Accessing and Using Public Data Resources with Bioconductor

Workshop Description

The goal of this workshop is to introduce Bioconductor packages for finding, accessing, and using large-scale public data resources including the Gene Expression Omnibus GEO, Sequence Read Archive SRA, the Genomic Data Commons GDC, and Bioconductor-hosted curated data resources for metagenomics, pharmacogenomics PharmacoDB, and The Cancer Genome Atlas.

Instructor names and contact information

• Levi Waldron (City University of New York, New York, NY, USA)
• Benjamin Haibe-Kains (Princess Margaret Cancer Center, Toronto, Canada)
• Sean Davis (Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA)

Pre-requisites

• Basic knowledge of R syntax
• Familiarity with the ExpressionSet and SummarizedExperiment classes
• Basic familiarity with ‘omics technologies such as microarray and NGS sequencing