Analysis of single cell RNASeq data
8 and 15 December
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methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.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.
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
08 December 2023 - 15 December 2023
Leuven - Park Inn by Radisson
Martelarenlaan 36
3010 Leuven
Belgium
08 December 2023 - 15 December 2023
Leuven - Park Inn by Radisson
The hotel is located 300m from Leuven Central Station. The hotel connects to Leuven Central Station by a pedestrian bridge.
08 December 2023 - 15 December 2023
Leuven - Park Inn by Radisson
Park Inn hotel has no own parking. It is possible to park underground in P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or in parking De Bond, Martelarenlaan 18, 3010 Leuven.
08 December 2023 - 15 December 2023
Leuven - Park Inn by Radisson
+32 16 61 66 02
sales.leuven@parkinn.com
The course takes place in the Park Inn by Radisson Leuven hotel next to the train station in Leuven.
Route description: http://www.parkinn.com/hotel-leuven/location