Package: pcaExplorer 3.1.1

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_3.1.1.tar.gz
pcaExplorer_3.1.1.zip(r-4.5)pcaExplorer_3.1.1.zip(r-4.4)pcaExplorer_2.99.1.zip(r-4.3)
pcaExplorer_3.1.1.tgz(r-4.4-any)pcaExplorer_2.99.1.tgz(r-4.3-any)
pcaExplorer_3.1.1.tar.gz(r-4.5-noble)pcaExplorer_3.1.1.tar.gz(r-4.4-noble)
pcaExplorer_3.1.1.tgz(r-4.4-emscripten)pcaExplorer_2.99.1.tgz(r-4.3-emscripten)
pcaExplorer.pdf |pcaExplorer.html✨
pcaExplorer/json (API)
NEWS

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

Peer review:

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

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

On BioConductor:pcaExplorer-3.1.1(bioc 3.21)pcaExplorer-3.0.0(bioc 3.20)

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

9.63 score 56 stars 180 scripts 794 downloads 26 mentions 17 exports 219 dependencies

Last updated 1 months agofrom:11c744f314. Checks:1 OK, 4 NOTE, 2 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 19 2025
R-4.5-winNOTEJan 19 2025
R-4.5-linuxNOTEJan 19 2025
R-4.4-winNOTEJan 19 2025
R-4.4-macNOTEJan 19 2025
R-4.3-winOUTDATEDOct 26 2024
R-4.3-macOUTDATEDOct 26 2024

Exports:correlatePCsdistro_exprgeneprofilergenespcaget_annotationget_annotation_orgdbhi_loadingslimmaquickpca2gomakeExampleDESeqDataSet_multifacpair_corrpca2gopcaExplorerpcaplotpcaplot3dpcascreeplotPCcorrstopGOtable

Dependencies:abindannotateAnnotationDbiAnnotationForgeapeaplotaskpassassertthatbase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrCategorycliclusterclusterProfilercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdoParallelDOSEdplyrDTeggenrichplotevaluatefansifarverfastmapfastmatchfgseafilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgclusgenefiltergeneLenDataBasegenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgoseqGOstatsgraphgridBasegridExtragridGraphicsGSEABasegsongtableheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemosdefmunsellnlmeNMFopensslpatchworkpermutepheatmappillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqapqvalueR.methodsS3R.ooR.utilsR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRcppEigenRCurlregistryreshape2restfulrRgraphvizRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorssassscalesscatterpieseriationshinyshinyAceshinyBSshinydashboardsnowsourcetoolsSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontsthreejstibbletidyrtidyselecttidytreetinytextopGOtreeioTSPtweenrtxdbmakerUCSC.utilsutf8vctrsveganviridisviridisLitewebshotwithrxfunXMLxml2xtableXVectoryamlyulab.utils

pcaExplorer User Guide

Federico Marini, Harald Binder

Rendered frompcaExplorer.Rmdusingknitr::rmarkdownon Jan 19 2025.

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

Up and running with r Biocpkg("pcaExplorer")

Federico Marini, Harald Binder

Rendered fromupandrunning.Rmdusingknitr::rmarkdownon Jan 19 2025.

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