Single Cell RNA-Seq Data Analyses Workshop


Navet, SciLifeLab Uppsala
SciLifeLab Uppsala, BMC C11, Husargatan 3
Uppsala, 75237 Sweden
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Single Cell RNA-Seq Data Analyses Workshop

February 12, 2024 @ 09:00 February 16, 2024 @ 17:00 CET

This workshop will introduce the best practice bioinformatics methods for analysing single cell RNA-seq data via a series of lectures and computer practicals. The total course duration is 5 days which includes 4 days of lectures and exercises followed by a “Bring Your Own Data” day where you get to practice your skills on a dataset of your choosing.

The course is organized by: National Bioinformatics Infrastructure Sweden (NBIS)

Responsible teachers: Åsa Björklund, Susanne Reinsbach, Roy Francis

Contact information:  

Important dates

Application open: 13 Nov 2023

Application closes: 17 Jan 2024

Confirmation to accepted participants: Weeks 3-4, 2024

Course fee

This on-site training event costs 3000 SEK for academic participants, invoiced to the participant’s organisation. If you accept a position and do not participate (no-show) you will still be invoiced 3000 SEK. Please note that NBIS cannot invoice individuals. We ask non-academic applicants to contact us regarding the fee. 

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
  • Comparison of analysis toolkits: Seurat, Scran and Scanpy

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.

Selection criteria

Due to limited space, the course accommodates a maximum of 25 participants. If we receive more applications, participants will be selected based on selection criteria such as correct entry requirements, motivation to attend the course as well as gender and geographical balance.

SciLifeLab Uppsala, BMC C11, Husargatan 3
Uppsala, 75237 Sweden
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Last updated: 2023-11-13

Content Responsible: Maria Bäckström(