Handling and analysis of high-throughput microbiome census data.

Bioconductor version: Development (3.0)

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>

To install this package, start R and enter:


To cite this package in a publication, start R and enter:



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, HighThroughputSequencing, MultipleComparisons, QualityControl, Software
Version 1.9.0
In Bioconductor since BioC 2.10 (R-2.15)
License AGPL-3
Depends R (>= 3.0.0)
Imports ade4 (>= 1.6.2), ape (>= 3.0.8), biom (>= 0.3.9), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.8.10), DESeq2(>= 1.0.19), foreach (>= 1.4), ggplot2 (>=, igraph (>=, methods (>= 3.0.0), 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 (>= 0.7.1), knitr (>= 1.3)
System Requirements
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source phyloseq_1.9.0.tar.gz
Windows Binary (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) phyloseq_1.9.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center