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

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

Paul J McMurdie  1 , Susan Holmes  1
Affiliations

Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking

Paul J McMurdie et al. Bioinformatics. .

Abstract

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/.

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Figures

Fig. 1.
Fig. 1.
Shiny-phyloseq Network panel. The Shiny-phyloseq interface is organized into panels from left to right, beginning with data selection, filtering/curation, transformation and then graphic-specific panels. The user input widgets are consolidated in a left-hand sidebar of each panel. The Select Dataset panel begins each session. Pre-loaded datasets are available by default, and users can optionally specify public datasets hosted on QIIME-DB (Caporaso et al., 2010), or upload private datasets in biom (McDonald et al., 2012) or binary ‘.RData’ (phyloseq) formats. The Filter panel supports user-defined data filtering. Shiny-phyloseq provides a separate panel for each major graphic function in phyloseq, including alpha diversity, sample- or OTU-networks, barplot, heatmap, phylogenetic tree, ordination and scatterplot. All relevant panels support customization of figure dimensions, color palette and download file format
See this image and copyright information in PMC

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Publication types