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.

Please note that you will not analyse your own data as part of the course. There will, however, be ample opportunity to discuss your 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 you will not require access to a powerful computer or install complex software on your 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.

Please note that we will operate this course virtually. Hybrid options are not currently available. We reserve the right to change the format of this course or cancel it.

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 successul applicants acquire/brush up on their basic skills in Python and the command line before attending the course. There are many tutorials available online and here are some that may be of help:

1. To complete the following suggested tutorials you may want to install Ubuntu for Windows Users if you are using a computer with a Windows Operating System.
2. Basic introduction to the Unix environment: https://swcarpentry.github.io/shell-novice/
3. 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. 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 23:59 on 17 November 2024. 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 02 December 2024. If you have any questions regarding the application process please contact Juanita Riveros. 

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
• course certificate on completion of the course

Financial assistance

Financial assistance is available for a limited number of participants on this course.

Registration fee waivers

We are able to offer a limited number of registration fee waivers for this course. If you receive a waiver, your registration fee will be reimbursed after you have completed the course.

You will need to apply for the fee waiver at the same time as submitting your application for the course, explaining why you require the waiver and how attending this course will benefit your career.

You will be informed about whether you have received the waiver at the same time as you hear about the application outcome for the course. If your course application is successful, you will need to pay the registration fee at the time you register. You will receive the waiver within a month of submitting your form. 

Terms and conditions

The scientific organisers will select the recipients of financial assistance during the course application selection process. Selection for financial support is based on scientific merit, your current work study or location, the reasons for needing financial support and the impact this event will have on your career. Priority will be given to applications from low and middle income countries.

Application for financial support will not affect the outcome of your course application.

Course materials

The course materials from the 2023 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2025 edition.

Posters

All participants are expected to present a poster that will be displayed virtually during the course. Successful applicants will be asked to submit their poster upon registration. 

All posters should:

•          PDF format
•          be in a portrait orientation
•          include your photograph and contact information

We expect the posters to act as a talking point between you, other participants, and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.