Package: iSEEde 1.5.0
Kevin Rue-Albrecht
iSEEde: iSEE extension for panels related to differential expression 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 differential expression results. This package does not perform differential expression. Instead, it provides methods to embed precomputed differential expression results in a SummarizedExperiment object, in a manner that is compatible with interactive visualisation in iSEE applications.
Authors:
iSEEde_1.5.0.tar.gz
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iSEEde.pdf |iSEEde.html✨
iSEEde/json (API)
NEWS
| # Install 'iSEEde' in R: |
| install.packages('iSEEde', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/isee/iseede/issues
On BioConductor:iSEEde-1.5.0(bioc 3.21)iSEEde-1.4.0(bioc 3.20)
softwareinfrastructuredifferentialexpressionbioconductorhacktoberfestiseeu
Last updated 4 months agofrom:81939ee147. Checks:5 OK, 2 NOTE, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 01 2025 |
| R-4.5-win | NOTE | Feb 01 2025 |
| R-4.5-mac | WARNING | Feb 01 2025 |
| R-4.5-linux | NOTE | Feb 01 2025 |
| R-4.4-win | OK | Feb 01 2025 |
| R-4.4-mac | OK | Feb 01 2025 |
| R-4.3-win | OK | Feb 01 2025 |
| R-4.3-mac | OK | Feb 01 2025 |
Exports:.cacheCommonInfo.createObservers.defineDataInterface.fullName.generateDotPlotData.generateTable.panelColor.refineParametersaverageLog2contrastResultscontrastResultsNamesDETableembedContrastResultsembedContrastResultsMethodsinitializeiSEEDESeq2ResultsiSEEedgeRResultsiSEELimmaResultslog2FoldChangeLogFCLogFCPlotMAPlotpValueVolcanoPlot
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkcurlDelayedArrayDESeq2digestdoParallelDTedgeRevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistviewerlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgconfigpngpromisesR6rappdirsRColorBrewerRcppRcppArmadillorintrojsrjsonrlangrmarkdownS4ArraysS4VectorssassscalesshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsnowsourcetoolsSparseArraystatmodSummarizedExperimentsystibbletinytexUCSC.utilsutf8vctrsviporviridisLitewithrxfunxtableXVectoryaml
Introduction to iSEEde
Rendered fromiSEEde.Rmdusingknitr::rmarkdownon Feb 01 2025.Last update: 2023-04-12
Started: 2022-12-02
Rounding numeric values
Rendered fromrounding.Rmdusingknitr::rmarkdownon Feb 01 2025.Last update: 2023-05-18
Started: 2023-04-12
Supported differential expression methods
Rendered frommethods.Rmdusingknitr::rmarkdownon Feb 01 2025.Last update: 2023-05-18
Started: 2022-12-06
Using annotations to facilitate interactive exploration
Rendered fromannotations.Rmdusingknitr::rmarkdownon Feb 01 2025.Last update: 2023-05-18
Started: 2022-12-08
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Extract contrast results embedded in a SummarizedExperiment object | contrastResults contrastResultsNames |
| Generics for Differential Expression Results | averageLog2 de-generics log2FoldChange pValue |
| The DETable class | .cacheCommonInfo,DETable-method .createObservers,DETable-method .defineDataInterface,DETable-method .fullName,DETable-method .generateTable,DETable-method .panelColor,DETable-method .refineParameters,DETable-method DETable DETable-class initialize,DETable-method |
| The iSEEDESeq2Results class | averageLog2,iSEEDESeq2Results-method embedContrastResults,DESeqResults-method embedContrastResults,iSEEDESeq2Results-method iSEEDESeq2Results iSEEDESeq2Results-class log2FoldChange,iSEEDESeq2Results-method pValue,iSEEDESeq2Results-method showAsCell,iSEEDESeq2Results-method |
| The iSEEedgeRResults class | averageLog2,iSEEedgeRResults-method embedContrastResults,iSEEedgeRResults-method embedContrastResults,TopTags-method iSEEedgeRResults iSEEedgeRResults-class log2FoldChange,iSEEedgeRResults-method pValue,iSEEedgeRResults-method showAsCell,iSEEedgeRResults-method |
| The iSEELimmaResults class | averageLog2,iSEELimmaResults-method embedContrastResults,iSEELimmaResults-method iSEELimmaResults iSEELimmaResults-class log2FoldChange,iSEELimmaResults-method pValue,iSEELimmaResults-method showAsCell,iSEELimmaResults-method |
| The LogFCLogFCPlot class | .cacheCommonInfo,LogFCLogFCPlot-method .createObservers,LogFCLogFCPlot-method .defineDataInterface,LogFCLogFCPlot-method .fullName,LogFCLogFCPlot-method .generateDotPlotData,LogFCLogFCPlot-method .panelColor,LogFCLogFCPlot-method .refineParameters,LogFCLogFCPlot-method initialize,LogFCLogFCPlot-method LogFCLogFCPlot LogFCLogFCPlot-class |
| The MAPlot class | .cacheCommonInfo,MAPlot-method .createObservers,MAPlot-method .defineDataInterface,MAPlot-method .fullName,MAPlot-method .generateDotPlotData,MAPlot-method .panelColor,MAPlot-method .refineParameters,MAPlot-method initialize,MAPlot-method MAPlot MAPlot-class |
| Generics for Embbedding Results into a SummarizedExperiment Object | embedContrastResults embedContrastResults,ANY-method embedContrastResults,data.frame-method embedContrastResultsMethods utils-SummarizedExperiment |
| The VolcanoPlot class | .cacheCommonInfo,VolcanoPlot-method .createObservers,VolcanoPlot-method .defineDataInterface,VolcanoPlot-method .fullName,VolcanoPlot-method .generateDotPlotData,VolcanoPlot-method .panelColor,VolcanoPlot-method .refineParameters,VolcanoPlot-method initialize,VolcanoPlot-method VolcanoPlot VolcanoPlot-class |
