Analysis of single cell RNASeq data
1/02/2024
8/02/2024
General context
Today it is possible to obtain genome-wide transcriptome data from single cells using high-throughput sequencing (scRNASeq). The main advantage of scRNASeq is that the cellular resolution and the genome wide scope makes it possible to address issues that are intractable using other methods, e.g. bulk RNASeq or single-cell RT-qPCR. These scRNASeq datasets can be used to unravel heterogenous cell populations, for the discovery of new cell types and states, the reconstruction of developmental trajectories and fate decisions, all previously masked in bulk transcriptome analyses. However, 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methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.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 discuss some of the advantages and pitfalls of scRNASeq and go through the whole scRNASeq analysis pipeline. We will teach you how to do proper quality control and filtering on gene level and cell level, how to do create tSNE plots, how to get potential markers for a subset of cells ...
Participants should have some experience with R. You can attend the Basic statistics in R training to get sufficient R background. Contact janick.mathys@vib.be if you want to follow the R introduction training.
Trainers
Janick Mathys
Program
9h30-12h00 Analysis via R of publicly available data: scater pipeline
12h00-13h00 Lunch
13h00-17h00 Analysis via R of publicly available data: Seurat pipeline
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
01 February 2024 - 08 February 2024
Leuven - Campus Gasthuisberg
Herestraat 49
3000 Leuven
Belgium
01 February 2024 - 08 February 2024
Leuven - Campus Gasthuisberg
01 February 2024 - 08 February 2024
Leuven - Campus Gasthuisberg
Please use Parking West - Follow 'Dagcentrum Onco' to get to the O&N buildings. Take the stairs on you left after exiting Parking West. You are now in front of buidling O&N4 and on the left you find O&N5.
01 February 2024 - 08 February 2024
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.