phyloseq
Handling and analysis of high-throughput microbiome census data
Bioconductor version: 3.23 · Package version: 1.56.0
phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("phyloseq")Details
| Maintainer | Paul J. McMurdie <joey711@gmail.com> |
| Author | Paul J. McMurdie [aut, cre], Susan Holmes [aut], Gregory Jordan [ctb], Scott Chamberlain [ctb] |
| License | AGPL-3 |
| URL | http://dx.plos.org/10.1371/journal.pone.0061217 |
| Bug Reports | https://github.com/joey711/phyloseq/issues |
| Downloads rank | 7797 |
| Source branch | RELEASE_3_23 |
| biocViews | Classification, Clustering, GeneticVariability, ImmunoOncology, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software |
Documentation
- Vignette for phyloseq: Analysis of high-throughput microbiome census data
- Example using Negative Binomial in Microbiome Differential Abundance Testing
- Basic storage, access, and manipulation of phylogenetic sequencing data with phyloseq
- phyloseq Frequently Asked Questions (FAQ)
Download
Follow the 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 (arm64) | phyloseq_1.56.0.tgz |
| macOS binary (x86_64) | phyloseq_1.56.0.tgz |
Dependencies
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)
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)
Enhances: doParallel (>= 1.0.10)
Reverse dependencies
Depends On Me (4): microbiome, MiscMetabar, phyloseqGraphTest, SIAMCAT
Imports Me (34): ADAPT, adaptiveGPCA, benchdamic, BRCore, breakaway, chem16S, combi, dar, DspikeIn, eDNAfuns, FinfoMDS, FLORAL, HMP2Data, holobiont, HybridMicrobiomes, MBECS, microbial, microbiomeDASim, mixKernel, multimedia, PathoStat, QsRutils, RCM, reconsi, RPA, Rsearch, SimBu, speedytax, SpiecEasi, SPsimSeq, structSSI, TaxaNorm, treeDA, zitools
Suggests Me (26): ANCOMBC, corncob, CrcBiomeScreen, decontam, demulticoder, FAVA, fido, file2meco, HMP16SData, lefser, LorMe, MeLSI, metacoder, MGnifyR, mia, MicrobiotaProcess, MIDASim, MMUPHin, parafac4microbiome, pctax, philr, phyloregion, radEmu, readyomics, SQMtools, strollur