Single-cell RNA-seq & network analysis using Galaxy and Cytoscape
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 cell cluster comparisons. In addition to running a basic pipeline, participants will explore single cell networks using Cytoscape.
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 discussion about their research challenges and problems with each other and the trainers at the ‘Talk with Trainers’.
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 08:00-17:30 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?
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
- Generate a network using Cytoscape and marker genes list from scRNA-seq analysis
Participants will be using a Galaxy resource in-depth. Participants may also be asked to do brief coding in R. Please ensure that you complete the free tutorials 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/
During this course you will learn about:
- Single cell RNA-seq experimental design
- Galaxy scRNA-seq pipeline
- Cytoscape network analysis
Wellcome Sanger Institute
University of Glasgow
The University of Edinburgh
University of California, San Francisco
|08:30 - 10:00||Keynote Lecture: Introduction to scRNA-seq Technologies||Kerstin Meyer|
|10:00 - 10:15||Break|
|10:15 - 11:00||Welcome to EMBL-EBI & Introductions!||Dayane Araújo|
|11:00 - 12:00||Q&A with Kerstin Meyer||Kerstin Meyer|
|13:00 - 14:00||Library Generation - Overview||Wendi Bacon|
|14:00 - 14:30||Introduction to Galaxy||Pablo Moreno|
|14:30 - 15:00||Q&A with Pablo Moreno||Pablo Moreno|
|15:00 - 15:30||Lightning Talks A|
|15:30 - 16:00||Break|
|16:00 - 17:30||Practical 1: Introduction to Galaxy||Pablo Moreno|
|08:00 - 09:00||Keynote Lecture: Applied scRNA-seq||Kristina Kirschner|
|09:00 - 10:30||Pipeline Overview||Wendi Bacon|
|10:30 - 11:00||Break|
|11:00 - 12:00||Experimental Design||Kristina Kirschner|
|13:00 - 14:00||Q&A with Kristina Kirschner||Kristina Kirschner|
|14:00 - 14:30||From Fasta to Matrix||Jonathan Manning|
|14:30 - 15:00||Q&A with Jonathan Manning||Jonathan Manning|
|15:00 - 15:30||Lightning Talks B|
|15:30 - 16:00||Break|
|16:00 - 18:00||Practical 2: From Fasta to Matrix||Jonathan Manning|
|08:00 - 09:00||Pre-processing & batch correction||Zhichao Miao|
|09:00 - 09:15||Morning Challenge||Wendi Bacon|
|09:15 - 10:00||Q&A with Zhichao Miao||Zhichao Miao|
|10:00 - 12:00||Practical 3: Pre-processing & batch correction||Wendi Bacon|
|13:00 - 14:00||Clustering, annotation and pseudotime inference tools for scRNA-seq data – a quick guide||Simone Webb|
|14:00 - 14:45||Q&A with Simone||Simone Webb|
|14:45 - 15:15||Lightning Talks C|
|15:15 - 15:45||Break|
|15:45 - 18:00||Practical 4: Cluster annotation & trajectories||Wendi Bacon|
|09:00 - 10:15||Designing your Analysis and Q&A||Tamir Chandra|
|10:15 - 10:45||Break|
|10:45 - 12:00||Network Analysis||Scooter Morris|
|13:00 - 14:00||Network Analysis Activity||Scooter Moris|
|14:00 - 15:00||Q&A with Scooter Morris||Scooter Moris|
|15:00 - 15:30||Break|
|15:30 - 17:30||Cytoscape Exploration||Scooter Moris|
|09:00 - 11:00||Talk to the trainers - Breakout chats||Kristina Kirschner, Tamir Chandra, Pablo Moreno, Jonathan Manning, Simone Webb, Zhichao Miao, Scooter Morris|
|11:00 - 11:15||Break|
|11:15 - 12:00||Cytoscape Exploration - Continued||Scooter Morris|
|13:00 - 14:00||Cytoscape Exploration - Continued||Scooter Morris|
|14:00 - 14:45||Future of Cytoscape||Scooter Morris|
|14:45 - 15:00||Wrap-up & Survey||Dayane Araújo|
Please note minor changes to the programme may occur.
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 history
- 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 midnight on Friday 26th February 2021.
Incomplete applications will not be considered.
All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by Friday 12th March 2021. If you have any questions regarding the application process please contact Meredith Willmott ( email@example.com ).
Participant 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. Further details will be provided following registration