Ludwig Geistlinger and Levi Waldron
CUNY School of Public Health 55 W 125th St, New York, NY 10027
This workshop gives an in-depth overview of existing methods for enrichment analysis of gene expression data with regard to functional gene sets, pathways, and networks. The workshop will help participants understand the distinctions between assumptions and hypotheses of existing methods as well as the differences in objectives and interpretation of results. It will provide code and hands-on practice of all necessary steps for differential expression analysis, gene set- and network-based enrichment analysis, and identification of enriched genomic regions and regulatory elements, along with visualization and exploration of results.
Basic knowledge of R syntax
Familiarity with the SummarizedExperiment class
Familiarity with the GenomicRanges class
Familiarity with high-throughput gene expression data as obtained with microarrays and RNA-seq
Familiarity with the concept of differential expression analysis (with e.g. limma, edgeR, DESeq2)