Single cell RNAseq data analysis

Github repository

 02-04 February 2022

 SciLifeLab Solna, Tomtebodavägen 23b, Stockholm, Sweden

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.


Course staff

Paulo Czarnewski (Course Leader)

Åsa Björklund (Course Leader)



Covered topics

All recorded lectures can be found in the MODULES page.

  • 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



Application open: 2021-11-05

Application deadline: 2021-12-16

Application form:

Course fee: This workshop has a fee of 1700kr 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.

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 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 analyze 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.


Course schedule can be found here.


All exercises can be found in here.


Precourse material
Please read carefully the Precourse material before the course start.



CC attribution share alike This course content is offered under a CC attribution share alike license. Content in this course can be considered under this license unless otherwise noted.