This set of materials includes those from the 2022 course Single-Cell RNA-seq Analysis using R; it covers the analysis of scRNA-seq data using R and command line tools. Lectures and practical sessions will cover both droplet-based and plate-based scRNA-seq analysis pipelines from raw reads to cell clusters. They will explore and interpret data using R as well as the Human Cell & Single Cell Expression Atlases.

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Using these materials

These course materials provide a mixture of pre-recorded lectures, presentations and practicals to help advance your skills in the analysis of single-cell RNA-seq 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.

If you would like to provide feedback on this set of course materials, please use the form on the Your feedback page.

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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

• Wendi Bacon, The Open University
• Dayane Araujo, EMBL-EBI

DOI: 10.6019/TOL.SingleCellMaterials-t.2021.00001.1