phyloseq

DOI: 10.18129/B9.bioc.phyloseq    

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")

Documentation

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, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version	1.22.3
In Bioconductor since	BioC 2.10 (R-2.15) (6 years)
License	AGPL-3
Depends	R (>= 3.4.0)
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 (>= 2.4)
LinkingTo
Suggests	BiocStyle(>= 2.4), DESeq2(>= 1.16.1), genefilter(>= 1.58), knitr (>= 1.16), 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, RPA
Imports Me	metavizr, PathoStat
Suggests Me	curatedMetagenomicData, philr
Build Report

Package Archives

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

Source Package	phyloseq_1.22.3.tar.gz
Windows Binary	phyloseq_1.22.3.zip
Mac OS X 10.11 (El Capitan)	phyloseq_1.22.3.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phyloseq
Package Short Url	http://bioconductor.org/packages/phyloseq/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive