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[Shiny-phyloseq](http://joey711.github.io/shiny-phyloseq/)

is an interactive web application that provides

a graphical user interface to the microbiome analysis package for R,

called [phyloseq](http://joey711.github.io/phyloseq/).

For details about using the phyloseq package directly,

see [The phyloseq Homepage](http://joey711.github.io/phyloseq/).

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](http://bioinformatics.oxfordjournals.org/content/early/2014/10/02/bioinformatics.btu616).

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](http://dx.plos.org/10.1371/journal.pone.0061217).

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](http://joey711.github.io/shiny-phyloseq/Install.html)

should also install missing/old packages.

Make sure that you first have installed

[the latest version of R](http://cran.r-project.org/).

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

```{r, eval=FALSE}

See the

[Shiny-phyloseq installation instructions](http://joey711.github.io/shiny-phyloseq/Install.html),

for further details.