Single Cell RNA-seq Analysis Using R

Date:

 Monday 5 Friday 9 October 2020

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application opens: 

Tuesday 11 February 2020

Application deadline: 

Friday 05 June 2020

Participation: 

Open application with selection

Contact: 

Meredith Willmott

Registration fee: 

£300 - Including meals and accommodation

Overview

This course covers the analysis of scRNA-seq data using R and command line tools. Participants will be guided through both droplet-based and plate-based scRNA-seq analysis pipelines from raw reads to cell clusters. They will explore and interpret data using R as well as the Human Cell & Single Cell Expression Atlases. Finally participants will put their knowledge into practice through a group challenge on the final two days.

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.

Audience

This course is aimed at 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 18 operating system and the R statistical packages. We recommend these free tutorials:



Syllabus, tools and resources

During this course you will learn about:

  • Single cell RNA-seq experimental design
  • scRNA-seq analysis pipelines for smart-seq and droplet-based data
  • EMBL-EBI Single Cell Expression Atlas Service
  • Human Cell Atlas data & Metadata standards
  • General principles of data management, data FAIRification and best practice for generating and working with single cell RNA sequencing and image-based transcriptomics data

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

Additional information

Accommodation will be provided at the Wellcome Genome Campus Conference Centre, Monday-Friday.  Please contact the Wellcome Genome Campus Conference Centre directly if you wish to arrange to stay additional nights around the course dates. 

All participants are expected to present a poster that will be displayed during the course outside the training room. Please send your poster in PDF format to Meredith Willmott (meredith@ebi.ac.uk) and we will print it on campus. 
All posters should:

  • be A2 in size - 420mm x 594 mm
  • be in a portrait orientation
  • include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. 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.

Programme

Day 1 – Monday 5 October 2020
Planning the Experiment
09:45-10:30 Arrival, Registration & Refreshments  
10:30-11:15 Welcome to EMBL-EBI & Introductions Wendi Bacon
11:15-12:00 Droplet-based Library Generation Overview Wendi Bacon
12:00-13:00 Experimental Design Tallulah Andrews
13:00-14:00 Lunch  
14:00-15:00 Keynote Lecture Tallulah Andrews
15:00-15:45 Getting set up - Infrastructure terms Xiaohui Zhao
15:45-16:15 Break  
16:15-18:15 Pipeline Overview Wendi Bacon
18:15 End of day  
19:15 Evening meal Hinxton Hall Restaurant
Day 2 – Tuesday 6 October 2020
Processing Data
09:00-09:15 Questions & Review Wendi Bacon
09:15-10:00 Dealing with Data Alex Holinski
10:00-10:45 FAIR Principles HCA Team
10:45-11:00 Lightning Talks A  
11:00-11:30 Break  
11:30-12:45 Raw Reads to Expression Matrix Xiaohui Zhao
12:45-13:00 Lightning Talks B  
13:00-14:00 Lunch  
14:00-15:00 Raw Reads to Expression Matrix Xiaohui Zhao
15:00-15:45 Cleaning the Expression Matrix & Batch Correction To be confirmed
15:45-16:00 Lightning Talks C  
16:00-16:30 Break  
16:30-18:30 Cleaning the Expression Matrix & Batch Correction To be confirmed
18:30 End of day  
19:00 Evening meal Hinxton Hall Restaurant
Day 3 – Wednesday 7 October 2020
Analysing Data
09:00-09:15 Questions & Review Wendi Bacon
09:15-11:00 Dimensionality Reduction Rasa Elmentaite
11:00-11:30 Break  
11:30-13:00 Identifying Marker Genes & Cluster Annotation Rasa Elmentaite
13:00-14:00 Lunch  
14:00-16:00 So I have some genes...what's next? Elo Madissoon
16:00-16:30 Break  
16:30-17:15 So I have some genes...what's next? Elo Madissoon
17:15-18:15 Designing your Analyses Tallulah Andrews
18:15-18:45 Discussion  
18:45 End of day  
19:15 Evening meal Hinxton Hall Restaurant
Day 4 – Thursday 8 October 2020
Applying the Pipeline
09:00-09:15 Questions & Review Wendi Bacon
09:15-11:00 Group Challenge Elo Madissoon
11:00-11:30 Break  
11:30-13:00 Diagnosing Dodgy Data To be confirmed
13:00-14:00 Lunch  
14:00-15:45 Group Challenge Elo Madissoon
15:45-16:15 Break  
16:15-18:00 Cell Atlases & Interpretation HCA & Gene Expression Teams
18:00 End of day  
18:30 Evening meal Red Lion Pub
Day 5 – Friday 9 October 2020
Applying the Pipeline
09:00-11:00 Group Challenge Elo Madissoon
11:00-11:30 Break  
11:30-13:00 Group Challenge Elo Madissoon
13:00-13:15 Wrap-up and Feedback Wendi Bacon
13:15-14:00 Lunch  
14:00 Bus to Cambridge