Single Cell RNA-seq data analysis


Air&Fire, SciLifeLab Stockholm
Tomtebodavägen 23A
Solna, Sweden
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Single Cell RNA-seq data analysis

February 2 @ 09:00 February 4 @ 17:00 CET

This workshop will introduce the best practice bioinformatics methods for processing and analyses of single cell RNA-seq data via a series of online lectures and computer practicals. The total course duration is 45 hours, including the online lectures (15 hours) to be watched in advance and practical workshop that will be held on site in Stockholm (30 hours). The practical session is divided into both analysis overview and a Bring-Your-Own-Data (BYOD) day.


2022-02-02 to 2022-02-04 on site (9:00 – 17:00)


Rooms Air & Fire

Tomtebodavägen 23b, SciLifeLab Solna, Stockholm, Sweden

Important dates

Application open: 2021-11-05

Application deadline: 2021-12-16

Course Leaders

Paulo Czarnewski & Åsa Björklund

Contact information for questions regarding the course


Course fee
This workshop has a fee of 1700kr and will be invoiced to the selected participants *. Applications without complete invoice information will not be considered. Course fees cover all coffee breaks, all lunches and 1 course dinner.

* Please note that NBIS cannot invoice individuals.

Topics covered will include

  • 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. We do accept application from other countries, but give priority to applicants from Swedish universities prior to applicants from industry and academics from other countries.

Please note that NBIS training events do not provide any formal university credits. The training content is estimated to correspond to a certain number of credits, however the estimated credits are just guidelines. If formal credits are crucial, the student needs to confer with the home department before submitting a course application in order to establish whether the course is valid for formal credits or not.

Practical exercises will be performed using either R or Python, so we only accept students that fulfill the entry requirements (see below). NBIS offers

Entry requirements

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

  • Your own laptop with the following specs:
    • Operating system Win10, OS X or Linux
    • At least 8 GB of RAM.
    • Operating system Win10, OS X or Linux
    • At least 30 GB of free storage
    • Have full access to your computer (admin permissions).
  • You are used to scripting in:
    • UNIX command line (bash)
    • Either R and/or Python
  • You already understand the basis of NGS technologies
  • You are able to analyze bulk RNA-sequencing data
  • 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.

Link to application

Tomtebodavägen 23A
Solna, Sweden
+ Google Map

Last updated: 2021-11-11

Content Responsible: David Gotthold(