DOI: 10.18129/B9.bioc.pcaExplorer  

This is the development version of pcaExplorer; for the stable release version, see pcaExplorer.

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

Bioconductor version: Development (3.19)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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, ShinyApps, Software, Visualization
Version 2.29.0
In Bioconductor since BioC 3.3 (R-3.3) (7.5 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, markdown, 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_2.29.0.tar.gz
Windows Binary pcaExplorer_2.29.0.zip
macOS Binary (x86_64) pcaExplorer_2.29.0.tgz
macOS Binary (arm64)
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: