Package: pcaExplorer 3.6.0

Federico Marini

pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach

This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.

Authors:Federico Marini [aut, cre]

pcaExplorer_3.6.0.tar.gz
pcaExplorer_3.6.0.zip(r-4.7)pcaExplorer_3.6.0.zip(r-4.6)pcaExplorer_3.6.0.zip(r-4.5)
pcaExplorer_3.6.0.tgz(r-4.6-any)pcaExplorer_3.6.0.tgz(r-4.5-any)
pcaExplorer_3.6.0.tar.gz(r-4.7-any)pcaExplorer_3.6.0.tar.gz(r-4.6-any)
pcaExplorer_3.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pcaExplorer/json (API)
NEWS

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

Bug tracker:https://github.com/federicomarini/pcaexplorer/issues

Pkgdown/docs site:https://federicomarini.github.io

On BioConductor:pcaExplorer-3.7.0(bioc 3.24)pcaExplorer-3.6.0(bioc 3.23)

immunooncologyvisualizationrnaseqdimensionreductionprincipalcomponentqualitycontrolguireportwritingshinyappsbioconductorprincipal-componentsreproducible-researchrna-seq-analysisrna-seq-datashinytranscriptomeuser-friendly

9.19 score 56 stars 198 scripts 689 downloads 26 mentions 17 exports 220 dependencies

Last updated from:27ac356e48 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING357
linux-devel-x86_64NOTE734
source / vignettesOK437
linux-release-x86_64NOTE719
macos-release-arm64NOTE475
macos-oldrel-arm64NOTE546
windows-develNOTE733
windows-releaseNOTE637
windows-oldrelNOTE642
wasm-releaseOK317

Exports:correlatePCsdistro_exprgeneprofilergenespcaget_annotationget_annotation_orgdbhi_loadingslimmaquickpca2gomakeExampleDESeqDataSet_multifacpair_corrpca2gopcaExplorerpcaplotpcaplot3dpcascreeplotPCcorrstopGOtable

Dependencies:abindaisdkannotateAnnotationDbiAnnotationForgeapeaplotaskpassassertthatbase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrCategorycigarillocliclusterclusterProfilercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdoParallelDOSEdplyrDTeggenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgclusgdtoolsgenefiltergeneLenDataBasegenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgoseqGOstatsgraphgridBasegridExtragridGraphicsGSEABasegsongtableheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemosdefnlmeNMFopensslotelpatchworkpermutepheatmappillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqapqvalueR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRCurlregistryreshape2restfulrRgraphvizRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscatterpieSeqinfoseriationshinyshinyAceshinyBSshinydashboardsnowsourcetoolsSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontsthreejstibbletidydrtidyrtidyselecttidytreetinytextopGOtreeioTSPtweenrtxdbmakerUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2xtableXVectoryamlyulab.utils

pcaExplorer User Guide

Federico Marini, Harald Binder

Rendered frompcaExplorer.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2024-09-20
Started: 2016-02-22

Up and running with r Biocpkg("pcaExplorer")

Federico Marini, Harald Binder

Rendered fromupandrunning.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2023-04-12
Started: 2019-02-12