This course covers the analysis of single cell RNA sequencing (scRNA-seq) data using Python and command line tools. Participants will be guided 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 as well as the Single Cell Expression Atlas. Finally, you will put their knowledge into practice through a group challenge on the last day.

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.

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: www.ee.surrey.ac.uk/Teaching/Unix
• Introduction to programming in Python: http://swcarpentry.github.io/python-novice-gapminder/ 

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

Please read our support page before starting your application. 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 23:59 GMT on 2 November 2025. Items marked * in the application are mandatory. Incomplete applications will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 17 November 2025.  If you have any questions regarding the application process, please contact Omotoke Labiyi.

Registration fees 

The registration fee includes: 

• access to the full five-day course programme
• access to a bespoke online course handbook
• secure community space on Slack
• virtual machine to work on that is accessed via the internet
• dedicated online support team
• certificate on completion of the course

* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your event organiser for more information.

Financial assistance
Financial assistance is available to a limited number of participants attending this course.

Registration fee waivers
A limited number of registration fee waivers are offered for this course.

• Application process:
  • Apply for the fee waiver alongside your course application.
  • Provide a brief explanation of why you require the waiver and how attending the course will benefit your career.
• Notification:
  • You will be informed of your waiver status at the same time as the outcome of your course application.
  • If awarded, the registration fee will be waived entirely.

Financial assistance terms and conditions

• Selection process: Recipients of financial assistance will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not impact the outcome of your course application.

Event terms and conditions

• Selection process: Recipients will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not affect your course application outcome.

Course materials

The materials for the 2025 course are available for you to browse. These provide a snapshot of the content that will be covered in the 2026 course.