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.

Responsible teachers: Åsa Björklund, Susanne Reinsbach, Roy Francis

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

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.