Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
Paul J. McMurdiea b✉, Susan Holmesa b
- aDepartment of Statistics, Stanford University, Stanford, CA 94305, USA
- bDepartment of Statistics, Stanford University Stanford, CA 94305, USA#TAB#
- ✉Corresponding author
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Abstract
UNLABELLED: 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 http://joey711.github.io/shiny-phyloseq/.
TL;DRA Shiny-based Web application 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. (Semantic Scholar)