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Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.19)

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 "4.4") and enter:

if (!require("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:

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) HTML R Script
Reference Manual PDF


biocViews Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.48.0
In Bioconductor since BioC 2.10 (R-2.15) (12.5 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)
System Requirements
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Suggests BiocStyle(>= 2.4), DESeq2(>= 1.16.1), genefilter(>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq(>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2)
Linking To
Enhances doParallel (>= 1.0.10)
Depends On Me microbiome, SIAMCAT, MiscMetabar, phyloseqGraphTest
Imports Me benchdamic, combi, dar, MBECS, microbiomeDASim, microbiomeMarker, PathoStat, RCM, reconsi, RPA, SimBu, SPsimSeq, HMP2Data, adaptiveGPCA, breakaway, chem16S, HTSSIP, HybridMicrobiomes, microbial, mixKernel, SigTree, SIPmg, speedytax, TaxaNorm, treeDA
Suggests Me CBEA, decontam, lefser, MGnifyR, mia, MicrobiotaProcess, MMUPHin, philr, HMP16SData, corncob, fido, file2meco, metacoder, pctax, phyloregion
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Follow Installation instructions to use this package in your R session.

Source Package phyloseq_1.48.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) phyloseq_1.48.0.tgz
macOS Binary (arm64)
Source Repository git clone
Source Repository (Developer Access) git clone
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