Accessing Public Data using R and Bioconductor

This little tutorial describes the tools used to access public data from the NCBI Gene Expression Omnibus and the Sequence Read Archive. Tools covered include GEOquery, GEOmetadb, and SRAdb. The tutorial materials include:

• PDF of the overview talk
• PDF version of the vignette
• The code extracted from the vignette (good for cut-and-paste)
• Sweave version of the vignette

Execute the following code to download the files using R and to set up your R session:

download.file('http://watson.nci.nih.gov/~sdavis/tutorials/publicdatatutorial/publicDataTutorial.R',destfile='publicDataTutorial.R')
download.file('http://watson.nci.nih.gov/~sdavis/tutorials/publicdatatutorial/publicDataTutorial.Rnw',destfile='publicDataTutorial.Rnw')
download.file('http://watson.nci.nih.gov/~sdavis/tutorials/publicdatatutorial/publicDataTutorial.pdf',destfile='publicDataTutorial.pdf')
library(BiocInstaller)
biocLite(c('GEOquery','GEOmetadb','SRAdb','RMySQL'))