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Bioconductor - phyloseq

phyloseq

This is the released version of phyloseq; for the devel version, see phyloseq.

Handling and analysis of high-throughput microbiome census data

Bioconductor version: Release (3.21)

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 "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("phyloseq")

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")

Details biocViews Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software Version 1.52.0 In Bioconductor since BioC 2.10 (R-2.15) (13.5 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) System Requirements URL http://dx.plos.org/10.1371/journal.pone.0061217 Bug Reports https://github.com/joey711/phyloseq/issues See More Suggests BiocStyle(>= 2.4), DESeq2(>= 1.16.1), genefilter(>= 1.58), knitr (>= 1.16), magrittr (>= 1.5), metagenomeSeq(>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) Linking To Enhances doParallel (>= 1.0.10) Depends On Me microbiome, SIAMCAT, MiscMetabar, phyloseqGraphTest Imports Me ADAPT, benchdamic, combi, dar, MBECS, microbiomeDASim, PathoStat, RCM, reconsi, RPA, SimBu, SPsimSeq, zitools, HMP2Data, adaptiveGPCA, BaHZING, breakaway, chem16S, FLORAL, holobiont, HybridMicrobiomes, microbial, mixKernel, multimedia, speedytax, TaxaNorm, treeDA Suggests Me ANCOMBC, decontam, lefser, MGnifyR, mia, MicrobiotaProcess, MMUPHin, philr, HMP16SData, corncob, demulticoder, FAVA, fido, file2meco, metacoder, MIDASim, parafac4microbiome, pctax, phyloregion, SQMtools Links To Me Build Report Build Report Package Archives

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

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