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Single cell RNA sequencing data analysis

National course. The course is open for PhD students, postdocs, researchers and other employees in need of single cell RNA-seq data analysis skills within all Swedish universities.

The course is organized by NBIS


Important dates

Application open: February 1

Application closes: April 23

Confirmation to accepted students: April 27

Responsible teacher: Åsa Björklund

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

How to apply

Course fee

A course fee* of 1700 SEK will be invoiced to accepted participants. This includes lunches, coffee and course dinner.

*Please note that NBIS cannot invoice individuals

Course content

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

Required for being able to follow the course and complete the computer exercises

  • 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 limited space the course can accommodate maximum of 25 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.