Analysis of single cell RNASeq data from 10x Genomics, Leuven
27 and 28 February 2023
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methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.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
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.
Niels Vandamme
Niels Vandamme heads the VIB Single Cell Core to cover complete experimental and computational workflows for single cell multi-omics. During his PhD, he studied heterogeneity and population dynamics in neural crest biology and cancer cell plasticity, using in vitro systems and genetically engineered mouse models at a single cell resolution. During his postdoctoral training, he gained expertise in computational models to analyze high-throughput single-cell data.
Program
Practical info
27 February 2023 - 28 February 2023
Leuven - Park Inn by Radisson
Martelarenlaan 36
3010 Leuven
Belgium
27 February 2023 - 28 February 2023
Leuven - Park Inn by Radisson
The hotel is located 300m from Leuven Central Station, just a short 5 minute walk.
27 February 2023 - 28 February 2023
Leuven - Park Inn by Radisson
Using your bike for longer distances? Check Cycle Highways.
27 February 2023 - 28 February 2023
Leuven - Park Inn by Radisson
Underground P1-Parking Station Leuven, Martelarenlaan 4, 3010 Leuven or parking De Bond, Martelarenlaan 18, 3010 Leuven.
27 February 2023 - 28 February 2023
Leuven - Park Inn by Radisson
+32 16 61 66 02
sales.leuven@parkinn.com