Analysis of single cell RNASeq data
5/11/2024
8/11/2024
General context
Single cell RNASeq delivers 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methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.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 the cells and create UMAP plots
- get potential markers for these clusters of cells
- identify genes that differentially expressed between conditions
The content is tailored to the needs of the participants. On the second day, participants can analyze their own data.
Participants should have some experience with R. You can attend the Basic statistics in R training 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
05 November 2024 - 08 November 2024
Ghent - VIB/UGent FSVM II
Technologiepark 75
9052 Zwijnaarde
Belgium
05 November 2024 - 08 November 2024
Ghent - VIB/UGent FSVM II
From Ghent Sint-Pieters station, you can take a bus to Technologiepark. Please check Routeplanner De Lijn for schedules.
05 November 2024 - 08 November 2024
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.
05 November 2024 - 08 November 2024
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.
05 November 2024 - 08 November 2024
Ghent - VIB/UGent FSVM II
Room L4