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README.md
In phyloseq: Handling and analysis of high-throughput microbiome census data
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 home page
the phyloseq FAQ
I recommend checking this page, and the issues tracker,
before posting new issues.
Bioconductor stable release.
the phyloseq Issue Tracker
This is the recommended location to post
(1) feature requests
(2) bug reports
(3) theoretical considerations
(4) other issues, feedback
(5) ask for help
Search previous posts,
and check the phyloseq FAQ
before posting a new issue.
Try the phyloseq package in your browser
Any scripts or data that you put into this service are public.
phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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 home page
the phyloseq FAQ
I recommend checking this page, and the issues tracker, before posting new issues.
Bioconductor stable release.
the phyloseq Issue Tracker
This is the recommended location to post
(1) feature requests (2) bug reports (3) theoretical considerations (4) other issues, feedback (5) ask for help
Search previous posts, and check the phyloseq FAQ before posting a new issue.
Try the phyloseq package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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