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

Bioconductor version: Release (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))


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:

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


biocViews DimensionReduction, GUI, ImmunoOncology, PrincipalComponent, QualityControl, RNASeq, ReportWriting, ShinyApps, Software, Visualization
Version 2.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL https://github.com/federicomarini/pcaExplorer https://federicomarini.github.io/pcaExplorer/
Bug Reports https://github.com/federicomarini/pcaExplorer/issues
See More
Suggests testthat, BiocStyle, markdown, airway, org.Hs.eg.db, htmltools
Linking To
Depends On Me
Imports Me ideal
Suggests Me GeDi
Links To Me
Build Report Build Report

Package Archives

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

Source Package pcaExplorer_2.30.0.tar.gz
Windows Binary pcaExplorer_2.30.0.zip (64-bit only)
macOS Binary (x86_64) pcaExplorer_2.30.0.tgz
macOS Binary (arm64) pcaExplorer_2.30.0.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