phyloseq

Installation

Please see the phyloseq installation instructions.

Tutorials

The complete list of phyloseq frontpage tutorials. There is also a separate repository of tutorials dedicated to extensions of phyloseq to other packages.

phyloseq-demo Repository

The phyloseq-demo repository contains many additional documentation materials created to support workshops on the use of phyloseq in microbiome research. These materials are available under an open-access copyright license.

Citing phyloseq Tools

A phyloseq GUI Web Application

McMurdie and Holmes (2014) Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking. Bioinformatics (Oxford, England) 31(2), 282–283.

Improved Normalization and Feature Detection:

Supplemental Materials Hosted on GitHub

(2013) Pre-print hosted on the arxiv prior to publication: PDF version 2 (12 Dec 2013), PDF version 1 (1 Oct 2013)

The phyloseq R package citation

McMurdie and Holmes (2013) phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE. 8(4):e61217

Description

The analysis of microbiological communities brings many challenges: the integration of many different types of data with methods from ecology, genetics, phylogenetics, network analysis, visualization and testing. The data itself may originate from widely different sources, such as the microbiomes of humans, soils, surface and ocean waters, wastewater treatment plants, industrial facilities, and so on; and as a result, these varied sample types may have very different forms and scales of related data that is extremely dependent upon the experiment and its question(s). The phyloseq package is a tool to import, store, analyze, and graphically display complex phylogenetic sequencing data that has already been clustered into Operational Taxonomic Units (OTUs), especially when there is associated sample data, phylogenetic tree, and/or taxonomic assignment of the OTUs. This package leverages many of the tools available in R for ecology and phylogenetic analysis (vegan, ade4, ape, picante), while also using advanced/flexible graphic systems (ggplot2) to easily produce publication-quality graphics of complex phylogenetic data. phyloseq uses a specialized system of S4 classes to store all related phylogenetic sequencing data as single experiment-level object, making it easier to share data and reproduce analyses. In general, phyloseq seeks to facilitate the use of R for efficient interactive and reproducible analysis of OTU-clustered high-throughput phylogenetic sequencing data.

More concretely, phyloseq provides:

• Import abundance and related data from popular OTU clustering pipelines:

  • See the tutorial page on importing data with phyloseq for more details
  • See the microbio_me_qiime tutorial page on importing directly from the microbio.me/qiime data server
  • Works with UPARSE, QIIME, mothur, BIOM, PyroTagger, RDP.
  • Additional importers planned for MG-RAST, CLoVR-16S, Genboree Microbiome, PANGEA, and others.

• Convenience analysis wrappers for common analysis tasks, e.g.

  • distance --> 44 distance methods supported (UniFrac, Jensen-Shannon, etc)
  • ordinate --> many supported methods, including constrained methods

• Microbiome plot functions using ggplot2 for powerful, flexible exploratory analysis:

  • plot_heatmap
  • plot_tree
  • plot_ordination
  • plot_net
  • plot_richness
  • plot_bar

• Modular, customizable preprocessing functions supporting fully reproducible work.

• Functions for merging data based on OTU/sample variables, and for supporting manually-imported data.

• Native R/C, parallelized implementation of UniFrac distance calculations.

• Multiple testing methods specific to high-throughput phylogenetic sequencing data.

• Examples for analysis and graphics using real published data.

• Some simple tree-based OTU clustering for building a combined OTU/tree data object "from scratch".

Additional features planned for the near-term are outlined at the future development page.

For news related to the latest development version, see:

phyloseq NEWS

The phyloseq package is actively and openly developed on GitHub:

I make lots of effort to cite/attribute author contributions within official package documentation, citations, and anywhere else it is appropriate. Please feel free to fork and contribute!