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Single cell RNA sequencing data analysis, 1 hp

National course open for PhD students (prioritized), postdocs, researchers and other employees in need of bioinformatic skills within all Swedish universities.

Application page

Important dates

Application open: June 19

Application deadline: August 28

Confirmation to accepted students: August 30

Responsible teachers: Åsa Björklund

If you don’t receive information according to the dates above, contact

Course fee

A course fee of 1300 SEK will be invoiced to accepted participants (includes coffee, lunches and course dinner). NOTE – Uppsala University cannot invoice individuals.

Course content

Course website

This course will cover the basic steps in single cell RNAseq (scRNAseq) processing and data analysis. Topics covered will include:

  • An overview of the current scRNAseq techniques
  • Basic overview of pipelines for processing raw reads into expression values
  • Quality control of scRNAseq data
  • Dimensionality reduction and clustering techniques
  • Data normalization
  • Differential gene expression for scRNAseq data
  • Examples on how to use these tools in a research project.

Entry requirements

  • Basic knowledge in Linux is a requirement. We will not teach Linux at the course and you may have considerable trouble to follow the practical sessions if you are not reasonably used to work in a Linux environment.
  • Be able to bring your own laptop with R installed for the practical computational exercises. Instructions on installation will be sent by email to accepted participants.
  • Some programming/scripting experience is required (preferably in R).
  • Experience working on the SNIC center Uppmax is desirable, but not required. We encourage accepted participants to do an Uppmax tutorial before the course.
  • Previous experience with RNA-seq analysis and/or participation in NGS/RNA-seq course is an advantage.

Due to space constraints for the computer exercises, there are a maximum number of allowed participants. If we receive more applications, participants will be selected based on several criteria. Selection criteria include correct entry requirements, motivation to attend the course as well as gender and geographical balance.