTable-method Man page
.multiSelectionRestricted Man page
.multiSelectionRestricted,ColumnDotPlot-method Man page
.multiSelectionRestricted,ComplexHeatmapPlot-method Man page
.multiSelectionRestricted,Panel-method Man page
.multiSelectionRestricted,RowDotPlot-method Man page
.multiSelectionRestricted,Table-method Man page
.multipleChoiceError Man page Source code
.nearestMatch Source code
.nearestPanelByName Source code
.nearestPanelByType Source code
.nearestValidChoice Source code
.nearestValidNamedChoice Source code
.nlevels Source code
.noSelection Man page
.nullColorMap Source code
.numericInput.iSEE Man page Source code
.onLoad Source code
.organizationHeight Man page
.organizationWidth Man page
.panelColor Man page
.panelColor,ColumnDataPlot-method Man page
.panelColor,ColumnDataTable-method Man page
.panelColor,ComplexHeatmapPlot-method Man page
.panelColor,FeatureAssayPlot-method Man page
.panelColor,ReducedDimensionPlot-method Man page
.panelColor,RowDataPlot-method Man page
.panelColor,RowDataTable-method Man page
.panelColor,SampleAssayPlot-method Man page
.panel_generation Source code
.panel_organization Source code
.populate_selection_environment Source code
.prepareBugsEasterEgg Source code
.prepare_SE Source code
.prioritizeDotPlotData Man page
.prioritizeDotPlotData,DotPlot-method Man page
.processMultiSelections Man page Source code
.process_heatmap_assay_colormap Source code
.process_heatmap_assay_row_transformations Source code
.process_heatmap_column_annotations_colorscale Source code
.process_heatmap_row_annotations_colorscale Source code
.process_selectby_choice Source code
.process_tooltip_field Source code
.radioButtons.iSEE Man page Source code
.radioButtonsHidden Source code
.refineParameters Man page
.refineParameters,ColumnDataPlot-method Man page
.refineParameters,ColumnDataTable-method Man page
.refineParameters,ColumnDotPlot-method Man page
.refineParameters,ColumnTable-method Man page
.refineParameters,ComplexHeatmapPlot-method Man page
.refineParameters,DotPlot-method Man page
.refineParameters,FeatureAssayPlot-method Man page
.refineParameters,Panel-method Man page
.refineParameters,ReducedDimensionPlot-method Man page
.refineParameters,RowDataPlot-method Man page
.refineParameters,RowDataTable-method Man page
.refineParameters,RowDotPlot-method Man page
.refineParameters,RowTable-method Man page
.refineParameters,SampleAssayPlot-method Man page
.refineParameters,Table-method Man page
.removeInvalidChoices Man page Source code
.renderOutput Man page
.renderOutput,ComplexHeatmapPlot-method Man page
.renderOutput,DotPlot-method Man page
.renderOutput,Panel-method Man page
.renderOutput,Table-method Man page
.replaceAssayColorMap Source code
.replaceColDataColorMap Source code
.replaceMissingWithFirst Man page Source code
.replaceRowDataColorMap Source code
.report_memory Source code
.requestActiveSelectionUpdate Man page Source code
.requestCleanUpdate Man page Source code
.requestUpdate Man page Source code
.retrieveOutput Man page Source code
.rowDataAllColorMap Source code
.rowDataColorMap Source code
.safe_nonzero_range Source code
.safe_reactive_bump Source code
.safe_reactive_init Source code
.sanitize_controlled_colormaps Source code
.scatter_plot Source code
.selectInput.iSEE Man page Source code
.selectInputHidden Man page Source code
.selectionColorMap Source code
.selectizeInput.iSEE Man page Source code
.selectizeInputHidden Source code
.self_select_boxes Source code
.setCachedCommonInfo Man page Source code
.set_colorby_when_none Source code
.set_colormap Source code
.set_nested_list Source code
.set_title Source code
.setdiffWithNames Source code
.setup_dimname_source_observer Source code
.setup_initial_state Source code
.showSelectionDetails Man page
.showSelectionDetails,ColumnTable-method Man page
.showSelectionDetails,RowTable-method Man page
.singleSelectionDimension Man page
.singleSelectionDimension,ColumnDotPlot-method Man page
.singleSelectionDimension,ColumnTable-method Man page
.singleSelectionDimension,Panel-method Man page
.singleSelectionDimension,RowDotPlot-method Man page
.singleSelectionDimension,RowTable-method Man page
.singleSelectionSlots Man page
.singleSelectionSlots,DotPlot-method Man page
.singleSelectionSlots,FeatureAssayPlot-method Man page
.singleSelectionSlots,Panel-method Man page
.singleSelectionSlots,SampleAssayPlot-method Man page
.singleSelectionValue Man page
.singleSelectionValue,DotPlot-method Man page
.singleSelectionValue,Panel-method Man page
.singleSelectionValue,Table-method Man page
.singleStringError Man page Source code
.sliderInput.iSEE Man page Source code
.snapshot_graph_linkedpanels Source code
.spawn_custom_methods Source code
.spawn_dynamic_multi_selection_list Source code
.spawn_dynamic_single_selection_list Source code
.spawn_multi_selection_graph Source code
.spawn_single_selection_graph Source code
.specific_help Source code
.square_plot Source code
.square_setup Source code
.substituteNullColorMap Source code
.textEval Man page Source code
.trackMultiSelection Man page Source code
.trackRelinkedSelection Man page Source code
.trackSingleSelection Man page Source code
.trackUpdate Man page Source code
.track_it_all Source code
.track_plotting_code Source code
.track_selection_code Source code
.transmitted_selection Source code
.update_dynamic_selection_source_panels Source code
.update_lasso Source code
.valid.Colormap Source code
.validLogicalError Man page Source code
.validNumberError Man page Source code
.validStringError Man page Source code
.violin_plot Source code
.violin_setup Source code
.whichGroupable Man page Source code
.whichNumeric Man page Source code
ColumnDataPlot Man page Source code
ColumnDataPlot-class Man page
ColumnDataTable Man page Source code
ColumnDataTable-class Man page
ColumnDotPlot-class Man page
ColumnTable-class Man page
ComplexHeatmapPlot Man page Source code
ComplexHeatmapPlot-class Man page
DotPlot-class Man page
ExperimentColorMap Man page Source code
ExperimentColorMap-class Man page
FeatureAssayPlot Man page Source code
FeatureAssayPlot-class Man page
Panel-class Man page
ReducedDimensionPlot Man page Source code
ReducedDimensionPlot-class Man page
RowDataPlot Man page Source code
RowDataPlot-class Man page
RowDataTable Man page Source code
RowDataTable-class Man page
RowDotPlot-class Man page
RowTable-class Man page
SampleAssayPlot Man page Source code
SampleAssayPlot-class Man page
Table-class Man page
[[,ColumnDotPlot,ANY,ANY-method Man page
[[,ColumnDotPlot-method Man page
[[,ComplexHeatmapPlot,ANY,ANY-method Man page
[[,ComplexHeatmapPlot-method Man page
[[,DotPlot,ANY,ANY-method Man page
[[,DotPlot-method Man page
[[,Panel,ANY,ANY-method Man page
[[,Panel-method Man page
[[,RowDotPlot,ANY,ANY-method Man page
[[,RowDotPlot-method Man page
[[<-,ColumnDotPlot,ANY,ANY-method Man page
[[<-,ColumnDotPlot-method Man page
[[<-,ComplexHeatmapPlot,ANY,ANY-method Man page
[[<-,ComplexHeatmapPlot-method Man page
[[<-,DotPlot,ANY,ANY-method Man page
[[<-,DotPlot-method Man page
[[<-,Panel,ANY,ANY-method Man page
[[<-,Panel-method Man page
[[<-,RowDotPlot,ANY,ANY-method Man page
[[<-,RowDotPlot-method Man page
aes-utils Man page
assay,ExperimentColorMap,character-method Man page
assay,ExperimentColorMap,numeric-method Man page
assayColorMap Man page
assayColorMap,ExperimentColorMap,character-method Man page
assayColorMap,ExperimentColorMap,missing-method Man page
assayColorMap,ExperimentColorMap,numeric-method Man page
assayColorMap<- Man page
assayColorMap<-,ExperimentColorMap,character-method Man page
assayColorMap<-,ExperimentColorMap,numeric-method Man page
assayNames,ExperimentColorMap-method Man page
assayNames<-,ExperimentColorMap,ANY-method Man page
assays,ExperimentColorMap-method Man page
assays<-,ExperimentColorMap,list-method Man page
cache-utils Man page
checkColormapCompatibility Man page Source code
class-utils Man page
class:ExperimentColorMap Man page
cleanDataset Man page
cleanDataset,SingleCellExperiment-method Man page
cleanDataset,SummarizedExperiment-method Man page
colData,ExperimentColorMap-method Man page
colData<-,ExperimentColorMap,ANY-method Man page
colDataColorMap Man page
colDataColorMap,ExperimentColorMap,character-method Man page
colDataColorMap,ExperimentColorMap,missing-method Man page
colDataColorMap<- Man page
colDataColorMap<-,ExperimentColorMap,character-method Man page
collapseBox Man page Source code
columnSelectionColorMap Man page Source code
constants Man page
createCustomPanels Man page
createCustomPlot Man page Source code
createCustomTable Man page Source code
createLandingPage Man page Source code
defaultTour Man page Source code
documentation-generics Man page
filterDT Man page Source code
filterDTColumn Man page Source code
getAllAppOptions Man page Source code
getAppOption Man page Source code
getPanelDefault Man page Source code
hidden-inputs Man page
iSEE Man page Source code
iSEE-package Man page
iSEE-pkg Man page
iSEEOptions Man page
initialize,ColumnDataPlot-method Man page
initialize,ColumnDataTable-method Man page
initialize,ColumnDotPlot-method Man page
initialize,ColumnTable-method Man page
initialize,ComplexHeatmapPlot-method Man page
initialize,DotPlot-method Man page
initialize,FeatureAssayPlot-method Man page
initialize,Panel-method Man page
initialize,ReducedDimensionPlot-method Man page
initialize,RowDataPlot-method Man page
initialize,RowDataTable-method Man page
initialize,RowDotPlot-method Man page
initialize,RowTable-method Man page
initialize,SampleAssayPlot-method Man page
initialize,Table-method Man page
interface-generics Man page
interface-wrappers Man page
jitterSquarePoints Man page Source code
jitterViolinPoints Man page Source code
lassoPoints Man page Source code
manage_commands Man page
merge_list Source code
metadata-plot-generics Man page
multi-select-generics Man page
multiSelectionToFactor Man page Source code
new_defaults Source code
observer-generics Man page
output-generics Man page
panelDefaults Man page Source code
plot-generics Man page
plot-utils Man page
prepareSpeechRecognition Source code
registerAppOptions Man page Source code
rowData,ExperimentColorMap-method Man page
rowData<-,ExperimentColorMap,ANY-method Man page
rowDataColorMap Man page
rowDataColorMap,ExperimentColorMap,character-method Man page
rowDataColorMap,ExperimentColorMap,missing-method Man page
rowDataColorMap<- Man page
rowDataColorMap<-,ExperimentColorMap,character-method Man page
rowSelectionColorMap Man page Source code
safegrep Source code
setup-generics Man page
show,ExperimentColorMap-method Man page
show,Panel-method Man page
single-select-generics Man page
specific-tours Man page
subsetPointsByGrid Man page Source code
synchronizeAssays Man page Source code
table-generics Man page
track-utils Man page
updateObject,ColumnDotPlot-method Man page
updateObject,ComplexHeatmapPlot-method Man page
updateObject,DotPlot-method Man page
updateObject,Panel-method Man page
updateObject,RowDotPlot-method Man page
updateObject,Table-method Man page
validate-utils Man page
visual-parameters-generics Man page
csoneson/SEE documentation built on Dec. 13, 2024, 6:43 p.m.

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