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.
McMurdie and Holmes (2014) Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking.
Bioinformatics (Oxford, England), 31(2), 282–283. DOI 10.1093/bioinformatics/btu616
McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data.
PLoS ONE 8(4):e61217.
While it is possible to host the server "back end" somewhere so that users only need to point their web browser to a link, it is also possible to launch both the back and front "ends" on your local machine. The server back end will be an R session on your own machine, while the front end is your web browser, pointed to the appropriate local URL.
Simply launching Shiny-phyloseq should also install missing/old packages. Make sure that you first have installed the latest version of R.
The following R code will launch Shiny-phyloseq on most systems.
install.packages("shiny")
shiny::runGitHub("shiny-phyloseq","joey711")See the Shiny-phyloseq installation instructions, for further details.