Single cell RNA-seq analysis
Single cell RNA-seq analysis
27 January 2026, 09h30-17h00
3 February 2026, 09h30-17h00
General context
Single-cell RNA sequencing (scRNA-seq) has revolutionized transcriptomics by allowing researchers to study gene expression at single-cell resolution. This level of detail is crucial for exploring cellular heterogeneity, discovering novel cell types, and investigating dynamic biological processes such as development and disease progression.
You will acquire the skills to analyze and interpret short-read scRNA-seq datasets. Through a combination of theory and hands-on exercises, we will guide you through the complete analysis pipeline from quality control and normalization to clustering, visualization, and differential expression analysis.
- Perform quality control and filtering at the cell level to ensure data reliability
- Apply normalization and noise-reduction techniques to enhance signal quality in scRNA-seq datasets
- Cluster cells based on gene expression profiles and visualize results using dimensionality reduction methods (e.g., UMAP)
- Identify marker genes for specific clusters to characterize distinct cell populations
- Analyze differential gene expression between experimental conditions to uncover biologically relevant changes
- Evaluate the effectiveness of preprocessing and clustering methods in revealing biological insights
The training combines theoretical instruction with hands-on activities. On the second day, participants are encouraged to bring their own data sets for practical application and feedback.
You should have experience with R, and we offer a free, online preparatory course that you can follow.
More information can be found on Basic Statistics in R. If this course is full, contact janick.mathys@vib.be to obtain a seat.
This course is part of the learning path Single cell data short reads and long reads.
AI methods used
This training introduces key machine learning methods, including dimensionality reduction, graph-based clustering approaches (e.g., Leiden/Seurat), and deep generative models (scVI encoder–decoder neural networks).
Trainers
Janick Mathys
Janick tries to help VIB scientists analyze their data by offering bioinformatics training and support. Next to organizing trainings, creating e-learning courses and teaching statistics, R, Python, Linux, HPC, bulk and single cell RNA-Seq analysis, she consults scientists and develops pipelines for omics analyses. Before joining VIB, she worked as a post-doc at KULeuven, doing research on transcriptomics and transcription regulation. She coordinated the Master of Bioinformatics program of KULeuven and taught the course on Biological Databases.
Robin Boiy
Robin Boiy leads the VIB Tech Satellite Antwerp, a hub facilitating access to cutting-edge single-cell technologies within the framework of VIB Single Cell Core and VIB Flow Core. During his PhD, he studied the function of extracellular vesicles in breast cancer, gaining expertise in functional biology and flow cytometry. At VIB Antwerp, Robin provides on-site support for single-cell RNA, ATAC, and multiome workflows, as well as high-parameter flow cytometry and FACS.
Program
Analysis via R of publicly available data: quality control
Lunch (provided)
Analysis via R of publicly available data: clustering
Follow up to Seurat pipeline: topics depend on needs of participants
Lunch (provided)
Analysis of own data under guidance of experts from Single Cell Core
Practical info
27 January 2026 - 03 February 2026
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
27 January 2026 - 03 February 2026
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp has a dense public transportation network. Buses and trams are available to take you to many different parts of the city. There are direct bus links to various other towns and cities as well. Plan your route using the De Lijn timetables.
- Campus Middelheim - Campus Groenenborger: around 7 min. on foot
- Campus Middelheim - Campus Drie Eiken: around 35 min.
- Campus Groenenborger - Campus Drie Eiken: around 45 min.
- Stadscampus - Campus Middelheim: around 45 min.
- Stadscampus - Campus Groenenborger: around 55 min.
- Stadscampus - Campus Drie Eiken: around 60 min.
Did you know Antwerp also has a water bus? You can use it to travel between the Antwerp city centre and nearby towns.
27 January 2026 - 03 February 2026
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp is a bike-friendly city. Get to know the smart and cheap way to travel around in Antwerp fot students.
For short trips in and around the city, a rental bike is ideal. Apart from the student bicycle and the Velo city bikes, there are several other bike rental options.
Do you need to cross the Scheldt? Check the availability of the bike lifts and escalators of the tunnels, or take Antwerp’s ferry service with your bike.
Cycling between campuses:
- Stadscampus - Campus Middelheim: 20 min.
- Stadscampus - Campus Groenenborger: 25 min.
- Stadscampus - Campus Drie Eiken: 30 min.
- Campus Middelheim - Campus Groenenborger: 4 min.
- Campus Middelheim - Campus Drie Eiken: 10 min.
- Campus Groenenborger - Campus Drie Eiken: 8 min.
The newest way to travel around Antwerp is by shared electric scooter.
27 January 2026 - 03 February 2026
Antwerp - Campus Drie Eiken UAntwerpen
It’s recommended to travel to and in Antwerp by public transport. If you are travelling by car, take the following into account:
- There are P+R zones where you can park on various main roads into Antwerp. They are ideal places to switch to bus, tram or bike a few kilometres from the campus.
- The Antwerp city centre and part of Linkeroever (Antwerp’s left bank) are a low-emission zone: highly polluting vehicles are not allowed into the city.
- Keep in mind that the zone around the Stadscampus is a residential area with a speed limit of 20 km/h. Pedestrians freely make use of the entire road.
- Take possible road works and events into account.
- Within Antwerp, you can make use of the taxi service.
Campus Drie Eiken en Campus Groenenborger have free university parking spots.
Carpooling is not only fun and ecological, but also good for your wallet and you get to meet new people. Are you looking for a car ride or a fellow passenger, occasionally or daily? Take a look at our carpool platform.