[![Travis-CI Build Status](https://travis-ci.org/waldronlab/MicrobiomeWorkshop.svg?branch=master)](https://travis-ci.org/waldronlab/MicrobiomeWorkshop)

# A workshop on microbiome data analysis in Bioconductor

Bioconductor provides significant resources for microbiome data acquisition, analysis, and visualization. This workshop introduces `curatedMetagenomicData`, a resource providing uniformly processed taxonomic and metabolic functional profiles for more than 5,000 whole metagenome shotgun sequencing samples from 26 publicly available studies, including the Human Microbiome Project, along with curated participant data. It demonstrates analysis of these data using the `dada2`, `phyloseq`, `treeDA`, `adaptiveGPCA` and `metagenomeSeq` packages for denoising, estimating differential abundance, alpha and beta diversities, ordinations, and other aspects of microbiome data analysis.
We also show the `treelapse` and `metavizr` packages for browsing and interactive visualization of microbiome profiles. Together, these packages provide easily linked components for data acquisition and flexible analysis of 16S rRNA and whole metagenome shotgun microbiome profiles. At the end of this workshop, users will be able to access publicly available metagenomic data and to perform differential abundance tests, visualization and
multivariate statistical analyses of these and other data in R/Bioconductor.

# Associated slides

Here are [the slides](https://github.com/waldronlab/presentations/blob/master/Passoli_2017-07-27_Bioc2017-MicrobiomeWorkshop.pptx?raw=true) presented by Edoardo Passoli on `curatedMetagenomicData`, and Justin Wagner on `metavizr`.