Single cell RNA-seq analysis
Single cell RNA-seq analysis
22 February 2027, 09h30-17h00
25 February 2027, 09h30-17h00
1 March 2027, 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.
Thomas Eekhout
Thomas Eekhout started his PhD in 2013 on plant cell cycle regulation in the group of prof. Lieven De Veylder. After obtaining his PhD in 2018 he did a short postdoc in the same group, after which he joined the plant single cell platform of prof. Bert De Rybel in the summer of 2020. Since then, he has loaded and analyzed over two hundred samples from over 20 species for both internal and external groups on different single cell technology platforms.
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
22 February 2027 - 01 March 2027
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
22 February 2027 - 01 March 2027
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
22 February 2027 - 01 March 2027
Ghent - VIB/UGent FSVM II
Looking for a custom cycling route? Try the online cycling route planner to easily and quickly identify the fastest, safest and/or most scenic route to any destination in Ghent.
Cycling route planner
Shared bicycles:
Several providers are active in the area.
Take a look at their platforms:
- Indigo Weel Pro app
- Bluebike
- DOTT
- BOLT eBikes
- Donkey Republic
There are also some public bicycle pumps at the park.
22 February 2027 - 01 March 2027
Ghent - VIB/UGent FSVM II
There is only one entrance to Technologiepark. At the entrance, please take a ticket - Parking is only allowed in regular parking spots (for instance in front of the building) and in the parking tower. Parking alongside the roads or in other places where there is no regular parking is prohibited.