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An interactive web application for demonstrating and using phyloseq.

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Shiny-phyloseq is an interactive web application that provides a graphical user interface to the microbiome analysis package for R, called phyloseq. For details about using the phyloseq package directly, see The phyloseq Homepage.


Shiny-phyloseq is provided under a free-of-charge, open-source license (A-GPL3). All we require is that you cite/attribute the following in any work that benefits from this code or application.

Citing the Web Application

McMurdie and Holmes (2014) Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking. Bioinformatics (Oxford, England) 31(2), 282–283.

Citing the R package "underneath the hood"

McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8(4):e61217.

Launch/Install Shiny-phyloseq

Simply launching Shiny-phyloseq will also install missing/old packages.

The following R code will launch Shiny-phyloseq on most systems.


See the Shiny-phyloseq installation page for further details regarding installation, and required packages.