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:
- Introduction to Galaxy: https://galaxyproject.org/tutorials/g101/
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
The Open University
The University of Edinburgh
University of Glasgow
EMBL-EBI
Wellcome Sanger Institute
EMBL-EBI
EMBL-EBI
Albert-Ludwigs-Universität Freiburg
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.