In this virtual course hosted by the EMBL European Bioinformatics Institute (EMBL-EBI), you will learn how to analyse single cell RNA sequencing data using Python and command line tools. Participants will be guided through droplet-based RNA-seq analysis pipelines from raw reads to cell clusters. You will explore and interpret single-cell RNA seq data using Python as well as the Single Cell Expression Atlas. Finally, you will put their knowledge into practice through a group challenge on the last day.

Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.

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.

Prerequisites

Some experience with Python is beneficial. During the course, some of the practicals will use a Linux-based command line interface. We recommend all successful applicants acquire/brush up on their basic skills in Python and the command line before attending the course.

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

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