Single cell RNAseq data analysis


Air&Fire, SciLifeLab Stockholm
Tomtebodavägen 23A
Solna, Sweden
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Single cell RNAseq data analysis

January 30 @ 08:00 February 3 @ 14:00 CET

This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data. The total course duration is 5 days, including the lectures and practical exercises that will be held on site in Stockholm.


Application open: 2022-11-25

Application deadline: 2022-12-21

Course Leaders

Paulo Czarnewski

Åsa Björklund


Course fee

This workshop has a fee of 2000kr and will be invoiced to the selected participants (Please note that NBIS cannot invoice individuals). Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner.

Course content

  • Overview of the current scRNAseq technologies
  • Basic overview of pipelines for processing raw reads into expression values
  • Quality control and normalization
  • Dimensionality reduction techniques
  • Data integration and batch correction
  • Differential gene expression
  • Clustering techniques
  • Celltype prediction
  • Trajectory inference analysis
  • Analysis of spatial transcriptomics datasets
  • Comparison of different analysis pipelines such as Seurat, Scran and Scanpy

Who can apply?

This is a national course. The course is open for PhD students, postdocs, group leaders and core facility staff within all Swedish universities. Even if we do accept application from other countries, we give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries.

Practical exercises will be performed using either R or Python, so we only accept students that fulfil the entry requirements below.

Entry requirements

  • You are used to program in either R and/or Python
  • You already understand the basis of NGS technologies
  • You are able to analyse bulk RNA-sequencing data
  • You are used to navigate and use UNIX command line (bash)
  • Have full access to your computer (admin permissions). Instructions on installation will be sent by email to accepted participants.

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.


January 30, 2023 @ 08:00 CET
February 3, 2023 @ 14:00 CET
Event Category:
Tomtebodavägen 23A
Solna, Sweden
+ Google Map

Last updated: 2023-01-24

Content Responsible: David Gotthold(