Single cell RNA sequencing analysis

Important dates 

  • Application open: September 13, 2019
  • Application deadline: December 16, 2019
  • Confirmation to accepted students: December 20, 2019

Application and more information can be found at:

Contact information  

Responsible teachers: Åsa Björklund and Paulo Czarnewski

Do you have any questions regarding the course, please email to or

Course fee

A course fee* of 2000 SEK will be invoiced to accepted participants. This includes lunches, coffee and course dinner.

*Please note that NBIS cannot invoice individuals

Course content

The first 3 days of the 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 technologies
  • 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
  • Trajectory analysis
  • Comparison of different analysis pipelines such as Seurat, Scran and Scanpy

On the fourth day we offer a “Bring your own data” day where you can analyse your data using the tools that you have discovered during the course, with TAs present to help you run the analyses and discuss your results. If you do not have your own data you can still select a public dataset of interest and analyse during that day.

Entry requirements

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

  • Basic knowledge in R/Linux.
  • 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).


  • 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.