Package: iSEEpathways 1.11.0

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_1.11.0.tar.gz
iSEEpathways_1.11.0.zip(r-4.7)iSEEpathways_1.11.0.zip(r-4.6)iSEEpathways_1.11.0.zip(r-4.5)
iSEEpathways_1.11.0.tgz(r-4.6-any)iSEEpathways_1.11.0.tgz(r-4.5-any)
iSEEpathways_1.11.0.tar.gz(r-4.7-any)iSEEpathways_1.11.0.tar.gz(r-4.6-any)
iSEEpathways_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iSEEpathways/json (API)

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

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

On BioConductor:iSEEpathways-1.11.0(bioc 3.24)iSEEpathways-1.10.0(bioc 3.23)

softwareinfrastructuredifferentialexpressiongeneexpressionguivisualizationpathwaysgenesetenrichmentgoshinyappsbioconductorhacktoberfestiseeiseeu

5.01 score 1 stars 17 scripts 268 downloads 28 exports 100 dependencies

Last updated from:c1607a555c. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

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bioc-checksWARNING302
linux-devel-x86_64NOTE458
source / vignettesOK463
linux-release-x86_64NOTE446
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macos-oldrel-arm64NOTE178
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wasm-releaseOK250

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

Dependencies:abindbase64encBiobaseBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkDelayedArraydigestdoParallelDTevaluatefarverfastmapfontawesomeforeachfsgenericsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelistviewermagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUInlmeotelpkgconfigpngpromisesR6rappdirsRColorBrewerRcpprintrojsrjsonrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsourcetoolsSparseArraySummarizedExperimenttinytexvctrsviporviridisLitewithrxfunxtableXVectoryaml

Introduction to iSEEpathways
Basics | Install iSEEpathways | Required knowledge | Asking for help | Citing iSEEpathways | Quick start to using to iSEEpathways | Reproducibility | Bibliography
Rendered fromiSEEpathways.Rmdusingknitr::rmarkdown

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

Integration with other panels
Scenario | Demonstration | Example data | Experimental metadata | Feature identifiers | Gene expression | Differential expression analysis | Pathways | Mapping pathways to genes | Gene set enrichment analysis | Displaying additional pathway information | Live app | Trading off memory usage for speed | Reproducibility | Bibliography
Rendered fromintegration.Rmdusingknitr::rmarkdown

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

Working with the Gene Ontology
Scenario | Demonstration | Example data | Pathway information | Live app | Reproducibility | Bibliography
Rendered fromgene-ontology.Rmdusingknitr::rmarkdown

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