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phyloseq

Handling and analysis of high-throughput microbiome census data


Bioconductor version: Release (3.18)

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 "4.3") and enter:


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

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

Details

biocViews Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.46.0
In Bioconductor since BioC 2.10 (R-2.15) (12 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
See More
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
Imports Me benchdamic, combi, HMP2Data, MBECS, microbiomeDASim, microbiomeMarker, PathoStat, PERFect, RCM, reconsi, RPA, SimBu, SPsimSeq
Suggests Me CBEA, decontam, HMP16SData, lefser, mia, MicrobiotaProcess, MMUPHin, philr
Links To Me
Build Report Build Report

Package Archives

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

Source Package phyloseq_1.46.0.tar.gz
Windows Binary phyloseq_1.46.0.zip
macOS Binary (x86_64) phyloseq_1.46.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/phyloseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phyloseq
Bioc Package Browser https://code.bioconductor.org/browse/phyloseq/
Package Short Url https://bioconductor.org/packages/phyloseq/
Package Downloads Report Download Stats