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-any)pcaExplorer_3.6.0.zip(r-4.6-any)pcaExplorer_3.6.0.zip(r-4.5-any)
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✨
DESCRIPTION |NEWS
card.svg |card.png
pcaExplorer/json (API)

# 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

9.18 score 56 stars 193 scripts 770 downloads 26 mentions 17 exports 219 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksWARNING289
linux-develNOTE705
source / vignettesOK467
linux-releaseNOTE730
macos-releaseNOTE602
macos-oldrelNOTE624
windows-develNOTE694
windows-releaseNOTE433
windows-oldrelNOTE647
wasm-releaseOK215

Exports:correlatePCsdistro_exprgeneprofilergenespcaget_annotationget_annotation_orgdbhi_loadingslimmaquickpca2gomakeExampleDESeqDataSet_multifacpair_corrpca2gopcaExplorerpcaplotpcaplot3dpcascreeplotPCcorrstopGOtable

Dependencies:abindaisdkannotateAnnotationDbiAnnotationForgeapeaplotaskpassassertthatbase64encBHBiasedUrnBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbslibcacachemcallrCategorycigarillocliclusterclusterProfilercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydendextendDESeq2digestdoParallelDOSEdplyrDTeggenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverforeachformatRfsfutile.loggerfutile.optionsgclusgdtoolsgenefiltergeneLenDataBasegenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggforceggfunggiraphggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgoseqGOstatsgraphgridBasegridExtragridGraphicsGSEABasegsongtableheatmaplyhighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemosdefnlmeNMFopensslotelpatchworkpheatmappillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqapqvalueR6rappdirsRBGLRColorBrewerRcppRcppArmadilloRcppEigenRCurlregistryreshape2restfulrRgraphvizRhtslibrjsonrlangrmarkdownrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscatterpieSeqinfoseriationshinyshinyAceshinyBSshinydashboardsnowsourcetoolsSparseArraySparseMstatmodstringistringrSummarizedExperimentsurvivalsyssystemfontsthreejstibbletidydrtidyrtidyselecttidytreetinytextopGOtreeioTSPtweenrtxdbmakerUCSC.utilsutf8vctrsviridisviridisLitewebshotwithrxfunXMLxml2xtableXVectoryamlyulab.utils

pcaExplorer User Guide
Getting started | Introduction | Citation info | Launching the application | How to provide your input data in r Biocpkg("pcaExplorer") | Up and running with r Biocpkg("pcaExplorer") | The controls sidebar | App settings | Plot export settings | The task menu | The app panels | Data Upload | Instructions | Counts Table | Data Overview | Samples View | Genes View | GeneFinder | PCA2GO | More on the pca2go parameter | Multifactor Exploration | Report Editor | About | Running pcaExplorer on published datasets | Running pcaExplorer on synthetic datasets | Functions exported by the package for standalone usage | pcaplot | pcaplot3d | pcascree | correlatePCs and plotPCcorrs | hi_loadings | genespca | topGOtable | pca2go | limmaquickpca2go | makeExampleDESeqDataSet_multifac | distro_expr | geneprofiler | get_annotation and get_annotation_orgdb | pair_corr | Further development | Session info
Rendered frompcaExplorer.Rmdusingknitr::rmarkdown

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

Up and running with r Biocpkg("pcaExplorer")
Setup | Start exploring - the beauty of interactivity | When you're done - the power of reproducibility | Session Info
Rendered fromupandrunning.Rmdusingknitr::rmarkdown

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