Virtual course

Single-cell RNA-seq & network analysis using Galaxy and Cytoscape

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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 cell cluster comparisons. In addition to running a basic pipeline, participants will explore single cell networks using Cytoscape.

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 discussion 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 08:00-17:30 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 cluster maps
  • Recognise decision-making steps along the analysis pipeline and justify your decisions, from experimental design to final visualisation
  • Generate a network using Cytoscape and marker genes list from scRNA-seq analysis
Course content

Participants will be using a Galaxy resource in-depth. Participants may also be asked to do brief coding in R. Please ensure that you complete the free tutorials before you attend the course:

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

During this course you will learn about:

  • Single cell RNA-seq experimental design
  • Galaxy scRNA-seq pipeline
  • Cytoscape network analysis



Kerstin Meyer
Wellcome Sanger Institute
Pablo Moreno
Kristina Kirschner
University of Glasgow
Jon Manning
Zhichao Miao
Simone Webb
Newcastle University
Tamir Chandra
The University of Edinburgh
Wendi Bacon
Scooter Morris
University of California, San Francisco


Day 1  
08:30 - 10:00 Keynote Lecture: Introduction to scRNA-seq Technologies Kerstin Meyer
10:00 - 10:15 Break  
10:15 - 11:00 Welcome to EMBL-EBI & Introductions! Dayane Araújo
11:00 - 12:00 Q&A with Kerstin Meyer Kerstin Meyer
  Lunch Break  
13:00 - 14:00 Library Generation - Overview Wendi Bacon
14:00 - 14:30 Introduction to Galaxy Pablo Moreno
14:30 - 15:00 Q&A with Pablo Moreno Pablo Moreno
15:00 - 15:30 Lightning Talks A  
15:30 - 16:00 Break  
16:00 - 17:30 Practical 1: Introduction to Galaxy Pablo Moreno
Day 2   Trainer
08:00 - 09:00 Keynote Lecture: Applied scRNA-seq Kristina Kirschner
09:00 - 10:30 Pipeline Overview Wendi Bacon
10:30 - 11:00 Break  
11:00 - 12:00 Experimental Design Kristina Kirschner
  Lunch Break  
13:00 - 14:00 Q&A with Kristina Kirschner Kristina Kirschner
14:00 - 14:30 From Fasta to Matrix Jonathan Manning
14:30 - 15:00 Q&A with Jonathan Manning Jonathan Manning
15:00 - 15:30 Lightning Talks B  
15:30 - 16:00 Break  
16:00 - 18:00 Practical 2: From Fasta to Matrix  Jonathan Manning
Day 3   Trainer
08:00 - 09:00 Pre-processing & batch correction Zhichao Miao
09:00 - 09:15 Morning Challenge Wendi Bacon
09:15 - 10:00 Q&A with Zhichao Miao Zhichao Miao
10:00 - 12:00 Practical 3: Pre-processing & batch correction Wendi Bacon
  Lunch Break  
13:00 - 14:00 Clustering, annotation and pseudotime inference tools for scRNA-seq data – a quick guide  Simone Webb
14:00 - 14:45 Q&A with Simone Simone Webb
14:45 - 15:15 Lightning Talks C  
15:15 - 15:45 Break  
15:45 - 18:00 Practical 4: Cluster annotation & trajectories Wendi Bacon
Day 4   Trainer
09:00 - 10:15 Designing your Analysis and Q&A Tamir Chandra
10:15 - 10:45 Break  
10:45 - 12:00 Network Analysis Scooter Morris
  Lunch Break  
13:00 - 14:00 Network Analysis Activity Scooter Moris
14:00 - 15:00 Q&A with Scooter Morris Scooter Moris
15:00 - 15:30 Break  
15:30 - 17:30 Cytoscape Exploration Scooter Moris
Day 5    
09:00 - 11:00 Talk to the trainers - Breakout chats Kristina Kirschner, Tamir Chandra, Pablo Moreno, Jonathan Manning, Simone Webb, Zhichao Miao, Scooter Morris
11:00 - 11:15 Break  
11:15 - 12:00 Cytoscape Exploration - Continued Scooter Morris
  Lunch Break  
13:00 - 14:00 Cytoscape Exploration - Continued Scooter Morris
14:00 - 14:45 Future of Cytoscape Scooter Morris
14:45 - 15:00 Wrap-up & Survey Dayane Araújo

Please note minor changes to the programme may occur. 

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 history
  • 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 midnight on Friday 26th February 2021. 

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 12th March 2021. If you have any questions regarding the application process please contact Meredith Willmott ( ).

Participant 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. Further details will be provided following registration

This course has ended

26 - 30 April 2021
Meredith Willmott

  • Wendi Bacon
  • Pablo Moreno

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