Analysis of single cell RNASeq data
Analysis of single cell RNASeq data
13 May 2025, 9h30-17h00
16 May 2025, 9h30-17h00
General context
Single cell RNASeq provides genome-wide transcriptome data from single cells. The data can be used to unravel heterogenous cell populations, to discover new cell types and states, and reconstruct developmental trajectories and fate decisions, all previously masked in bulk transcriptome analyses. To analyze scRNASeq data, novel methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.
In this course, we will go through the whole pipeline to analyze short-read scRNASeq data. We will teach you how to:
- do proper quality control and filtering on gene level and cell level
- remove as much noise as possible
- cluster your cells and create UMAP plots
- get potential markers for these subsets of cells
- identify genes that are differentially expressed genes between conditions
The content of the course is tailored to the participants 'needs. On the second day, participants can bring their own data to analyze.
Participants should have some experience with R. Send a mail to janick.mathys@vib.be to get a seat for the Basic statistics in R training in February or March to get sufficient R background.
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
9h30-12h00 Analysis via R of publicly available data: quality control
12h00-13h00 Lunch
13h00-17h00 Analysis via R of publicly available data: clustering
9h30-12h00 Follow up to Seurat pipeline: topics depend on needs of participants
12h00-13h00 Lunch
13h00-17h00 Analysis of own data under guidance of experts from Single Cell Core
Practical info
13 May 2025 - 16 May 2025
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
13 May 2025 - 16 May 2025
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
13 May 2025 - 16 May 2025
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.
13 May 2025 - 16 May 2025
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.
13 May 2025 - 16 May 2025
Ghent - VIB/UGent FSVM II
FSVM II / CMB building
room: L4 on the 4th floor