- Home
- Bioconductor 3.4
- Software Packages
- phyloseq
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
In most cases, you don't need to download the package archive at all.
phyloseq
|
|
|
|
|
|
|
|
Handling and analysis of high-throughput microbiome census data
Bioconductor version: Release (3.4)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("phyloseq")
Documentation
| 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) |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Clustering, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Sequencing, Software |
| Version | 1.19.1 |
| In Bioconductor since | BioC 2.10 (R-2.15) (5 years) |
| License | AGPL-3 |
| Depends | R (>= 3.3.0) |
| Imports | BiocGenerics(>= 0.18.0), ade4 (>= 1.7.4), ape (>= 3.4), biomformat(>= 1.0.0), Biostrings(>= 2.40.0), cluster (>= 2.0.4), data.table (>= 1.9.6), 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 (>= 2.3.5), Biobase |
| LinkingTo | |
| Suggests | BiocStyle(>= 2.0.0), DESeq2(>= 1.12.0), genefilter(>= 1.54), testthat (>= 1.0.2), knitr (>= 1.13), metagenomeSeq(>= 1.14), rmarkdown (>= 0.9.6) |
| 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 | curatedMetagenomicData, RPA |
| Imports Me | PathoStat |
| Suggests Me | philr |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | phyloseq_1.19.1.tar.gz |
| Windows Binary | phyloseq_1.19.1.zip |
| Mac OS X 10.9 (Mavericks) | phyloseq_1.19.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/phyloseq/tree/release-3.4 |
| Package Short Url | http://bioconductor.org/packages/phyloseq/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
