Starting single cell RNA-seq analysis (Virtual)


 Monday 1 Friday 5 June 2020


Virtual - EMBL-EBI, Hinxton,  CB10 1SD, United Kingdom

Application opens: 

Wednesday 23 October 2019

Application deadline: 

Friday 24 January 2020


Open application with selection


Meredith Willmott

Registration fee: 


Registration closed

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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 using data extracted from the Single Cell Expression Atlas. In addition to running a basic pipeline, participants will explore the variety of options within the Galaxy resource and individually analyse a given dataset. The results will be compared across the cohort to assess reproducibility and demonstrate the effect of analytical choice on research output. Finally, participants will learn about data submission, resources, and standards within the single cell field. 

Please note that participants will not be able to use their own data during the course practicals. However, there will be plenty of time to discuss their research and exchange ideas with other participants and the trainers. Opportunities will include poster sessions, evening discussions and small group chats with the trainers.


This course is aimed at researchers who are generating, planning on generating, or working with single cell RNA sequencing data. 


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:

Syllabus, tools and resources

During this course you will learn about:

  • Single cell RNA-seq experimental design
  • EMBL-EBI Single Cell Expression Atlas Service
  • Galaxy scRNA-seq pipelines, including: Seurat, SC3, scanpy, and Scater
  • Case study of single cell data
  • Human Cell Atlas data & metadata standards
  • General principles of data management, data FAIRification and best practice for generating and working with single cell RNA sequencing and image-based transcriptomics data


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 on other datasets
  • Recognise decision-making steps along the analysis pipeline and justify your choices
  • Employ appropriate data standards for repository submission and contribution to global cell atlases
  • Define best practice for managing cellular resolution data


Pre-course work
Pre-course Keynote 1.1 – Introduction to scRNA-Seq technologies Kerstin Meyer
Pre-course Keynote 1.2 – Research Applications Kerstin Meyer
Day 1 – Monday 1 June 2020
09:45-11:45 Welcome, course introduction & scRNA-Seq Lab Tutorial Wendi Bacon
13:00-13:30 Live question & answers Kerstin Meyer
16:00-16:30 Check-in & social (optional) Wendi Bacon
Day 2 – Tuesday 2 June 2020
09:45 Morning challenge Wendi Bacon
10:00 Keynote 2.1 - Experimental design Kristina Kirschner
13:00 Raw reads to DEM lecture Jonathan Manning
16:00 Check-in & social (optional) Wendi Bacon
Day 3 – Wednesday 3 June 2020
09:45 Morning Challenge Wendi Bacon
10:00 Keynote 2.2 - Research applications Kristina Kirschner
11:30-12:00 Live questions & answers Kristina Kirschner
13:00 Filtering, Normalisation & Batch Correction Jongeun Park
  Filtering, Normalisation & Batch Correction Jongeun Park
16:00 Check-in (optional) Wendi Bacon
Day 4 – Thursday 4 June 2020
09:45 Morning Challenge Wendi Bacon
10:00 Spatial transcriptomics Wendi Bacon
13:00 Dimension Reduction, Cluster Mapping and Finding Marker Genes Vladimir Uzun
14:00 Dimension Reduction, Cluster Mapping and Finding Marker Genes practical Vladimir Uzun
16:00 Check-in (optional) Wendi Bacon
Day 5 – Friday 5 June 2020
09:45 Morning Challenge Wendi Bacon
10:15 Designing your analysis Tamir Chandra
13:00 Cell Atlases Nancy George, Silvie Fexova &  Enrique Sapena Ventura
15:00 Final wrap-up Wendi Bacon