phyloseq-demo

Extended Documentation

This repository hosts extended examples of the phyloseq package, created by the phyloseq author, but with a size and/or scope that makes them unsuitable for including among the core tutorials on the phyloseq main page.

This repository is also intended to host user-provided tutorials of their new/interesting datasets and analysis. Contributions should be in the form of a standard GitHub Pull Request, preferably created using R markdown with the .rmd source and the .md and .html output already built, as well as any necessary input data that is not otherwise open and web-facing. The pull requests can be made to either the master or gh-pages branch, but most things added to the master branch will be migrated to the gh-pages by me so that it can be directly accessed by users as web content, so please consider just directing your pull requests toward the gh-pages branch. Also, I will decline or omit examples that are not reproducible. The .rmd source should be able to completely rebuild the examples you've shown by anyone that has downloaded the repo to their machine, with any tweaks or data-access being as transparent as possible.

Demo Index

An index of the currently available demos can be found at

the phyloseq demonstration index

Overview and Slides

A good place to start might be

the overview demo

or the

presentation-style demo

(created by pandoc)

Core Examples, Main Page

See the official phyloseq package home page for key details and key tutorials, as well as to make suggestions, raise issues, or contribute code.

Demo Materials

This repository originally hosted material for a workshop session regarding the use of the phyloseq package for microbiome census data in R. The original materials were expected to support a a 75 - 120 minute interactive workshop demonstration. Those materials are archived as a "snapshot" branch for interested users, though some of the code may be slightly outdated already. The best, most-current place to start browsing extended tutorials/examples is right here from this main page.s

The Bioconductor Conference (BioC 2012) was held on July 24-25, 2012, at the Fred Hutchinson Cancer Research Center - Seattle, WA