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 (3.23)
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 [aut, cre], Susan Holmes [aut], Gregory Jordan [ctb], Scott Chamberlain [ctb]
Maintainer: Paul J. McMurdie <joey711 at gmail.com>
citation("phyloseq")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| 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) | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software |
| Version | 1.56.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 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, DspikeIn, FinfoMDS, MBECS, microbiomeDASim, PathoStat, RCM, reconsi, RPA, SimBu, SpiecEasi, SPsimSeq, zitools, HMP2Data, adaptiveGPCA, BRCore, breakaway, chem16S, eDNAfuns, FLORAL, holobiont, HybridMicrobiomes, microbial, mixKernel, multimedia, QsRutils, Rsearch, speedytax, structSSI, TaxaNorm, treeDA |
| Suggests Me | ANCOMBC, CrcBiomeScreen, decontam, lefser, MeLSI, MGnifyR, mia, MicrobiotaProcess, MMUPHin, philr, HMP16SData, OMA, corncob, demulticoder, FAVA, fido, file2meco, LorMe, metacoder, MIDASim, parafac4microbiome, pctax, phyloregion, radEmu, readyomics, SQMtools, strollur |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | phyloseq_1.56.0.tar.gz |
| Windows Binary (x86_64) | phyloseq_1.56.0.zip |
| macOS Binary (big-sur-x86_64) | phyloseq_1.56.0.tgz |
| macOS Binary (sonoma-arm64) | phyloseq_1.56.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/phyloseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/phyloseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/phyloseq/ |
| Package Short Url | https://bioconductor.org/packages/phyloseq/ |
| Package Downloads Report | Download Stats |