Single-Cell RNA-Seq Data Analysis
March 31, 2025 @ 08:00 – April 3, 2025 @ 17:00 CEST
National course open for PhD students, postdocs, researchers and other employees in all Swedish universities, in need of single cell RNAseq analysis skills. We also welcome applications from outside of Sweden and from the non-academic sector, for more info contact us!
Course dates: 31 March 2025 – 3 April 2025 and 10 April 2025
Important dates and information
Application opens: 2024-12-18
Application closes: 2025-02-28
Confirmation to accepted students: 2025-03-07
Course Leader and teachers: Åsa Björklund (CL), Susanne Reinsbach (CL), Jennifer Fransson (CL)
In case you miss information on any of the above dates, please contact: edu.sc [at] nbis.se
Course fee
This online training event has no fee for academic participants. However, if you accept a position at the workshop and do not participate (no-show) you will be invoiced 3000 SEK. For non-academic participants a course fee* of 12000 SEK will be invoiced.
*Please note that NBIS cannot invoice individuals
Course content
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” (BYOD) day where you get to practice your skills on a dataset of your choosing. Please note that the BYOD section will take place the week after the lectures.
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
- Cell type prediction
- Trajectory inference analysis
- Comparison of Seurat, Bioconductor and Scanpy toolkits
Learning Outcomes
Upon completion of this course, you will be able to run analysis on your own data, select appropriate analysis methods and interpret the results.
Entry requirements
The following is a list of skills required for being able to follow the course and complete the exercises:
- You are familiar with basic UNIX command line (bash)
- You are familiar with either R and/or Python
- You already understand the basics of NGS technologies
- You are familiar with analyses of bulk RNA-sequencing data
- You have full access to your computer (admin permissions). Instructions on installation will be sent by email to accepted participants.
The course accommodates a maximum of 25 participants. If we receive more applications, participants will be selected based on selection criteria, including (but not limited to) correct entry requirements, motivation to attend the course, as well as gender and geographical balance.
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