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

iSEEde_1.11.0.tar.gz
iSEEde_1.11.0.zip(r-4.7)iSEEde_1.11.0.zip(r-4.6)iSEEde_1.11.0.zip(r-4.5)
iSEEde_1.11.0.tgz(r-4.6-any)iSEEde_1.11.0.tgz(r-4.5-any)
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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

5.18 score 1 stars 19 scripts 23 exports 113 dependencies

Last updated from:ce821d1f93. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING233
linux-devel-x86_64NOTE454
source / vignettesOK387
linux-release-x86_64NOTE443
macos-release-arm64NOTE279
macos-oldrel-arm64NOTE208
windows-develNOTE518
windows-releaseNOTE553
windows-oldrelNOTE519
wasm-releaseOK233

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

Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkDelayedArrayDESeq2digestdoParallelDTedgeRevaluatefarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvigraphIRangesiSEEisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalistviewerlocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUInlmeotelpkgconfigpngpromisesR6rappdirsRColorBrewerRcppRcppArmadillorintrojsrjsonrlangrmarkdownS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsnowsourcetoolsSparseArraystatmodSummarizedExperimenttinytexvctrsviporviridisLitewithrxfunxtableXVectoryaml

Rounding numeric values
Example data | Differential expression | Set a default rounding configuration | Configuring rounding in individual panels | Reproducibility | Bibliography
Rendered fromrounding.Rmdusingknitr::rmarkdown

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
Rendered frommethods.Rmdusingknitr::rmarkdown

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
Rendered fromannotations.Rmdusingknitr::rmarkdown

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
Rendered fromiSEEde.Rmdusingknitr::rmarkdown

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

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