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Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.3)

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


biocViews Classification, Clustering, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 2.10 (R-2.15) (4 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
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