Virtual course
Single-cell RNA-seq analysis with Python
2027
This course covers the analysis of single-cell RNA sequencing (scRNA-seq) data using Python and command-line tools. You will be guided through droplet-based scRNA-seq analysis pipelines from raw reads to cell clusters. You will then explore and interpret single-cell RNA-seq data using Python as well as the Single Cell Expression Atlas. Finally, you will put your knowledge into practice through a group challenge on the last day.
Virtual course
You 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 you will need to watch, read, or work through to get the most out of the live training event.
In the week before the course, there will be a brief induction session. Computational practicals will be run on EMBL-EBI's virtual training infrastructure, meaning you will not require access to a powerful computer or install complex software on your own machine.
You’ll need to be available between the hours of 09:00 – 17:30 UK time each day of the course. The course trainers will be available to assist, answer questions, and provide further explanations during these times.
Who is this course for?
This course is aimed at wet-lab researchers who are generating, planning on generating, or working with single-cell RNA sequencing data. You are required to have basic experience with a Unix/Linux command line. Basic knowledge of Python is essential.
We recommend these free tutorials:
What will I learn?
Course content
During this course, you will learn about:
- scRNA-seq experimental design
- scRNA-seq analysis pipelines for droplet-based data
- EMBL-EBI Single Cell Expression Atlas Service
- Single-cell data submission
Learning outcomes
After the 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
Trainers
Lizzie Bridget Divala
EMBL-EBI Vinicius Maracaja-Coutinho
Universidad de Chile Jiawei Wang
University of Bath Iris Diana Yu
EMBL-EBI
Programme
Time
Topic
Trainer
Day one – Monday 12 April 2027 – Planning the Experiment
09:00 – 09:45
Introduction to EMBL-EBI and icebreaker
Lizzie Divala
09:45 – 10:00
Break
10:00 – 10:45
Introduction to single cell technologies
Silvie Fexova
10:45 – 12:30
Wet and dry lab overview
Marisa Loach and Kayleigh Smith
12:30 – 13:30
Lunch break
13:30 – 15:15
Experimental design (lecture and Q&A)
Tallulah Andrews
15:15 – 15:30
Break
15:30 – 16:30
Getting set up: data set, workflow, and environment setup
Iris Yu
Day two – Tuesday 13 April 2027
09:00 – 10:30
Raw reads to expression matrix (lecture and practicals)
Jinzheng Ren and Jiawei Wang
10:30 – 10:45
Break
10:45 – 12:00
QC, pre-processing, and, normalisation (lecture and practicals)
Iris Yu
12:00 – 13:00
Lunch break
13:00 – 13:45
QC, pre-processing, and normalisation (practicals continued.)
Iris Yu
13:45 – 15:45
Batch correction and data set integration (lecture and practicals)
Jinzheng Ren, Daniel Guerrero Romero, and Brandon Schellhaas
15:45 – 16:00
Break
16:00 – 16:45
Posters and networking
Day three – Wednesday 14 April 2027 – Analysing data
09:00 – 10:00
Dimensionality reduction, clustering, and annotation (lecture and practicals)
Jinzheng Ren, Daniel Guerrero Romero, and Brandon Schellhaas
10:00 – 10:15
Break
10:15 – 11:15
Dimensionality reduction, clustering, and annotation (practicals continued)
Jinzheng Ren, Daniel Guerrero Romero, and Brandon Schellhaas
11:15 – 12:30
Differential expression and abundance analysis (lecture and Q&A)
Andrian Yang
12:30 – 13:30
Lunch break
13:30 – 14:30
Differential expression (practical)
Andrian Yang
14:30 – 15:30
Abundance analysis (practical)
Andrian Yang
15:30 – 16:30
Posters and networking
Day four – Thursday 15 April 2027 – Applying the pipeline
09:00 – 10:00
Multi-omics (lecture and Q&A)
Vinicius Maracaja-Coutinho
10:10 – 10:15
Break
10:15 – 11:15
scATAC-seq (lecture and Q&A)
Garth Ilsey
11:15 – 12:15
The state of the art and the future of single-cell transcriptomics (lecture and Q&A)
TBC
12:15 – 13:00
Lunch break and group photo
13:00 – 14:00
Single-cell resources at EMBL-EBI
Liora Vilmovsky
14:00 – 15:00
Project work
Project mentors
15:00 – 15:30
Break
15:30 – 16:00
Project work
Project mentors
Day five – Friday 16 April 2027
09:00 – 10:00
Project work
Project mentors
10:00 – 10:20
Break
10:20 – 12:00
Project work
Project mentors
12:00 – 13:00
Lunch break
13:00 – 14:00
Project work wrap-up
Project mentors
14:00 – 15:00
Final Q&A with project mentors
15:00 – 15:30
Course wrap-up and feedback
Lizzie Divala
You will need to submit all your documents during the application process by 23:59 UK time on 10 January 2027.
You will then be informed of the status of your application (successful, waiting list, unsuccessful) by 22 January 2027.
If you have any questions regarding the application process, please contact your Event Organiser, Toke Labiyi.
