Virtual course

Single-cell RNA-seq analysis using Galaxy

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 trajectories, for mammalian and plant genomes.

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 discussions 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 09:00 - 17:00 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 trajectories
  • Recognise decision-making steps along the analysis pipeline and justify your decisions, from experimental design to final visualisation
Course content

Participants will be using Galaxy through the course, and may also be asked to do some brief coding in R. Please ensure that you complete this free tutorial before you attend the course:

There are other tutorials here, although they are not required: https://galaxyproject.org/learn/

Trainers

Wendi Bacon
The Open University
Tamir Chandra
The University of Edinburgh
Kristina Kirschner
University of Glasgow
Jonathan Manning
EMBL-EBI
Kerstin Meyer
Wellcome Sanger Institute
Zhichao Miao
EMBL-EBI
Pablo Moreno
EMBL-EBI
Mehmet Tekman
Albert-Ludwigs-Universität Freiburg
Simone Webb
Newcastle University

Programme

All timings are in GMT. 

 

Time  

Subject  

Trainer

Day one - 7 March 2022

09:30 - 10:15

Welcome to EMBL-EBI and introductions

Dayane Araújo

10:15 - 11:30 

Local and systemic response to SARS-CoV-2 infection in children and adults lecture and Q&A

Kerstin Meyer

11:30 - 12:00

Lightning talks group one

Participants

12:00 - 13:00

Lunch break 

 

13:00 - 13:30

Introduction to Galaxy

Pablo Moreno

13:30 - 14:00

Q&A session with Pablo

Pablo Moreno

14:00 - 15:00

Practical one: Introduction to Galaxy

Pablo Moreno

15:00 - 15:30

Break

 

15:30 - 16:30 

Library generation - overview

Wendi Bacon 

Day two - 8 March 2022

08:45 - 09:30 

Understanding complex cellular interactions in senescence using single-cell seq approaches

Kristina Kirschner

09:30 - 10:00

Q&A with Kristina Kirschner

Kristina Kirschner

10:00 - 10:45

From fasta to matrix lecture and Q&A

Jonathan Manning

10:45 - 11:00 Break  

11:00 - 11:30

Lightning talks group two

Participants

11:30 - 12:00

Socialising/networking

Dayane Araújo

12:00 - 13:00

Lunch break

 

13:00 - 14:30

Pipeline overview 

Wendi Bacon

14:30 - 15:30 

Experimental design of single-cell studies

Kristina Kirschner

15:30 - 16:00

Break 

 

16:00 - 16:30 

Q&A on experimental design 

 Kristina Kirschner

Day three - 9 March 2022

09:00 - 09:15

Morning activity

 

09:15 - 09:45

Practical two: From fasta to matrix

Jonathan Manning

09:45 - 10:00 Break  

10:00 - 12:00

Practical two: From fasta to matrix continued

Jonathan Manning

12:00 - 13:00

Lunch break

 

13:00 - 14:30

Practical two: From fasta to matrix continued

Jonathan Manning 

14:30 - 15:00

Socialising/Networking

 

15:00 - 15:30

Break

 

15:30 - 16:00

Lightning talks group three

Participants

Day four - 10 March 2022

09:00 - 09:45

Pre-processing & batch correction 

Zhichao Miao

09:45 - 10:00

Morning activity

Dayane Araújo

10:00 - 10:30

Pre-processing & batch correction Q&A

Zhichao Miao

10:30 - 12:00 

Practical three: Filter, plot & explore

Wendi Bacon 

12:00 - 13:00

Lunch break

 

13:00 - 14:30 

Practical three: Filter, plot & explore

Wendi Bacon 

14:30 - 15:30 

Clustering, annotation and pseudotime inference tools for scRNA-seq data – a quick guide 

Simone Webb

15:30 - 16:00

Break

 

16:00 - 16:30

Q&A with Simone Webb

Simone Webb

Day five - 11 March 2022

09:00 - 11:00

Practical four: Trajectory analysis using Python

Wendi Bacon 

11:00 - 12:00

Practical five: Analysis of plant scRNA-seq data with Scanpy

Mehmet Tekman

12:00 - 13:00

Lunch break

 

13:00 - 14:15

Designing your analysis and Q&A

Tamir Chandra

14:15 - 14:30

Break and group photo

 

14:30 - 15:30 

Talk to the trainers  

All trainers 

15:30 - 15:45

Wrap-up

Dayane Araujo

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 experience
    • 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 7 January.

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) by 17 January.

This course has ended

07 - 11 March 2022
£200
Contact
Sophie Spencer

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

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