During this course, you will learn about the analysis of single-cell RNA sequencing (scRNA-seq) data using both Python and command line tools. We will guide you through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. You will explore and interpret single-cell RNA-seq data using Python and the Single Cell Expression Atlas. Finally, you will put your knowledge into practice through a group challenge on the last day.

Single-cell RNA-seq analysis with Python 2027 is currently in development. Sign up for alerts to hear as this course develops.

Who is this course for?

This course is aimed at wet-lab researchers who are generating, planning on generating, or working with single cell RNA sequencing data.

Participants are required to have basic experience with a Unix/Linux command line. Basic knowledge of Python is essential.  We recommend you go through these free tutorials before attending the course:

• Basic introduction to the Unix environment
• Introduction to programming in Python

What will I learn?

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

Course content

During this course you will learn about:

• Single cell RNA-seq experimental design
• scRNA-seq analysis pipelines for droplet-based data
• EMBL-EBI Single Cell Expression Atlas Service
• Single cell data submission

Trainers

This course opens applications on 28 September 2026. Click to register your interest using the button on the right-hand side of this course website to hear as the course develops.