Package: iSEEpathways 1.5.0
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:
iSEEpathways_1.5.0.tar.gz
iSEEpathways_1.5.0.zip(r-4.5)iSEEpathways_1.5.0.zip(r-4.4)iSEEpathways_1.5.0.zip(r-4.3)
iSEEpathways_1.5.0.tgz(r-4.4-any)iSEEpathways_1.5.0.tgz(r-4.3-any)
iSEEpathways_1.5.0.tar.gz(r-4.5-noble)iSEEpathways_1.5.0.tar.gz(r-4.4-noble)
iSEEpathways_1.5.0.tgz(r-4.4-emscripten)iSEEpathways_1.5.0.tgz(r-4.3-emscripten)
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')) |
Bug tracker:https://github.com/isee/iseepathways/issues
On BioConductor:iSEEpathways-1.5.0(bioc 3.21)iSEEpathways-1.4.0(bioc 3.20)
softwareinfrastructuredifferentialexpressiongeneexpressionguivisualizationpathwaysgenesetenrichmentgoshinyappsbioconductorhacktoberfestiseeiseeu
Last updated 2 months agofrom:d58f5a5dcf. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:.cacheCommonInfo.createObservers.defineDataInterface.defineInterface.defineOutput.fullName.generateOutput.generateTable.isBrushable.multiSelectionActive.multiSelectionCommands.multiSelectionDimension.panelColor.refineParameters.renderOutput.showSelectionDetailsembedPathwaysResultsembedPathwaysResultsMethodsfeaturesStatsFgseaEnrichmentPlotinitializeiSEEfgseaResultspathwaysListpathwaysResultspathwaysResultsNamesPathwaysTablepathwayTypesimulateExampleData
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkcurlDelayedArraydigestdoParallelDTevaluatefansifarverfastmapfontawesomeforeachfsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelistviewermagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgconfigpngpromisesR6rappdirsRColorBrewerRcpprintrojsrjsonrlangrmarkdownS4ArraysS4VectorssassscalesshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsourcetoolsSparseArraySummarizedExperimentsystibbletinytexUCSC.utilsutf8vctrsviporviridisLitewithrxfunxtableXVectoryamlzlibbioc
Integration with other panels
Rendered fromintegration.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2023-09-04
Started: 2023-02-16
Introduction to iSEEpathways
Rendered fromiSEEpathways.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2023-09-21
Started: 2022-12-02
Working with the Gene Ontology
Rendered fromgene-ontology.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2023-09-04
Started: 2023-02-16
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 class | embedPathwaysResults,iSEEfgseaResults-method featuresStats,iSEEfgseaResults-method iSEEfgseaResults iSEEfgseaResults-class pathwaysList,iSEEfgseaResults-method pathwayType,iSEEfgseaResults-method |
| The iSEEpathwaysResults class | iSEEpathwaysResults iSEEpathwaysResults-class show,iSEEpathwaysResults-method |
| Generics for Pathway Analysis Results | featuresStats pathway-generics pathwaysList pathwayType |
| Extract contrast results embedded in a SummarizedExperiment object | pathwaysResults 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 Data | simulateExampleData |
| Generics for Embbedding Pathway Analysis Results into a SummarizedExperiment Object | embedPathwaysResults embedPathwaysResults,data.frame-method embedPathwaysResultsMethods utils-SummarizedExperiment |
