Ludwig Geistlinger, Marcel Ramos, Sehyun Oh, Workshop 200: Copy number variation analysis with BioC

200: Copy number variation analysis with Bioconductor
Ludwig Geistlinger (CUNY School of Public Health), Marcel Ramos (Roswell Park Comprehensive Cancer Center), Sehyun Oh (City University of New York)
11:00 AM - 11:55 AM EDT on Tuesday, 28 July
WORKSHOP
This workshop gives an overview of Bioconductor solutions for the analysis of copy number variation (CNV) data. The workshop introduces Bioconductor core data structures for efficient representation, access, and manipulation of CNV data, and how to use these containers for structured downstream analysis of CNVs and integration with gene expression and quantitative phenotypes. Participants will be provided with code and hands-on practice for a comprehensive set of typical analysis steps including exploratory analysis, summarizing individual CNV calls across a population, overlap analysis with functional genomic regions and regulatory elements, expression quantitative trait loci (eQTL) analysis, and genome-wide association analysis (GWAS) with quantitative phenotypes. As an advanced application example, the workshop also introduces allele-specific absolute copy number analysis and how it is incorporated in genomic cancer analysis for the estimation of tumor characteristics such as tumor purity and ploidy.
Moderator: Erica Feick