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README.md
<link href="http://joey711.github.com/phyloseq/markdown.css" rel="stylesheet"></link> # [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.