Example data | Differential expression | Set a default rounding configuration | Configuring rounding in individual panels | Reproducibility | Bibliography
Package: iSEEde 1.11.0
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_1.11.0.tar.gz
iSEEde_1.11.0.zip(r-4.7-any)iSEEde_1.11.0.zip(r-4.6-any)iSEEde_1.11.0.zip(r-4.5-any)
iSEEde_1.11.0.tgz(r-4.6-any)iSEEde_1.11.0.tgz(r-4.5-any)
iSEEde_1.11.0.tar.gz(r-4.7-any)iSEEde_1.11.0.tar.gz(r-4.6-any)
iSEEde_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
iSEEde/json (API)
| # 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-1.11.0(bioc 3.24)iSEEde-1.10.0(bioc 3.23)
softwareinfrastructuredifferentialexpressionbioconductorhacktoberfestiseeu
Last updated from:ce821d1f93. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 207 | ||
| linux-devel | NOTE | 420 | ||
| source / vignettes | OK | 306 | ||
| linux-release | NOTE | 446 | ||
| macos-release | NOTE | 271 | ||
| macos-oldrel | NOTE | 342 | ||
| windows-devel | NOTE | 362 | ||
| windows-release | NOTE | 511 | ||
| windows-oldrel | NOTE | 358 | ||
| wasm-release | OK | 170 |
Exports:.cacheCommonInfo.createObservers.defineDataInterface.fullName.generateDotPlotData.generateTable.panelColor.refineParametersaverageLog2contrastResultscontrastResultsNamesDETableembedContrastResultsembedContrastResultsMethodsinitializeiSEEDESeq2ResultsiSEEedgeRResultsiSEELimmaResultslog2FoldChangeLogFCLogFCPlotMAPlotpValueVolcanoPlot
Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkDelayedArrayDESeq2digestdoParallelDTedgeRevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistviewerlocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUInlmeotelpkgconfigpngpromisesR6rappdirsRColorBrewerRcppRcppArmadillorintrojsrjsonrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsnowsourcetoolsSparseArraystatmodSummarizedExperimenttinytexvctrsviporviridisLitewithrxfunxtableXVectoryaml
Rounding numeric values
Last update: 2023-05-18
Started: 2023-04-12
Supported differential expression methods
Implementation | User-facing storage and access | Additional considerations | Example data | Supported methods | Limma | DESeq2 | edgeR | Live app | Comparing two contrasts | Reproducibility | Bibliography
Last update: 2023-05-18
Started: 2022-12-06
Using annotations to facilitate interactive exploration
Example data | Annotating data | Differential expression | Live app | Reproducibility | Bibliography
Last update: 2023-05-18
Started: 2022-12-08
Introduction to iSEEde
Basics | Install iSEEde | Required knowledge | Asking for help | Citing iSEEde | Quick start to using to iSEEde | Reproducibility | Bibliography
Last update: 2023-04-12
Started: 2022-12-02
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 |
