phyloseq

Handling and analysis of high-throughput microbiome census data.

Bioconductor version: Release (2.12)

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>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("phyloseq")

To cite this package in a publication, start R and enter:

    citation("phyloseq")

Documentation

PDF	R Script	Analysis examples using phyloseq
PDF	R Script	Basic data manipulation using phyloseq
PDF		phyloseq_classes_7.pdf
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, Clustering, GeneticVariability, HighThroughputSequencing, MultipleComparisons, QualityControl, Software
Version	1.4.5
In Bioconductor since	BioC 2.10 (R-2.15)
License	AGPL-3
Depends	R (>= 2.15.2), methods, ade4 (>= 1.4.17), picante (>= 1.5.2)
Imports	ape (>= 3.0.7), Biostrings(>= 2.26.3), foreach (>= 1.4), ggplot2 (>= 0.9.3), igraph (>= 0.6.5.2), multtest(>= 2.14), plyr (>= 1.8), reshape (>= 0.8.4), RJSONIO (>= 1.0.1), scales (>= 0.2.3), vegan (>= 2.0.6)
Suggests	genefilter(>= 1.40), testthat (>= 0.7)
System Requirements
URL	http://dx.plos.org/10.1371/journal.pone.0061217
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source	phyloseq_1.4.5.tar.gz
Windows Binary	phyloseq_1.4.5.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	phyloseq_1.4.5.tgz
Package Downloads Report	Download Stats

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