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This is the development version of phyloseq; for the stable release version, see phyloseq.

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Development (3.4)

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>

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


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HTML R Script Basic storage, access, and manipulation of phylogenetic sequencing data with phyloseq
HTML R Script Example using Negative Binomial in Microbiome Differential Abundance Testing
HTML R Script phyloseq Frequently Asked Questions (FAQ)
HTML R Script Vignette for phyloseq: Analysis of high-throughput microbiome census data
PDF   Reference Manual


biocViews Classification, Clustering, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.17.2
In Bioconductor since BioC 2.10 (R-2.15) (4.5 years)
License AGPL-3
Depends R (>= 3.2.0)
Imports BiocGenerics(>= 0.14.0), ade4 (>= 1.7.2), ape (>= 3.1.1), biomformat(>= 0.4.0), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.6), foreach (>= 1.4.2), ggplot2 (>= 2.1.0), igraph (>= 0.7.0), methods (>= 3.1.0), multtest(>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.3.0), vegan (>= 2.0.10), Biobase
Suggests BiocStyle(>= 1.6), DESeq2(>= 1.8), genefilter(>= 1.50), testthat (>= 0.10), knitr (>= 1.10), metagenomeSeq(>= 1.10), rmarkdown (>= 0.7)
Enhances doParallel (>= 1.0.1)
Depends On Me RPA
Imports Me
Suggests Me philr
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