phyloseq

Handling and analysis of high-throughput microbiome census data.

Bioconductor version: Release (2.14)

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 <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

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

Details

biocViews Classification, Clustering, GeneticVariability, HighThroughputSequencing, MultipleComparisons, QualityControl, Software
Version 1.8.1
In Bioconductor since BioC 2.10 (R-2.15)
License AGPL-3
Depends R (>= 3.0.0)
Imports ade4 (>= 1.6.2), ape (>= 3.1.1), biom (>= 0.3.9), Biostrings(>= 2.28.0), cluster (>= 1.14.4), data.table (>= 1.9.2), DESeq2(>= 1.4.0), foreach (>= 1.4.2), ggplot2 (>= 0.9.3.1), igraph (>= 0.6.5.2), methods (>= 3.0.0), multtest(>= 2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.2.3), vegan (>= 2.0.10)
Suggests genefilter(>= 1.42.0), testthat (>= 0.7.1), knitr (>= 1.3)
System Requirements
URL http://dx.plos.org/10.1371/journal.pone.0061217
Depends On Me
Imports Me
Suggests Me

Package Downloads

Package Source phyloseq_1.8.1.tar.gz
Windows Binary phyloseq_1.8.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) phyloseq_1.8.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center