Single cell RNA-seq analysis
Single cell RNA-seq analysis
17 November 2026, 09h30-17h00
20 November 2026, 09h30-17h00
24 November 2026, 09h30-12h30
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.
Program
Single cell RNASeq introduction and quality control
Lunch (provided)
Seurat pipeline in R: quality control and clustering
Seurat pipeline in R: clustering and batch correction
Lunch (provided)
Seurat pipeline: batch correction and downstream analysis
Downstream analysis and analysis of own data with expert guidance
Practical info
17 November 2026 - 24 November 2026
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
17 November 2026 - 24 November 2026
Leuven - Campus Gasthuisberg
Leuven train station is approximately 4 km from the campus Gasthuisberg. Buses depart very regularly to the Gasthuisberg Campus from Leuven train station.
For tickets and up to date schedules visit website De Lijn or use the De Lijn App.
Exit at the very last bus stop ‘Gasthuisberg Campus) make sure not to exit at ‘Gasthuisberg Kliniek =
hospital)
Once you get off the bus, go to your right and go up the street until you see stairs to your left. Climb the stairs all the way up between two buildings. Look for the signs containing blue circles and white numbers and follow them all the way from 2 up to number 12. You will cross several buildings and the walk will take max. 10 minutes. When you reach number 12, you have reached O&N 5, where you can find the reception.
17 November 2026 - 24 November 2026
Leuven - Campus Gasthuisberg
The Gasthuisberg campus is west of the Leuven ring. Our buildings are situated behind the hospital (see black arrow near ‘RING NOORD’ on the map). If you come from the city center, you will arrive on campus from the east side (taking Mgr. Van Waeyenberglaan and roundabout Het Teken). If you come from Heverlee or Campus Arenberg, you will arrive from the west side (taking the Celestijnenlaan and Taborweg). When you arrive uphill at the intersection with the Rega Institute and the Red Cross building, you need to take the road down to the bicycle parking at Rega Institute (see map) where you can park. Next, follow the ‘Onderwijs & Navorsing blue route’ description below (start point is #9).
17 November 2026 - 24 November 2026
Leuven - Campus Gasthuisberg
You arrive via the E314 highway – EXIT 16
After 200 m, keep left to drive underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
You arrive via the Leuven ring road
At the roundabout, take the exit towards ‘Spoed / Ziekenhuis’.
Follow the ring around Campus Gasthuisberg and pass the entrance of SPOED.
Continue right until you arrive at a second roundabout.
Follow the directions for E314.
Near the Fire Brigade Station, make a U-turn and follow the directions for ‘Ziekenhuis’.
Keep left and drive downhill, underneath the roundabout and into the tunnel.
Keep left and follow the arrows to Parking West.
Next, leave the parking at level +1 using the big stairs near the vending machines.
Follow the red carpet and arrows to 'Onco Dagcentrum' to get to the O&N buildings. Take the stairs on your left after exiting Parking West. You are now in front of the O&N4 building; on the left you will find O&N5.