phyloseq
Handling and analysis of high-throughput microbiome census data
Bioconductor version: Release (3.19)
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 "4.4") 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 | 1.48.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (12.5 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 | SIAMCAT, microbiome, MiscMetabar, phyloseqGraphTest |
| Imports Me | MBECS, PathoStat, RCM, RPA, SPsimSeq, SimBu, benchdamic, combi, dar, microbiomeDASim, microbiomeMarker, reconsi, HMP2Data, adaptiveGPCA, breakaway, chem16S, holobiont, HTSSIP, HybridMicrobiomes, microbial, mixKernel, multimedia, SigTree, SIPmg, speedytax, TaxaNorm, treeDA |
| Suggests Me | CBEA, MGnifyR, MMUPHin, MicrobiotaProcess, decontam, lefser, mia, philr, HMP16SData, corncob, fido, file2meco, parafac4microbiome, pctax, phyloregion |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | phyloseq_1.48.0.tar.gz |
| Windows Binary (x86_64) | phyloseq_1.48.0.zip (64-bit only) |
| macOS Binary (x86_64) | phyloseq_1.48.0.tgz |
| macOS Binary (arm64) | |
| 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 |