DOI: 10.18129/B9.bioc.pcaExplorer  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see pcaExplorer.

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

Bioconductor version: 3.16

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.

Author: Federico Marini [aut, cre]

Maintainer: Federico Marini <marinif at uni-mainz.de>

Citation (from within R, enter citation("pcaExplorer")):


To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script pcaExplorer User Guide
HTML R Script Up and running with pcaExplorer
PDF   Reference Manual
Text   NEWS


biocViews DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, Software, Visualization
Version 2.24.0
In Bioconductor since BioC 3.3 (R-3.3) (7 years)
License MIT + file LICENSE
Imports DESeq2, SummarizedExperiment, GenomicRanges, IRanges, S4Vectors, genefilter, ggplot2 (>= 2.0.0), heatmaply, plotly, scales, NMF, plyr, topGO, limma, GOstats, GO.db, AnnotationDbi, shiny (>= 0.12.0), shinydashboard, shinyBS, ggrepel, DT, shinyAce, threejs, biomaRt, pheatmap, knitr, rmarkdown, base64enc, tidyr, grDevices, methods
Suggests testthat, BiocStyle, airway, org.Hs.eg.db, htmltools
URL https://github.com/federicomarini/pcaExplorer https://federicomarini.github.io/pcaExplorer/
BugReports https://github.com/federicomarini/pcaExplorer/issues
Depends On Me
Imports Me ideal
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package pcaExplorer_2.24.0.tar.gz
Windows Binary pcaExplorer_2.24.0.zip
macOS Binary (x86_64) pcaExplorer_2.24.0.tgz
macOS Binary (arm64) pcaExplorer_2.24.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pcaExplorer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pcaExplorer
Bioc Package Browser https://code.bioconductor.org/browse/pcaExplorer/
Package Short Url https://bioconductor.org/packages/pcaExplorer/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: