The Single cell RNA-seq analysis using Python course, which  focused on the analysis of single cell RNA sequencing (scRNA-seq) data using Python and command line tools, ran in February 2025. Here, we have made the course materials available for you to access any time.

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Using these materials

These course materials provide a mixture of pre-recorded lectures, presentations and practicals to help advance your knowledge and skills in the analysis of biological data. You may select your topic of interest from the Course content page to view the relevant materials or work your way through all the course materials. 

To find out more about the trainers who created these materials, follow the links from the Course content page or go directly to the Trainer biographies page. You can also find the software requirements for the practicals in the Technical help sheet.

In the Further learning section you may explore the details about the EMBL-EBI’s free access online tutorials and webinars on a variety of life sciences topics.

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Learning outcomes

After this course you should be able to:

• Explain the steps in the scRNA-seq pipeline
• Repeat the course analysis of scRNA-seq data from extraction to cluster maps
• Recognise decision-making steps along the analysis pipeline and justify your decisions, from experimental design to final visualisation
• Employ appropriate data standards for repository submission and contribution to global cell atlases

Material collection editors

• Jiawei Wang, EMBL-EBI
• Piv Gopalasingam, EMBL-EBI
• Iris Diana Yu, EMBL-EBI

DOI: 10.6019/TOL.SingleCellPython-t.2023.00001.1