Single cell RNA-seq data analysis with Chipster (2020-10-28)

27-28 October 2020 two half-days, Online Register here


This two half-days practical course (October 27, October 28) introduces single cell RNA-seq data analysis methods, tools and file formats to all researchers who are planning to use single cell RNA-seq data for their own projects. The course will cover the processing of transcript counts from quality control and filtering to dimensional reduction, clustering, and differential expression analysis. In addition, it will cover how to do integrated analysis of two samples.

Seurat v3 tools embedded in user-friendly Chipster software will be used for the practical tutorials and hands-on sessions.

Successful completion will be awarded with 0.5 ECTS.

Learning objectives

  • Obtaining an overview and discuss a variety of aspects of single cell RNA-seq data analysis

  • Gaining experience with Seurat v3 tools available in Chipster to undertake analysis of single cell RNA-seq data

  • Understanding the advantages and limitations of single cell RNA-seq data analysis


The free and user-friendly Chipster software is used in the exercises, so no previous knowledge of Unix or R is required, and the course is thus suitable for everybody who is planning to use single cell RNA-seq.

Participants will be provided with the access to pre-recorded lessons two weeks before the online training as an introductionary overview of the main concepts and first steps with Chipster software. Participants will be expected to view these recordings and perform a short Chipster exercise before attending the online sessions.

Time Plan

Both days consist of interleaved lectures and hands-on exercises followed by a wrap-up and question session on each topic. A 15 min coffee break is held in between.

Date Time Topic
Tue, 27 Oct 8.45 Virtual coffee & get together
  9.15 Introduction to Chipster
    Introduction to single cell RNA-seq
    Preprocessing and quality control
    Dimensional reduction
  13.00 End of day 1
Wed, 28 Oct 8.45 Virtual coffee & get together, re-cap
  9.15 Clustering and finding marker genes, visualisation
    Analysis of two samples
Finding common cell types
Finding conserved cluster marker genes
Finding genes which are differentially expressed in a cell-type specific manner
    Conclusion & final discussion
  13.00 End of course


The registration is closed.


Eija Korpelainen with Maria Lehtivaara


The course will be held online. Access will be available for registered participants only.


Roland Krause