18 - 20 March 2024
Application deadline:
06 March 2024
Cancellation deadline:
06 March 2024
Rachel Marcone, Geert van Geest and Tania Wyss
Omics data analysis
Academic: 300 CHF
For-profit: 1500 CHF
0.75 ECTS credits

Next course(s):
29 - 31 Oct 2024 Bellinzona

The videos of the lectures can be found on the SIB YouTube channel.


Single-cell RNA sequencing (scRNAseq) allows researchers to study gene expression at the single cell level. For example, scRNAseq can help to identify expression patterns that differ between conditions within a cell-type. To generate and analyze scRNAseq data, several methods are available, all with their strengths and weaknesses depending on the researchers’ needs. This 3-day course will cover the main technologies as well as the main aspects to consider while designing a scRNAseq experiment. In addition, it will cover the theoretical background of analysis methods with hands-on practical data analysis sessions applied to droplet-based methods.


This course is intended for life scientists and bioinformaticians familiar with "Next Generation Sequencing" who want to acquire the necessary skills to analyse scRNA-seq gene expression data.

Learning objectives

At the end of the course, participants will be able to:

  • distinguish advantages and pitfalls of scRNAseq
  • design their own scRNA-seq experiment
  • apply a downstream analysis using R




Attendees should have a Wi-Fi enabled computer. An online R and RStudio environment will be provided. However, in case you wish to perform the practical exercises on your own computer, please take a moment to install the following before the course:

  • R version > 4.2.
  • Latest RStudio version, the free version is perfectly fine.


The program will be communicated in due time. Program of past occurences can be found on GitHub.


The registration fees for academics are 300 CHF and 1500 CHF for for-profit companies. While participants are registered on a first come, first served basis, exceptions may be made to ensure diversity and equity, which may increase the time before your registration is confirmed.

Applications will close once the places will be filled. Deadline for registration and free-of-charge cancellation is set to 06/03/2024. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Venue and Time

This course will take place at the University of Bern.

It will start at 9:15 CET and end around 17:15 CET every day.

Precise information will be provided to the participants in due time.

Additional information

Coordination: Grégoire Rossier, SIB Training group.

We will recommend 0.75 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

SIB abides by the ELIXIR Code of Conduct. Participants of SIB courses are also required to abide by the same code.

For more information, please contact training@sib.swiss.