phyloseq

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Development (3.24)

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 [aut, cre], Susan Holmes [aut], Gregory Jordan [ctb], Scott Chamberlain [ctb]

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

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

Paul J. McMurdie, Susan Holmes. phyloseq: Handling and analysis of high-throughput microbiome census data. doi:10.18129/B9.bioc.phyloseq, R package version 1.57.0, https://bioconductor.org/packages/phyloseq.

Generated from the package metadata; it may differ from the package's own citation.

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

## The following initializes the development version of Bioconductor
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")

Vignette for phyloseq: Analysis of high-throughput microbiome census data	HTML	R Script
Example using Negative Binomial in Microbiome Differential Abundance Testing	HTML	R Script
Basic storage, access, and manipulation of phylogenetic sequencing data with phyloseq	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	1.57.0
In Bioconductor since	BioC 2.10 (R-2.15) (14.5 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, MiscMetabar, phyloseqGraphTest, SIAMCAT
Imports Me	ADAPT, adaptiveGPCA, benchdamic, BRCore, breakaway, chem16S, combi, dar, DspikeIn, eDNAfuns, FinfoMDS, FLORAL, holobiont, HybridMicrobiomes, MBECS, microbial, microbiomeDASim, mixKernel, multimedia, PathoStat, QsRutils, RCM, reconsi, RPA, Rsearch, SimBu, speedytax, SpiecEasi, SPsimSeq, structSSI, TaxaNorm, treeDA, zitools
Suggests Me	ANCOMBC, corncob, CrcBiomeScreen, DAssemble, decontam, demulticoder, FAVA, fido, file2meco, hilldiv3, HMP16SData, lefser, LorMe, MeLSI, metacoder, MGnifyR, mia, MicrobiotaProcess, MIDASim, MMUPHin, parafac4microbiome, pctax, philr, phylobar, phyloregion, radEmu, readyomics, SQMtools, strollur
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	phyloseq_1.57.0.tar.gz
Windows Binary (x86_64)	phyloseq_1.57.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	phyloseq_1.57.0.tgz
macOS Binary (sonoma-arm64)	phyloseq_1.57.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phyloseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/phyloseq
Package Short Url	https://bioconductor.org/packages/phyloseq/
Package Downloads Report	Download Stats