DOI: 10.18129/B9.bioc.phyloseq    

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.6)

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")):


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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, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.22.3
In Bioconductor since BioC 2.10 (R-2.15) (6 years)
License AGPL-3
Depends R (>= 3.4.0)
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 (>= 2.4)
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, RPA
Imports Me metavizr, PathoStat
Suggests Me curatedMetagenomicData, philr
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