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Handling and analysis of high-throughput microbiome census data.

Bioconductor version: Release (3.1)

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Author: Paul J. McMurdie <mcmurdie at>, Susan Holmes <susan at>, with contributions from Gregory Jordan and Scott Chamberlain

Maintainer: Paul J. McMurdie <mcmurdie at>

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HTML R Script phyloseq analysis vignette
HTML R Script phyloseq and DESeq2 on Colorectal Cancer Data
HTML R Script phyloseq basics vignette
PDF   Reference Manual
Text   NEWS


biocViews Classification, Clustering, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.12.2
In Bioconductor since BioC 2.10 (R-2.15) (3.5 years)
License AGPL-3
Depends R (>= 3.1.0)
Imports BiocGenerics(>= 0.14.0), ade4 (>= 1.7.2), ape (>= 3.1.1), biom (>= 0.3.9), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.4), DESeq2(>= 1.4.0), foreach (>= 1.4.2), ggplot2 (>= 1.0.0), igraph (>= 0.7.0), methods (>= 3.1.0), multtest(>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.10)
Suggests genefilter(>= 1.42.0), testthat (>= 0.8), knitr (>= 1.3)
Enhances doParallel (>= 1.0.1)
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