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:

• Introduction to Galaxy: https://galaxyproject.org/tutorials/g101/

There are other tutorials here, although they are not required: https://galaxyproject.org/learn/

Trainers

Please read our page on application advice before starting your application. In order to be considered for a place on this course, you must do the following:

• Complete the online application form providing answers as directed
• Ensure you add relevant information to the "Application submission" section where you are asked to provide three 100-word paragraphs that cover your:
  • scientific biography/work experience
  • current research interests
• Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course

Please submit all documents during the application process by 7 January.

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by 17 January.