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

 

   

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.2)

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

Maintainer: Paul J. McMurdie <mcmurdie at alumni.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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("phyloseq")

 

HTML phyloseq analysis vignette
HTML phyloseq and DESeq2 on Colorectal Cancer Data
HTML phyloseq basics vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Clustering, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software
Version 1.14.0
In Bioconductor since BioC 2.10 (R-2.15) (4 years)
License AGPL-3
Depends R (>= 3.1.0)
Imports BiocGenerics(>= 0.14.0), ade4 (>= 1.7.2), ape (>= 3.1.1), biom (>= 0.3.9), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.4), foreach (>= 1.4.2), ggplot2 (>= 1.0.0), igraph (>= 0.7.0), methods (>= 3.1.0), multtest(>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.10), Biobase
LinkingTo
Suggests DESeq2(>= 1.8), genefilter(>= 1.50), testthat (>= 0.10), knitr (>= 1.10), metagenomeSeq(>= 1.10)
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
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source phyloseq_1.14.0.tar.gz
Windows Binary phyloseq_1.14.0.zip
Mac OS X 10.6 (Snow Leopard) phyloseq_1.14.0.tgz
Mac OS X 10.9 (Mavericks) phyloseq_1.14.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/phyloseq/tree/release-3.2
Package Short Url http://bioconductor.org/packages/phyloseq/
Package Downloads Report Download Stats

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