Package: iSEEpathways 1.3.0

Kevin Rue-Albrecht

iSEEpathways: iSEE extension for panels related to pathway analysis

This package contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels or modes facilitating the analysis of pathway analysis results. This package does not perform pathway analysis. Instead, it provides methods to embed precomputed pathway analysis results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.

Authors:Kevin Rue-Albrecht [aut, cre], Thomas Sandmann [ctb], Charlotte Soneson [aut], Federico Marini [ctb], Denali Therapeutics [fnd]

iSEEpathways_1.3.0.tar.gz
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iSEEpathways.pdf |iSEEpathways.html✨
iSEEpathways/json (API)
NEWS

# Install 'iSEEpathways' in R:
install.packages('iSEEpathways', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/isee/iseepathways/issues

On BioConductor:iSEEpathways-1.3.0(bioc 3.20)iSEEpathways-1.2.0(bioc 3.19)

bioconductor-package

28 exports 1.08 score 113 dependencies

Last updated 2 months agofrom:fbcecb00be

Exports:.cacheCommonInfo.createObservers.defineDataInterface.defineInterface.defineOutput.fullName.generateOutput.generateTable.isBrushable.multiSelectionActive.multiSelectionCommands.multiSelectionDimension.panelColor.refineParameters.renderOutput.showSelectionDetailsembedPathwaysResultsembedPathwaysResultsMethodsfeaturesStatsFgseaEnrichmentPlotinitializeiSEEfgseaResultspathwaysListpathwaysResultspathwaysResultsNamesPathwaysTablepathwayTypesimulateExampleData

Dependencies:abindanytimeaskpassbase64encBHBiobaseBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkcurlDelayedArraydigestdoParallelDTevaluatefansifarverfastmapfontawesomeforeachfsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelistviewermagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgconfigpngpromisesR6rappdirsRColorBrewerRcpprintrojsrjsonrlangrmarkdownS4ArraysS4VectorssassscalesshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsourcetoolsSparseArraySummarizedExperimentsystibbletinytexUCSC.utilsutf8vctrsviporviridisLitewithrxfunxtableXVectoryamlzlibbioc

Integration with other panels

Kevin Rue-Albrecht

Rendered fromintegration.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-09-04
Started: 2023-02-16

Introduction to iSEEpathways

Kevin Rue-Albrecht

Rendered fromiSEEpathways.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-09-21
Started: 2022-12-02

Working with the Gene Ontology

Kevin Rue-Albrecht

Rendered fromgene-ontology.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-09-04
Started: 2023-02-16

Readme and manuals

Help Manual

Help pageTopics
The FgseaEnrichmentPlot class.cacheCommonInfo,FgseaEnrichmentPlot-method .createObservers,FgseaEnrichmentPlot-method .defineDataInterface,FgseaEnrichmentPlot-method .defineInterface,FgseaEnrichmentPlot-method .defineOutput,FgseaEnrichmentPlot-method .fullName,FgseaEnrichmentPlot-method .generateOutput,FgseaEnrichmentPlot-method .isBrushable,FgseaEnrichmentPlot-method .multiSelectionActive,FgseaEnrichmentPlot-method .multiSelectionCommands,FgseaEnrichmentPlot-method .multiSelectionDimension,FgseaEnrichmentPlot-method .panelColor,FgseaEnrichmentPlot-method .refineParameters,FgseaEnrichmentPlot-method .renderOutput,FgseaEnrichmentPlot-method .showSelectionDetails,FgseaEnrichmentPlot-method FgseaEnrichmentPlot FgseaEnrichmentPlot-class initialize,FgseaEnrichmentPlot-method
The iSEEfgseaResults classembedPathwaysResults,iSEEfgseaResults-method featuresStats,iSEEfgseaResults-method iSEEfgseaResults iSEEfgseaResults-class pathwaysList,iSEEfgseaResults-method pathwayType,iSEEfgseaResults-method
The iSEEpathwaysResults classiSEEpathwaysResults iSEEpathwaysResults-class show,iSEEpathwaysResults-method
Generics for Pathway Analysis ResultsfeaturesStats pathway-generics pathwaysList pathwayType
Extract contrast results embedded in a SummarizedExperiment objectpathwaysResults pathwaysResultsNames
The PathwaysTable class.cacheCommonInfo,PathwaysTable-method .createObservers,PathwaysTable-method .defineDataInterface,PathwaysTable-method .defineInterface,PathwaysTable-method .fullName,PathwaysTable-method .generateTable,PathwaysTable-method .multiSelectionActive,PathwaysTable-method .multiSelectionCommands,PathwaysTable-method .multiSelectionDimension,PathwaysTable-method .panelColor,PathwaysTable-method .refineParameters,PathwaysTable-method .showSelectionDetails,PathwaysTable-method initialize,PathwaysTable-method PathwaysTable PathwaysTable-class
Simulate Example DatasimulateExampleData
Generics for Embbedding Pathway Analysis Results into a SummarizedExperiment ObjectembedPathwaysResults embedPathwaysResults,data.frame-method embedPathwaysResultsMethods utils-SummarizedExperiment