Virtual course

Single-cell RNA-seq analysis using R

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 last two days of the course.

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.

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.

Prerequisites

Participants will require a basic knowledge of the Unix command line, the Ubuntu operating system and specialised 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
Western University
Wendi Bacon
The Open University
Nancy George
EMBL-EBI
Vitalii Kleshchevnikov
Wellcome Sanger Institute
Silvie Korena Fexova
EMBL-EBI
Ana-Maria Cujba
Wellcome Sanger Institute
Iguaracy Pinheiro de Sousa
EMBL-EBI
Daniel O'Hanlon
EMBL-EBI

Programme

All times in the programme are listed in BST

 

Time

Topic

Trainer

Day one Monday 3 October 2022

Planning the experiment

09:00 10:00

Keynote lecture

Tallulah Andrews

10:00 10:30

Break

 

10:30 11:15

Welcome to EMBL-EBI and introductions

Dayane Araujo

11:15 12:00

Library generation overview 

Wendi Bacon

12:00 13:00

Lunch break

 

13:00 14:15

Experimental design 

Tallulah Andrews

14:15 16:00

Pipeline overview 

Wendi Bacon

16:00 16:30

Break

 

16:00 16:30

Q&A

Tallulah Andrews


 

Time

Topic

Trainer

Day two Tuesday 4 October 2022

Processing data

08:40 09:15 

Getting set up: infrastructure terms

Iguaracy Pinheiro de Sousa and Daniel O'Hanlon

09:15 09:30 

Morning challenge 

Dayane Araujo 

09:30 10:00  

Lightning talks: round A 

Delegates 

10:00 10:30  

Break  

 

10:30 11:30  

Raw reads to expression matrix 

Iguaracy Pinheiro de Sousa and Daniel O'Hanlon

11:30 12:00  

Lightning talks: round B 

 

12:00 13:00  

Lunch break  

 

13:00 13:15 

Q&A

Iguaracy Pinheiro de Sousa and Daniel O'Hanlon

13:15 14:45  

Practical one: Raw reads to expression matrix 

Iguaracy Pinheiro de Sousa and Daniel O'Hanlon

14:45 15:15  

Lightning talks: round C 

 

15:15 15:45  

Break  

 

15:45 16:45  

Cell Atlases 

Nancy George and Silvia Fexova

16:45 17:30  

Cell Atlas activity 

Nancy George and Silvia Fexova

 

Time

Topic

Trainer

Day three Wednesday 5 October 2022

Analysing data

08:15 09:00  

Pre-processing and dimensionality reduction 

Ana-Maria Cujba

09:00 09:15 

Morning challenge 

Dayane Araujo 

09:15 10:15  

Practical two: Pre-processing and dimensionality reduction 

Ana-Maria Cujba

10:15 10:45  

Break  

 

10:45 11:30 

Practical two: Pre-processing and dimensionality reduction 

Ana-Maria Cujba

11:30 12:00 

Q&A 

Ana-Maria Cujba

12:00 13:00  

Lunch break  

 

13:00 14:00  

From UMAP to annotation 

Ana-Maria Cujba

14:00 15:00  

Practical three: From UMAP to  annotation 

Ana-Maria Cujba

15:00 15:30  

Break  

 

15:30 16:30 

Practical three: From UMAP to  annotation 

Ana-Maria Cujba

16:30 17:30  

Q&A 

Ana-Maria Cujba


 

Time

Topic

Trainer

Day four Thursday 6 October 2022

Applying the pipeline

08:15 09:00  

Spatial mapping of cell types (pre-recording) 

Vitalii Kleshchevnikov 

09:00 09:30 

Q&A 

Vitalii Kleshchevnikov 

09:30 10:30  

Online tools and follow-up  

TBC

10:30 11:00 

Break 

 

11:00 12:00 

Group project 

All trainers 

12:00 13:00  

Lunch break  

 

13:00 15:00  

Group project 

All trainers 

15:00 15:30  

Break 

 

15:30 17:30  

Talk with the trainers rounds 

All trainers

 

Time

Topic

Trainer

Day five Friday 7 October 2022

Putting it into practice

09:15 – 10:00  

Group project 

All trainers

10:00 10:30  

Break 

 

10:30  12:00  

Group project presentations 

All trainers

12:00  13:00  

Lunch break and group photo 

 

13:00  14:00  

Designing your analysis  

Tallulah Andrews 

14:00  15:00  

Q&A 

Tallulah Andrews 

15:00  15:30  

Survey and end of course

Dayane Araujo

Please read our page on application support 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 midnight on Friday 24 June 2022. 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 Friday 15 July 2022. If you have any questions regarding the application process please contact Jane Reynolds.

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. Successful applicants will be required to submit their talks upon registration.

Applications closed
24 June 2022

03 - 07 October 2022
£200.00
Contact
Jane Reynolds
Open application with selection
30 places

Organisers
  • Wendi Bacon
    The Open University
  • Dayane Araujo
    EMBL-EBI

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