This course covers the analysis of scRNA-seq data using R and command line tools. Participants will be guided through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. They will explore and interpret data using R as well as the Single Cell Expression Atlas. Finally, participants will put their knowledge into practice through a group challenge on the last two days of the course.

Please note that participants will not analyse their own data as part of the course. There will, however, be ample opportunity to discuss their research and ideas with other course participants and 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 asynchronous communication via Slack.

Pre-recorded material may be provided before the course starts that participants will need to watch, read or work through to gain the most out of the actual training event. 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 – 17:30 BST each day of the course. Trainers will be available to assist, answer questions, and provide further explanations during these times.

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

Participants will require a basic knowledge of the Unix command line, the Ubuntu operating system and specialised R statistical packages. We recommend these free tutorials:

• Basic introduction to the Unix environment
   
• Basic R concept tutorials

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
• Human Cell Atlas data & metadata standards

Trainers

Please read our page on application support 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.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
• Upload one 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 midnight on Friday 24 June 2022. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 15 July 2022. If you have any questions regarding the application process please contact Jane Reynolds.

Flash talks

All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Successful applicants will be required to submit their talks upon registration.