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

DOI: 10.18129/B9.bioc.phyloseq

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (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 <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>

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 1.20.0

In Bioconductor since BioC 2.10 (R-2.15) (5.5 years)

License AGPL-3

Depends R (>= 3.3.0)

Imports BiocGenerics(>= 0.18.0), ade4 (>= 1.7.4), ape (>= 3.4), biomformat(>= 1.0.0), Biostrings(>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.9.6), 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 (>= 2.3.5), Biobase

LinkingTo

Suggests BiocStyle(>= 2.0.0), DESeq2(>= 1.12.0), genefilter(>= 1.54), testthat (>= 1.0.2), knitr (>= 1.13), metagenomeSeq(>= 1.14), rmarkdown (>= 0.9.6)

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 curatedMetagenomicData, RPA

Imports Me metavizr, PathoStat

Suggests Me philr

Build Report