phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
phyloseq
phyloseq
Quick Install
In R terminal:
if(!requireNamespace("BiocManager")){
install.packages("BiocManager")
}
BiocManager::install("phyloseq")See the phyloseq installation page for further details, examples.
Article on Improved Microbiome Analysis
McMurdie and Holmes (2014) Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible PLoS Computational Biology 10(4): e1003531
Presubmission versions ahead of acceptance (2013): PDF version 2, PDF version 1
Peer-reviewed articles about phyloseq
McMurdie and Holmes (2014) Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking. Bioinformatics (Oxford, England) 31(2), 282–283.
McMurdie and Holmes (2013) phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data PLoS ONE 8(4):e61217
Other resources
The phyloseq project also has a number of supporting online resources, including (but probably not limited to)
the phyloseq FAQ
I recommend checking this page, and the issues tracker, before posting new issues.
the phyloseq Issue Tracker
This is the recommended location to post
- feature requests
- bug reports
- theoretical considerations
- other issues, feedback
- ask for help
Search previous posts, and check the phyloseq FAQ before posting a new issue.