pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

Software status

R build status

| Platforms | OS | R CMD check | |:----------------:|:----------------:|:----------------:| | Travis CI | Linux | Travis CI build status | | Bioc (devel) | Multiple | Bioconductor-devel Build Status | | Bioc (release) | Multiple | Bioconductor-release Build Status |

pcaExplorer is a Bioconductor package containing a Shiny application for analyzing expression data in different conditions and experimental factors.

It is a general-purpose interactive companion tool for RNA-seq analysis, which guides the user in exploring the Principal Components of the data under inspection.

pcaExplorer provides tools and functionality to detect outlier samples, genes that show particular patterns, and additionally provides a functional interpretation of the principal components for further quality assessment and hypothesis generation on the input data.

Moreover, a novel visualization approach is presented to simultaneously assess the effect of more than one experimental factor on the expression levels.

Thanks to its interactive/reactive design, it is designed to become a practical companion to any RNA-seq dataset analysis, making exploratory data analysis accessible also to the bench biologist, while providing additional insight also for the experienced data analyst.


pcaExplorer can be easily installed using BiocManager::install():

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

or, optionally,

# or alternatively...

Quick start

This command loads the pcaExplorer package


The pcaExplorer app can be launched in different modes:

Additional parameters and objects that can be provided to the main pcaExplorer function are:


For additional details regarding the functions of pcaExplorer, please consult the documentation or write an email to

Bug reports/Issues/New features

Please use for reporting bugs, issues or for suggesting new features to be implemented.

Try the pcaExplorer package in your browser

Any scripts or data that you put into this service are public.

pcaExplorer documentation built on Nov. 8, 2020, 5:29 p.m.