GHGA Summer School on Gene Set Enrichment Analysis with R
Date: 2nd - 5th June 2025
Instructors: Zuguang Gu (DKFZ - main instructor) and Kübra Narci (GHGA, DKFZ - assistant)
Language: English
Content:
Gene Set Enrichment Analysis (GSEA) is a fundamental technique in biological data analysis. It is commonly used to associate biological functions with a list of genes, offering valuable insights into the biological context of experimental results. This workshop will provide a comprehensive introduction to GSEA methods with hands-on practice using R and Bioconductor packages. The following topics will be covered:
1) accessing and utilizing gene set resources with Bioconductor packages;
2) ORA and GSEA,
3) applications of GSEA in genomics;
4) pathway-based GSEA approaches;
5) single-sample GSEA approaches, and
6) visualization of GSEA results.
Recommended audience: master students, PhD and postdoc with R skills
Location: Meeting room 4th floor (04.MC.100) Mathematikon (Berliner Str. 41, 69120 Heidelberg)
- Please, use the entrance via Berliner Str. 41. The entrance is on the left from the Restaurant named “Bräustadel”. We are on the 4th floor in the seminar room 04.MC.100 at the AI Health Innovation Cluster Department.
- 🚎: The next Tram stop is “Bunsengymnasium”. Tram Line 21 and 24 stop there (From Main Station it is direction “Handschuhsheim”)
- 🚗: For temporary parking, the parking garage for Aldi and Rewe can be used. Fees apply.
Free of charge but limited to 20 participants. We are already fully booked, if you want to sign up for the waiting list, please, contact us!
Objetives and short learning program:
09:30 - 12:30 - lunch break* - 13:30 - 16:30
The course is designed with a focus on bioinformaticians. In the course we will cover the methological aspects as well as the practical code implementations. You will learn how to run the gene set enrichment analysis using CRAN/Bioconductor packages, also you will learn how to implement these algorithms from scratch in R, as some of the algorithms are not only restricted in GSEA analysis, but more universal to data science. I hope the course helps you to improve your bioinformatics skills, not only as a package runner.
These are the rough plans:
day 1: gene sets resources, over-representation analysis
day 2: gene set enrichment analysis, pathway enrichment analysis
day 3: single-sample-based GSEA, GSEA in genomics
day 4: clustering, simplification and visualization of GSEA results
* We will not provide lunch or drinks during the learning sessions nor the lunch break. The are restaurants, cafes and supermakts close to the veneu for lunch options on your own. Please, feel free to bring your own drinks for the learning sessions.
Materials and prerequisites:
- Please, bring your own computer and lots of enthusiasm!
- In order to have internet is crucial to have a DKFZ dienst or eduroam access.
- The workshop only requires very basic R skills. You need to know:
- basic data types in R such as vectors, data frames, lists, matrices, factors...
- some basic R functions, such as read.table, t.test, plot...
- all advanced data types from Bioconductor will be introduced during the course.
Organiser:
German Human Genome-Phenome Archive (GHGA)
powered by the German Cancer Research Center (DKFZ)
