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phyloseq | An R package for reproducible interactive analysis and graphics of microbiome census data

A package dedicated to the object-oriented representation and analysis of microbiome census data in R. Phyloseq supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics, all in a manner that is easy to document, share, and modify. It simplifies many of the common data management and preprocessing tasks required during analysis of phylogenetic sequencing data. The phyloseq package also provides a set of powerful analysis and graphics functions, building upon related packages available in R and Bioconductor. It includes or supports some of the most commonly-needed ecology and phylogenetic tools, including a consistent interface for calculating ecological distances and performing dimensional reduction.

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phyloseq forum

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phyloseq classification

phyloseq specifications

Unique identifier:
OMICS_01520
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU Affero General Public License version 3
Version:
1.16.2
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable

phyloseq distribution

versioning

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No versioning.

phyloseq support

Documentation

Maintainer

  • Paul J. McMurdie <>

Credits

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Publications

Institution(s)

Department of Statistics, Stanford University, Stanford, CA, USA; The Roslin Institute, University of Edinburgh, UK

Funding source(s)

This work was supported by grant NIH-R01GM086884.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.