Package: shinyDSP 1.5.0

Seung J. Kim

shinyDSP: A Shiny App For Visualizing Nanostring GeoMx DSP Data

This package is a Shiny app for interactively analyzing and visualizing Nanostring GeoMX Whole Transcriptome Atlas data. Users have the option of exploring a sample data to explore this app's functionality. Regions of interest (ROIs) can be filtered based on any user-provided metadata. Upon taking two or more groups of interest, all pairwise and ANOVA-like testing are automatically performed. Available ouputs include PCA, Volcano plots, tables and heatmaps. Aesthetics of each output are highly customizable.

Authors:Seung J. Kim [aut, cre], Marco Mura [aut, fnd]

shinyDSP_1.5.0.tar.gz
shinyDSP_1.5.0.zip(r-4.7)shinyDSP_1.5.0.zip(r-4.6)shinyDSP_1.5.0.zip(r-4.5)
shinyDSP_1.5.0.tgz(r-4.6-any)shinyDSP_1.5.0.tgz(r-4.5-any)
shinyDSP_1.5.0.tar.gz(r-4.7-any)shinyDSP_1.5.0.tar.gz(r-4.6-any)
shinyDSP_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
shinyDSP/json (API)

# Install 'shinyDSP' in R:
install.packages('shinyDSP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/kimsjune/shinydsp/issues

Pkgdown/docs site:https://joonkim.ca

On BioConductor:shinyDSP-1.5.0(bioc 3.24)shinyDSP-1.4.0(bioc 3.23)

differentialexpressiongeneexpressionshinyappsspatialtranscriptomics

4.48 score 1 stars 5 scripts 278 downloads 1 exports 248 dependencies

Last updated from:fed273cb7f. Checks:1 NOTE, 9 OK. Indexed: yes.

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bioc-checksNOTE259
linux-devel-x86_64OK456
source / vignettesOK493
linux-release-x86_64OK532
macos-release-arm64OK218
macos-oldrel-arm64OK267
windows-develOK341
windows-releaseOK376
windows-oldrelOK353
wasm-releaseOK219

Exports:shinyDSP

Dependencies:abindAnnotationDbiAnnotationHubaroma.lightaskpassassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionbiomaRtBiostringsbitbit64bitopsblobbootbroombsiconsbslibcachemCairocarcarDatacigarillocirclizeclicliprclueclustercodetoolscolorspacecommonmarkComplexHeatmapcorrplotcowplotcpp11crayoncrosstalkcurlDBIdbplyrDelayedArraydeldirDerivdichromatdigestdoBydoParalleldplyrdqrngDTEDASeqedgeRevaluateExperimentHubfarverfastmapfilelockFNNfontawesomeforeachforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesGetoptLongggalluvialggbeeswarmggplot2ggpubrggrastrggrepelggsciggsignifGlobalOptionsgluegridExtragtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2hwriterinterpIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelimmalme4lmtestlocfitmagickmagrittrmapprojmapsMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmclustcompmemoisemgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslotelpalspatchworkpbkrtestpheatmappillarpkgconfigpngpolynomprettyunitsprogresspromisespurrrpwalignquantregR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRCurlRdpackreadrreformulasrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsRSpectraRSQLiterstatixrsvdrtracklayerRtsneruvRUVSeqS4ArraysS4VectorsS7sassScaledMatrixscalesscaterscuttleSeqinfoshapeshinyshinycssloadersshinyjsshinyvalidateshinyWidgetsShortReadSingleCellExperimentsitmosnowsourcetoolsSparseArraySparseMSpatialExperimentstandRstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontstextshapingtibbletidyrtidyselecttimeDatetinytextzdburcautf8uwotvctrsviporviridisviridisLitevroomwithrxfunXMLxml2xtableXVectoryamlzoo

shinyDSP tutorial
Introduction | Installation | Usage | User interface | Loading data | QC | PCA | Normalization | Table | Volcano plots | Heatmap | Data processing and analysis | Session Info
Rendered fromshinyDSP.Rmdusingknitr::rmarkdown

Last update: 2025-06-12
Started: 2025-01-30

shinyDSP internal data processing pipeline explained
Introduction | Data import | Variable(s) selection | Selecting groups to analyze | Applying QC filters | PCA | Design matrix | Creating a DGEList | Comparison between all biological groups | Fitting a linear regression model with limma | Tables of top differentially expressed genes | Volcano plot and heatmap
Rendered fromshinyDSP_secondary.Rmdusingknitr::rmarkdown

Last update: 2025-06-12
Started: 2025-02-03