phyloseq

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

Handling and analysis of high-throughput microbiome census data

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DOI: 10.18129/B9.bioc.phyloseq

Bioconductor version: Development (3.23)

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 gmail.com>, Susan Holmes <susan at stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Maintainer: Paul J. McMurdie <joey711 at gmail.com>

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

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("phyloseq")

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

Documentation

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

browseVignettes("phyloseq")

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

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software

Version 1.55.0

In Bioconductor since BioC 2.10 (R-2.15) (13.5 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

URL http://dx.plos.org/10.1371/journal.pone.0061217

Bug Reports https://github.com/joey711/phyloseq/issues

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