Analysis of single cell RNASeq data
Analysis of single cell RNASeq data
04 March 2025, 9h00-17h00
11 March 2025, 9h00-17h00
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, 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methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.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 needs of the participants. 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 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.
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
04 March 2025 - 11 March 2025
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
04 March 2025 - 11 March 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 March 2025 - 11 March 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 March 2025 - 11 March 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.
04 March 2025 - 11 March 2025
Leuven - Campus Gasthuisberg
O&N5-5th floor room 347 of campus Gasthuisberg.
Route description Campus Gasthuisberg - Groep Biomedische Wetenschappen KU Leuven
For those who do not have a badge to access O&N5: take the crossing between O&N4 and O&N5 and take the elevator in the foyer to the 5th floor.