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.

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 posters on their research topics.

Virtual course

This course will now be held virtually, it was previously advertised as an on-site course. Hybrid options are not currently available. We reserve the right to change the format of this course or cancel it, due to the ongoing coronavirus pandemic.

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.

Trainers will be available to assist, answer questions, and provide further explanations during the course.

Who is this course for?

This course is aimed at researchers with little-to-no experience in big data analysis who are generating, planning on generating, or working with single-cell RNA sequencing data.
 

Participants may also be asked to do brief coding in R or Python. 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/ 

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


There are many packages for analysing single cell data – Seurat Satija et al. 2015, Scanpy Wolf et al. 2018, Monocle Trapnell et al. 2014, Scater McCarthy et al. 2017, and so forth. We’re working with Scanpy, because currently Galaxy hosts the most Scanpy tools of all of those options.

Course content

During this course you will learn about:

  • Single cell RNA-seq experimental design
  • Galaxy scRNA-seq pipeline

Trainers

Wendi Bacon
The Open University
Nancy George
EMBL-EBI
Silvie Korena Fexova
EMBL-EBI
Zhichao Miao
EMBL-EBI
Mehmet Tekman
Albert-Ludwigs-Universität Freiburg
Iris Diana Yu
EMBL-EBI
Julia Jakiela
University of Edinburgh
Iguaracy Pinheiro de Sousa
EMBL-EBI

Programme

All times in the programme are listed in GMT.

Time

Topic

Trainer

Day one  Monday 6 February 2023

09:00 – 09:45

Welcome and introduction to EMBL-EBI

Dayane Araújo

09:45 10:00

Break

 

10:00 – 11:00

Keynote

TBC

11:00 – 12:00

Library generation: overview

Wendi Bacon

12:00 13:00

Lunch break

 

13:00 – 14:30

Pipeline overview

Wendi Bacon

14:30 – 15:00

Introduction to Galaxy

 

15:00 15:30

Break

 

15:30 – 16:30

Practical one: introduction to Galaxy

Pablo Moreno

16:30

End of the day 

 

Time

Topic

Trainer

Day two Tuesday 7 February 2023

09:00 – 10:00

From fasta to matrix

Iris Diana Yu

10:00 10:30

Break

 

10:30 – 12:00

Practical two: from fasta to matrix

Iris Diana Yu

12:00 13:00

Lunch break

 

13:00 – 15:30

Practical two: from fasta to matrix

Iris Diana Yu

15:30 16:00

Break

 

16:00 – 16:30

Networking

 

16:30

End of the day

 

Time

Topic

Trainer

Day three Wednesday 8 February 2023

09:00 – 10:00

Experimental design of single-cell studies

TBC

10:00 10:30

Break

 

10:30 – 11:30

Pre-processing and batch correction

Zhichao Miao

11:30 – 12:00

Networking

 

12:00 13:00

Lunch break

 

13:00 – 15:00

Practical three: filter, plot, and explore

Wendi Bacon

15:00 15:30

Break

 

15:30 – 16:30

Practical three: filter, plot, and explore

Wendi Bacon

16:30

End of the day

 

Time

Topic

Trainer

Day four Thursday 9 February 2023

09:00 – 10:00

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

Simone Webb

10:00 10:30

Break

 

10:30 – 12:00

Practical four: trajectory analysis using Python

Wendi Bacon

12:00 13:00

Lunch break

 

13:00 – 14:00

Practical four: Monoclone3 for trajectory analysis

Julia Jakiela

14:00 –15:30

Practical five: bulk deconvolution 

Mehmet Tekman

15:30 16:00

Break

 

16:00 –17:00

Designing your analysis

Iguaracy Pinheiro de Sousa 

17:00

End of the day

 

Time

Topic

Trainer

Day five  Friday 10 February 2023

09:00 – 10:30

Single-cell data submission 

Single cell Expression Atlas team

10:30 11:00

Break

 

11:00 – 12:00

Single-cell expression atlas

Single cell Expression Atlas

12:00 13:00 

Lunch break and group photo

 

13:00 – 13:30

Closing remarks

 

13:30

End of the day

 

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 23:59 on 27 November 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 12 December 2022. If you have any questions regarding the application process please contact Jane Reynolds.

Course materials

The course materials from the 2022 edition of the course are now live and available for you to use. They provide a mixture of pre-recorded lectures, presentations, and practicals from the course, and will give you a snapshot of what to expect in the 2023 edition.

Posters

All participants are expected to present a poster virtually. Successful applicants will be provided with further information and asked to submit this upon registration. 

We expect the posters to act as a talking point between you, other participants and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the gathered participants.

 

Applications closed
27 November 2022

06 - 10 February 2023
Online
£200.00
Contact
Jane Reynolds
Open application with selection
35 places

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

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