Analysis of single cell RNASeq data
2/04/2024
9/04/2024
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methods are required and some of the underlying assumptions for the methods developed for bulk RNASeq experiments are no longer valid.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
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: 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
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
Universiteitsplein 1
2610 Antwerpen
Belgium
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp has a dense public transportation network. Buses and trams are available to take you to many different parts of the city. There are direct bus links to various other towns and cities as well. Plan your route using the De Lijn timetables.
- Campus Middelheim - Campus Groenenborger: around 7 min. on foot
- Campus Middelheim - Campus Drie Eiken: around 35 min.
- Campus Groenenborger - Campus Drie Eiken: around 45 min.
- Stadscampus - Campus Middelheim: around 45 min.
- Stadscampus - Campus Groenenborger: around 55 min.
- Stadscampus - Campus Drie Eiken: around 60 min.
Did you know Antwerp also has a water bus? You can use it to travel between the Antwerp city centre and nearby towns.
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
Antwerp is a bike-friendly city. Get to know the smart and cheap way to travel around in Antwerp fot students.
For short trips in and around the city, a rental bike is ideal. Apart from the student bicycle and the Velo city bikes, there are several other bike rental options.
Do you need to cross the Scheldt? Check the availability of the bike lifts and escalators of the tunnels, or take Antwerp’s ferry service with your bike.
Cycling between campuses:
- Stadscampus - Campus Middelheim: 20 min.
- Stadscampus - Campus Groenenborger: 25 min.
- Stadscampus - Campus Drie Eiken: 30 min.
- Campus Middelheim - Campus Groenenborger: 4 min.
- Campus Middelheim - Campus Drie Eiken: 10 min.
- Campus Groenenborger - Campus Drie Eiken: 8 min.
The newest way to travel around Antwerp is by shared electric scooter.
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
It’s recommended to travel to and in Antwerp by public transport. If you are travelling by car, take the following into account:
- There are P+R zones where you can park on various main roads into Antwerp. They are ideal places to switch to bus, tram or bike a few kilometres from the campus.
- The Antwerp city centre and part of Linkeroever (Antwerp’s left bank) are a low-emission zone: highly polluting vehicles are not allowed into the city.
- Keep in mind that the zone around the Stadscampus is a residential area with a speed limit of 20 km/h. Pedestrians freely make use of the entire road.
- Take possible road works and events into account.
- Within Antwerp, you can make use of the taxi service.
Campus Drie Eiken en Campus Groenenborger have free university parking spots.
Carpooling is not only fun and ecological, but also good for your wallet and you get to meet new people. Are you looking for a car ride or a fellow passenger, occasionally or daily? Take a look at our carpool platform.
02 April 2024 - 09 April 2024
Antwerp - Campus Drie Eiken UAntwerpen
Neuron Room, Building V of the University of Antwerp (UA), Parking 4, Universiteitsplein 1, 2610 Antwerpen.
Via public transport: from Antwerp Central Station take bus 17 to UZA and get out at the last stop. Walk around the hospital building via the right side and pass building T (see map in the link below).
By car: see map