phyloseq

DOI: 10.18129/B9.bioc.phyloseq    

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.13)

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>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML	R Script	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)
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version	1.36.0
In Bioconductor since	BioC 2.10 (R-2.15) (9.5 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)
LinkingTo
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)
SystemRequirements
Enhances	doParallel (>= 1.0.10)
URL	http://dx.plos.org/10.1371/journal.pone.0061217
BugReports	https://github.com/joey711/phyloseq/issues
Depends On Me	microbiome, SIAMCAT
Imports Me	ANCOMBC, combi, gramm4R, HMP2Data, metavizr, microbiomeDASim, PathoStat, PERFect, RCM, reconsi, RPA, SPsimSeq
Suggests Me	decontam, HMP16SData, metagenomeFeatures, mia, MicrobiotaProcess, MMUPHin, philr
Links To Me
Build Report

Package Archives

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

Source Package	phyloseq_1.36.0.tar.gz
Windows Binary	phyloseq_1.36.0.zip
macOS 10.13 (High Sierra)	phyloseq_1.36.0.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