DOI: 10.18129/B9.bioc.phyloseq    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see phyloseq.

Handling and analysis of high-throughput microbiome census data

Bioconductor version: 3.8

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 <joey711 at>, Susan Holmes <susan at>, with contributions from Gregory Jordan and Scott Chamberlain

Maintainer: Paul J. McMurdie <joey711 at>

Citation (from within R, enter citation("phyloseq")):


To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))

For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script analysis vignette
HTML R Script phyloseq and DESeq2 on Colorectal Cancer Data
HTML R Script phyloseq basics vignette
HTML R Script phyloseq Frequently Asked Questions (FAQ)
PDF   Reference Manual
Text   NEWS


biocViews Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.26.1
In Bioconductor since BioC 2.10 (R-2.15) (7 years)
License AGPL-3
Depends R (>= 3.3.0)
Imports ade4 (>= 1.7.4), ape (>= 5.0), Biobase(>= 2.36.2), BiocGenerics(>= 0.22.0), biomformat(>= 1.0.0), Biostrings(>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), foreach (>= 1.4.3), ggplot2 (>= 2.1.0), igraph (>= 1.0.1), methods (>= 3.3.0), multtest(>= 2.28.0), plyr (>= 1.8.3), reshape2 (>= 1.4.1), scales (>= 0.4.0), vegan (>= 2.5)
Suggests BiocStyle(>= 2.4), DESeq2(>= 1.16.1), genefilter(>= 1.58), knitr (>= 1.16), metagenomeSeq(>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2)
Enhances doParallel (>= 1.0.10)
Depends On Me microbiome, SIAMCAT
Imports Me metavizr, PathoStat, RPA
Suggests Me curatedMetagenomicData, decontam, HMP16SData, metagenomeFeatures, philr
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package phyloseq_1.26.1.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) phyloseq_1.26.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: