Virtual course

Single-cell RNA-seq analysis using R

Welcome to the new EMBL-EBI Training site. Please tell us what you think!

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 final two days.

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.

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 18 operating system and the R statistical packages. We recommend these free 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:

Trainers

Tallulah Andrews
Wellcome Trust Sanger Institute
Wendi Bacon
EMBL-EBI, UK
Rasa Elmentaite
Wellcome Sanger Institute
Nancy George
EMBL-EBI, UK
Veronika Kedlian
Wellcome Sanger Institute
Gerda Kildisiute
Wellcome Sanger Institute
Vitalii Kleshchevnikov
Wellcome Sanger Institute
Elo Madissoon
EMBL-EBI, UK
Enrique Sapena Ventura
EMBL-EBI, UK
Xiaohui Zhao
University of Cambridge

Programme

Day 1

Planning the Experiment

09:00 - 10:00 Keynote Lecture Tallulah Andrews
10:00 - 10:30 Break  
10:30 - 11:00 Welcome to EMBL-EBI and Introductions Wendi Bacon
11:00 - 12:00 Library Generation Overview Wendi Bacon
12:00 - 13:00 Lunch Break  
13:00 - 14:00 Experimental Design Tallulah Andrews
14:00 - 16:00 Pipeline Overview Wendi Bacon
16:00 - 16:30 Break  
16:30 - 17:30 Q&A with Tallulah Tallulah Andrews
 

Day 2

Processing Data

08:00 - 09:00 Getting set up: infrastructure terms Xiaohui Zhao
09:00 - 09:15 Morning Challenge Wendi Bacon
09:15 - 09:45 Q&A with Xiaohui Zhao Xiaohui Zhao
09:45 - 10:15 Lightning Talks Round A Delegates
10:15 - 10:45 Break  
10:45 - 11:30 Raw reads to expression matrix Xiaohui Zhao
11:30 - 12:00 Lightning Talks Round B  
12:00 - 13:00 Lunch Break  
13:00 - 13:15 Q&A with Xiaohui Zhao Xiaohui Zhao
13:15 - 14:45 Practical 1: Raw reads to expression matrix Xiaohui Zhao
14:45 - 15:15 Lightning Talks Round C  
15:15 - 15:45 Break  
15:45 - 16:45 Cell Atlases Nancy George & Enrique Sapena Ventura
16:45 - 17:30 Cell Atlas Activity Nancy George & Enrique Sapena Ventura
 

Day 3

Analysing Data

08:15 - 09:00 Pre-processing and dimensionality reduction Rasa Elmentaite
09:00 - 09:15 Morning Challenge Wendi Bacon
09:15 - 10:15 Practical 2: Pre-processing & dimensionality reduction Rasa Elmentaite & Gerda Kildisiute
10:15 - 10:45 Break  
10:45 - 11:30 Practical 2: Pre-processing & dimensionality reduction Rasa Elmentaite & Gerda Kildisiute
11:30 - 12:00 Q&A with Rasa & Gerda Rasa Elmentaite & Gerda Kildisiute
12:00 - 13:00 Lunch Break  
13:00 - 14:00 From UMAP to annotation Gerda Kildisiute
14:00 - 15:00 Practical 3: From UMAP to annotation Gerda Kildisiute & Rasa Elmentaite
15:00 - 15:30 Break  
15:30 - 17:00 Practical 3: From UMAP to annotation Gerda Kildisiute & Rasa Elmentaite
17:00 - 17:30 Q&A with Gerda & Rasa Gerda Kildisiute & Rasa Elmentaite
 

Day 4

Putting it into practice

08:30 - 09:00 Spatial Transcriptomics Vitalii Kleshchevnikov
09:00 - 09:30 Q&A with Vitalii Vitalii Kleshchevnikov
09:30 - 10:30 So I have some genes... what's next? Elo Madissoon
10:30 - 11:00 Break  
10:30 - 12:00 Group Challenge Elo Madissoon, Xiaohui Zhao, Rasa Elmentaite,  Gerda Kildisiute, Vitalii Kleshchevnikov, Veronika Kedlian 
12:00 - 13:00 Lunch Break  
13:00 - 15:00 Group Challenge Elo Madissoon, Xiaohui Zhao, Rasa Elmentaite,  Gerda Kildisiute, Vitalii Kleshchevnikov, Veronika Kedlian 
15:00 - 15:30 Break  
15:30 - 17:30 Talk with the Trainers Rounds Elo, Rasa, Gerda, Xiaohui, Tallulah, Enrique & Nancy
 

Day 5

Putting it into practice

09:15- 10:00 Group Challenge Elo Madissoon, Xiaohui Zhao, Rasa Elmentaite,  Gerda Kildisiute, Vitalii Kleshchevnikov, Veronika Kedlian 
10:00 - 10:30 Break  
10:30 - 12:00 Group Challenge Elo Madissoon, Xiaohui Zhao, Rasa Elmentaite,  Gerda Kildisiute, Vitalii Kleshchevnikov, Veronika Kedlian 
12:00 - 13:00 Lunch Break  
13:00 - 14:00 Designing your analysis Tallulah Andrews
14:00 - 15:00 Q&A with Tallulah Tallulah Andrews
15:00 - 15:30 Survey & Goodbyes Wendi Bacon

Registration is now closed. 

This course has ended

01 - 05 February 2021
Contact
Meredith Willmott

Organisers
  • Wendi Bacon
    EMBL-EBI, UK
  • Xiaohui Zhao
    University of Cambridge

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