phyloseq

DOI: 10.18129/B9.bioc.phyloseq    

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.8)

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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("phyloseq", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("phyloseq")

 

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 1.26.0
In Bioconductor since BioC 2.10 (R-2.15) (6.5 years)
License AGPL-3
Depends R (>= 3.3.0)
Imports ade4 (>= 1.7.4), ape (>= 5.0), Biobase(>= 2.36.2), BiocGenerics(>= 0.22.0), biomformat(>= 1.0.0), Biostrings(>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.10.4), 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 (>= 2.5)
LinkingTo
Suggests BiocStyle(>= 2.4), DESeq2(>= 1.16.1), genefilter(>= 1.58), knitr (>= 1.16), metagenomeSeq(>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2)
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 microbiome, SIAMCAT
Imports Me metavizr, PathoStat, RPA
Suggests Me curatedMetagenomicData, decontam, HMP16SData, philr
Links To Me
Build Report  

Package Archives

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

Source Package phyloseq_1.26.0.tar.gz
Windows Binary phyloseq_1.26.0.zip
Mac OS X 10.11 (El Capitan) phyloseq_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/phyloseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phyloseq
Package Short Url http://bioconductor.org/packages/phyloseq/
Package Downloads Report Download Stats

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