Analysis of single-cell RNASeq data
Analysis of single-cell RNASeq data
04 November 2025, 9h00-17h00
13 November 2025, 9h00-17h00
General context
Single-cell RNA sequencing (scRNA-seq) has transformed transcriptomics by enabling the study of gene expression at the resolution of individual cells. This level of detail is essential for researchers aiming to understand cellular heterogeneity, identify novel cell types, or explore dynamic biological processes such as development or disease progression. However, analyzing scRNA-seq data requires specialized tools and approaches that differ significantly from bulk RNA-seq workflows.
This introductory course is designed for early-stage researchers, including PhD students, postdocs, and technical staff, who are new to single-cell transcriptomics.
Participants will gain hands-on experience with the complete analysis pipeline - from quality control and normalization to clustering, visualization, and differential expression analysis. By the end of the course, attendees will be equipped with the foundational skills needed to analyze and interpret scRNA-seq datasets using current best practices independently.
- Perform quality control and filtering on the cell levels to ensure high-quality scRNA-seq data.
- Apply normalization and noise reduction techniques to improve signal clarity in scRNA-seq datasets.
- Cluster cells based on gene expression and visualize the results using dimensionality reduction methods such as UMAP.
- Identify marker genes for specific cell clusters to characterize distinct cell types.
- Analyze differential gene expression between experimental conditions to uncover biologically relevant changes.
- Evaluate the effectiveness of preprocessing and clustering methods in revealing meaningful biological insights.
The training combines theoretical instruction with hands-on activities tailored to participants’ needs. On the second day, participants are encouraged to bring their own datasets for practical application and feedback
- Basic knowledge of R programming and ability to work with RStudio – understanding of syntax, data structures, data handling, and basic plotting. Can be acquired by completing the training: Basic Statistics in R
- A basic understanding of the practical setup of single-cell experiments is required; participants without this background can follow our free hands-on workshop How to start with single-cell transcriptomics
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
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
04 November 2025 - 13 November 2025
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
04 November 2025 - 13 November 2025
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.
04 November 2025 - 13 November 2025
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).
04 November 2025 - 13 November 2025
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.