# \[phyloseq\](http://joey711.github.com/phyloseq/) \[!\[Travis-CI Build Status\](https://travis-ci.org/joey711/phyloseq.svg?branch=master)\](https://travis-ci.org/joey711/phyloseq) !\[phyloseq\](inst/extdata/phyloseq.png) ## Quick Install In R terminal: \`\`\` if(!requireNamespace("BiocManager")){ install.packages("BiocManager") } BiocManager::install("phyloseq") \`\`\` See \[the phyloseq installation page\](http://joey711.github.io/phyloseq/install.html) for further details, examples. ## Article on Improved Microbiome Analysis McMurdie and Holmes (2014) \[Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible\](http://dx.plos.org/10.1371/journal.pcbi.1003531) \*PLoS Computational Biology\* 10(4): e1003531 Presubmission versions ahead of acceptance (2013): \[PDF version 2\](http://arxiv.org/pdf/1310.0424v2.pdf), \[PDF version 1\](http://arxiv.org/pdf/1310.0424v1.pdf) ## Peer-reviewed articles about phyloseq McMurdie and Holmes (2014) \[Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking\](http://bioinformatics.oxfordjournals.org/content/early/2014/10/02/bioinformatics.btu616). \*Bioinformatics (Oxford, England)\* 31(2), 282–283\. McMurdie and Holmes (2013) \[phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data\](http://dx.plos.org/10.1371/journal.pone.0061217) \*PLoS ONE\* 8(4):e61217 ## Other resources The phyloseq project also has a number of supporting online resources, including (but probably not limited to) ### \[the phyloseq home page\](http://joey711.github.com/phyloseq/) ### \[the phyloseq FAQ\](https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-FAQ.html) I recommend checking this page, and the issues tracker, before posting new issues. ### \[Bioconductor stable release\](http://bioconductor.org/packages/release/bioc/html/phyloseq.html). ### \[the phyloseq Issue Tracker\](https://github.com/joey711/phyloseq/issues) 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 \[the phyloseq FAQ\](https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-FAQ.html) before posting a new issue.