To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

phyloseq

 

   

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

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Development (3.5)

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 <mcmurdie at stanford.edu>, Susan Holmes <susan at stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Maintainer: Paul J. McMurdie <mcmurdie at stanford.edu>

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

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 1.19.1
In Bioconductor since BioC 2.10 (R-2.15) (4.5 years)
License AGPL-3
Depends R (>= 3.2.0)
Imports BiocGenerics(>= 0.14.0), ade4 (>= 1.7-2), ape (>= 3.1.1), biomformat(>= 0.4.0), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.6), foreach (>= 1.4.2), ggplot2 (>= 2.1.0), igraph (>= 0.7.0), methods (>= 3.1.0), multtest(>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.3.0), vegan (>= 2.0.10), Biobase
LinkingTo
Suggests BiocStyle(>= 1.6), DESeq2(>= 1.8), genefilter(>= 1.50), testthat (>= 0.10), knitr (>= 1.10), metagenomeSeq(>= 1.10), rmarkdown (>= 0.7)
SystemRequirements
Enhances doParallel (>= 1.0.1)
URL http://dx.plos.org/10.1371/journal.pone.0061217
BugReports https://github.com/joey711/phyloseq/issues
Depends On Me curatedMetagenomicData, RPA
Imports Me PathoStat
Suggests Me philr
Build Report  

Package Archives

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

Package Source phyloseq_1.19.1.tar.gz
Windows Binary
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/phyloseq
Package Short Url http://bioconductor.org/packages/phyloseq/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: