Bioconductor provides significant resources for microbiome data acquisition, analysis, and visualization. This workshop introduces the common analyses of differential abundance and ordination using the phyloseq, edgeR, and DESeq2. It will utilize the curatedMetagenomicData package, a resource providing uniformly processed taxonomic and metabolic functional profiles for more than 6,000 whole metagenome shotgun sequencing samples from 26 publicly available studies, including the Human Microbiome Project. At the end of this workshop, users will be able to access publicly available metagenomic data and to perform differential abundance tests, ordination, and visualization of microbiome data in R/Bioconductor.
I will briefly introduce the topic and scope of the workshop, and brief (10-minute) talks by two active microbiome researchers in my lab:
1. Audrey Renson will summarize results from an analysis of sociodemographic patterning of the oral microbiome in the New York City Health and Nutrition Examination Study (NYC-HANES). https://www.biorxiv.org/content/early/2017/10/25/189225
2. Lucas Schiffer will demonstrate the use of curatedMetagenomicData for meta-analysis of health outcomes. Free link to article at Nature Methods: http://rdcu.be/A27v
Then we will supervise a hands-on workshop on analyzing microbiome data in R/Bioconductor. This workshop will build on the workshop I gave for Bioc2017 at the Dana-Farber Cancer Institute, and will be available from: https://github.com/waldronlab/microbiomeworkshop.
Plan to come prepared for hands-on data analysis, with your laptop and the following software installed:
* R and R Studio
* > BiocInstaller::biocLite("waldronlab/microbiomeworkshop", dependencies=TRUE) #install all workshop materials and packages from within R