Virtual course

Single-cell RNA-seq analysis using Galaxy

This course utilises Galaxy pipelines, an online open-access resource that allows even the most computer-phobic bench scientists to analyse their biological data. Participants will be guided through the droplet-based scRNA-seq analysis pipelines from raw reads to trajectories, for mammalian and plant genomes.

Please note that although participants will not be able to use their own data during the course practicals, there will be ample time to discuss their research and ideas with both course participants and trainers.  As part of this, participants will present lightning talks on their research topics. Near the end of the course, participants will engage in small group discussions about their research challenges and problems with each other and the trainers at the ‘Talk with trainers’.

Virtual course

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 communication via Slack

Pre-recorded material will be made available to registered participants prior to the start of the course and in the week before the course there will be a brief induction session. Computational practicals will run on EMBL-EBI’s virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines.

Participants will need to be available between the hours of 09:00 - 17:00 GMT each day of the course. Trainers will be available to assist, answer questions, and further explain the analysis during these times.

Who is this course for?

This course is aimed at researchers with little-to-no experience in big data analysis and who are generating, planning on generating, or working with single-cell RNA sequencing data.

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 trajectories
  • Recognise decision-making steps along the analysis pipeline and justify your decisions, from experimental design to final visualisation

Course content

Participants will be using Galaxy through the course, and may also be asked to do some brief coding in R. Please ensure that you complete this free tutorial before you attend the course:

There are other tutorials here, although they are not required:


Wendi Bacon
The Open University
Tamir Chandra
The University of Edinburgh
Kristina Kirschner
University of Glasgow
Jonathan Manning
Kerstin Meyer
Wellcome Sanger Institute
Zhichao Miao
Pablo Moreno
Mehmet Tekman
Albert-Ludwigs-Universität Freiburg
Simone Webb
Newcastle University
This course has ended

07 - 11 March 2022
Sophie Spencer

  • Dayane Rodrigues Araujo
  • Wendi Bacon
    The Open University

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