phyloseq

DOI:10.18129/B9.bioc.phyloseq

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, seephyloseq.

Handling and analysis of high-throughput microbiome census data

Bioconductor version: 3.14

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 , Susan Holmes , with contributions from Gregory Jordan and Scott Chamberlain

Maintainer: Paul J. McMurdie

Installation

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

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

For older versions of R, please refer to the appropriateBioconductor 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	1.38.0
In Bioconductor since	BioC 2.10 (R-2.15) (10 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),集群(>= 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,benchdamic,combi,gramm4R,HMP2Data,metavizr,microbiomeDASim,microbiomeMarker,PathoStat,PERFect,RCM,reconsi,RPA,SPsimSeq
Suggests Me	decontam,HMP16SData,mia,MicrobiotaProcess,MMUPHin,philr
Links To Me
Build Report

Package Archives

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Source Package	phyloseq_1.38.0.tar.gz
Windows Binary	phyloseq_1.38.0.zip
macOS 10.13 (High Sierra)	phyloseq_1.38.0.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	//www.anjoumacpherson.com/packages/phyloseq/
Package Downloads Report	Download Stats