E8: Analysis of Genomics Data with R/Bioconductor – 45038

(2 hrs/week, 2 CP; Spring 2025, Lecture and exercises)

Florian Geier, Robert Ivanek, Kloc Michal, Panagiotis Papasaikas, Julien Roux, Jenny Charlotte Soneson, Michael Stadler

The R/Bioconductor framework is the most widely used analysis tool for sequence-based
bioinformatics. The lecture gives an overview of typical Bioconductor based analysis pipelines
including:
 

• Bioconductor data containers
• Analysis of bulk RNA-seq data (differential gene expression analysis)
• Preprocessing and analysis of single-cell-RNA-seq data (filtering, dimensionality reduction, batch correction, clustering, differential expression)
• Analysis of ChIP-seq and ATAC-seq datasets (peak finding, differential binding/accessibility)

Each lecture is organized around one analysis question using publicly available data. It consists of 1-hour lecture and 1-hour hands on practical. Participants should bring along their laptops. Solid programming skills in R (on the level of E7: Introduction to R) are required.