Package: iSEEde 1.3.0

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:Kevin Rue-Albrecht [aut, cre], Thomas Sandmann [ctb], Denali Therapeutics [fnd]

iSEEde_1.3.0.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'))

Peer review:

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

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

bioconductor-package

23 exports 0.49 score 125 dependencies

Last updated 2 months agofrom:ed9ba77ab7

Exports:.cacheCommonInfo.createObservers.defineDataInterface.fullName.generateDotPlotData.generateTable.panelColor.refineParametersaverageLog2contrastResultscontrastResultsNamesDETableembedContrastResultsembedContrastResultsMethodsinitializeiSEEDESeq2ResultsiSEEedgeRResultsiSEELimmaResultslog2FoldChangeLogFCLogFCPlotMAPlotpValueVolcanoPlot

Dependencies:abindanytimeaskpassbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkcurlDelayedArrayDESeq2digestdoParallelDTedgeRevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistviewerlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgconfigpngpromisesR6rappdirsRColorBrewerRcppRcppArmadillorintrojsrjsonrlangrmarkdownS4ArraysS4VectorssassscalesshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsnowsourcetoolsSparseArraystatmodSummarizedExperimentsystibbletinytexUCSC.utilsutf8vctrsviporviridisLitewithrxfunxtableXVectoryamlzlibbioc

Introduction to iSEEde

Kevin Rue-Albrecht

Rendered fromiSEEde.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2023-04-12
Started: 2022-12-02

Rounding numeric values

Kevin Rue-Albrecht

Rendered fromrounding.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2023-05-18
Started: 2023-04-12

Supported differential expression methods

Kevin Rue-Albrecht

Rendered frommethods.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2023-05-18
Started: 2022-12-06

Using annotations to facilitate interactive exploration

Kevin Rue-Albrecht

Rendered fromannotations.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2023-05-18
Started: 2022-12-08

Readme and manuals

Help Manual

Help pageTopics
Extract contrast results embedded in a SummarizedExperiment objectcontrastResults contrastResultsNames
Generics for Differential Expression ResultsaverageLog2 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 classaverageLog2,iSEEDESeq2Results-method embedContrastResults,DESeqResults-method embedContrastResults,iSEEDESeq2Results-method iSEEDESeq2Results iSEEDESeq2Results-class log2FoldChange,iSEEDESeq2Results-method pValue,iSEEDESeq2Results-method showAsCell,iSEEDESeq2Results-method
The iSEEedgeRResults classaverageLog2,iSEEedgeRResults-method embedContrastResults,iSEEedgeRResults-method embedContrastResults,TopTags-method iSEEedgeRResults iSEEedgeRResults-class log2FoldChange,iSEEedgeRResults-method pValue,iSEEedgeRResults-method showAsCell,iSEEedgeRResults-method
The iSEELimmaResults classaverageLog2,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 ObjectembedContrastResults 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