Shiny-phyloseq: Web Application for Interactive Microbiome Analysis With Provenance Tracking

Bioinformatics. 2015 Jan 15;31(2):282-3. doi: 10.1093/bioinformatics/btu616. Epub 2014 Sep 26.


We have created a Shiny-based Web application, called Shiny-phyloseq, for dynamic interaction with microbiome data that runs on any modern Web browser and requires no programming, increasing the accessibility and decreasing the entrance requirement to using phyloseq and related R tools. Along with a data- and context-aware dynamic interface for exploring the effects of parameter and method choices, Shiny-phyloseq also records the complete user input and subsequent graphical results of a user's session, allowing the user to archive, share and reproduce the sequence of steps that created their result-without writing any new code themselves.

Availability and implementation: Shiny-phyloseq is implemented entirely in the R language. It can be hosted/launched by any system with R installed, including Windows, Mac OS and most Linux distributions. Information technology administrators can also host Shiny--phyloseq from a remote server, in which case users need only have a Web browser installed. Shiny-phyloseq is provided free of charge under a GPL-3 open-source license through GitHub at

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Computer Graphics*
  • Data Interpretation, Statistical*
  • Humans
  • Microbiota*
  • Phylogeny*
  • Software*
  • Web Browser