These materials include those from the course Single-cell RNA-seq & network analysis using Galaxy and Cytoscape, which ran in April 2021. The materials utilise Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data, demonstrate the droplet-based single-cell RNA-seq analysis pipelines from raw reads to cell cluster comparisons and explores single-cell networks using Cytoscape.

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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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Course 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 on other datasets
• Recognise decision-making steps along the analysis pipeline and justify your choices
• Employ appropriate data standards for repository submission and contribution to global cell atlases
• Define best practice for managing cellular resolution data

Material collection editors

• Wendi Bacon, EMBL-EBI, UK
• Pablo Moreno, EMBL-EBI, UK

DOI: 10.6019/TOL.SCGalaxyMaterials-t.2021.00001.1