Posters
If selected for this course, you will be asked to submit your poster upon registration. We expect the posters to act as a talking point between you, other attendees, 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 group.
Registration fees
Payment must be completed within 14 days of receiving your acceptance email. Failure to do so may result in your place being offered to someone else on the waitlist.
Your registration fee includes:
- access to the full five-day course programme
- access to a bespoke online course handbook
- secure community space on Slack
- virtual machine to work on that is accessed via the internet
- dedicated online support team
- certificate on completion of the course
Academia
£250.00
Industry*
£350.00
* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your Event Organiser for more information.
Financial assistance
Financial assistance is available to a limited number of participants attending this course. For full details, please refer to our dedicated support page for information on available fee waivers, travel grants, and financial assistance.
Accessibility
The EMBL-EBI Training team is committed to making our events inclusive and accessible to all participants. Please read our dedicated support page to find out how we may be able to support you with any accessibility requirements.
Event terms and conditions
By applying and registering for events hosted by EMBL-EBI Training, you are adhering to our terms and conditions. We recommend that you read through these before submitting your details.
Course materials
The materials for the 2026 course are available for you to browse. These provide a snapshot of the content that will be covered in the 2027 course..
EMBL-EBI
Universidad de Chile
University of Bath
EMBL-EBI
Programme
Time | Topic | Trainer |
Day one – Monday 12 April 2027 – Planning the Experiment | ||
09:00 – 09:45 | Introduction to EMBL-EBI and icebreaker | Lizzie Divala |
09:45 – 10:00 | Break | |
10:00 – 10:45 | Introduction to single cell technologies | Silvie Fexova |
10:45 – 12:30 | Wet and dry lab overview | Marisa Loach and Kayleigh Smith |
12:30 – 13:30 | Lunch break |
|
13:30 – 15:15 | Experimental design (lecture and Q&A) | Tallulah Andrews |
15:15 – 15:30 | Break | |
15:30 – 16:30 | Getting set up: data set, workflow, and environment setup | Iris Yu |
Day two – Tuesday 13 April 2027 | ||
09:00 – 10:30 | Raw reads to expression matrix (lecture and practicals) | Jinzheng Ren and Jiawei Wang |
10:30 – 10:45 | Break | |
10:45 – 12:00 | QC, pre-processing, and, normalisation (lecture and practicals) | Iris Yu |
12:00 – 13:00 | Lunch break |
|
13:00 – 13:45 | QC, pre-processing, and normalisation (practicals continued.) | Iris Yu |
13:45 – 15:45 | Batch correction and data set integration (lecture and practicals) | Jinzheng Ren, Daniel Guerrero Romero, and Brandon Schellhaas |
15:45 – 16:00 | Break | |
16:00 – 16:45 | Posters and networking | |
Day three – Wednesday 14 April 2027 – Analysing data | ||
09:00 – 10:00 | Dimensionality reduction, clustering, and annotation (lecture and practicals) | Jinzheng Ren, Daniel Guerrero Romero, and Brandon Schellhaas |
10:00 – 10:15 | Break |
|
10:15 – 11:15 | Dimensionality reduction, clustering, and annotation (practicals continued) | Jinzheng Ren, Daniel Guerrero Romero, and Brandon Schellhaas |
11:15 – 12:30 | Differential expression and abundance analysis (lecture and Q&A) | Andrian Yang |
12:30 – 13:30 | Lunch break |
|
13:30 – 14:30 | Differential expression (practical) | Andrian Yang |
14:30 – 15:30 | Abundance analysis (practical) | Andrian Yang |
15:30 – 16:30 | Posters and networking |
|
Day four – Thursday 15 April 2027 – Applying the pipeline | ||
09:00 – 10:00 | Multi-omics (lecture and Q&A) | Vinicius Maracaja-Coutinho |
10:10 – 10:15 | Break |
|
10:15 – 11:15 | scATAC-seq (lecture and Q&A) | Garth Ilsey |
11:15 – 12:15 | The state of the art and the future of single-cell transcriptomics (lecture and Q&A) | TBC |
12:15 – 13:00 | Lunch break and group photo |
|
13:00 – 14:00 | Single-cell resources at EMBL-EBI | Liora Vilmovsky |
14:00 – 15:00 | Project work | Project mentors |
15:00 – 15:30 | Break |
|
15:30 – 16:00 | Project work | Project mentors |
Day five – Friday 16 April 2027 | ||
09:00 – 10:00 | Project work | Project mentors |
10:00 – 10:20 | Break |
|
10:20 – 12:00 | Project work | Project mentors |
12:00 – 13:00 | Lunch break |
|
13:00 – 14:00 | Project work wrap-up | Project mentors |
14:00 – 15:00 | Final Q&A with project mentors |
|
15:00 – 15:30 | Course wrap-up and feedback | Lizzie Divala |
You will need to submit all your documents during the application process by 23:59 UK time on 10 January 2027.
You will then be informed of the status of your application (successful, waiting list, unsuccessful) by 22 January 2027.
If you have any questions regarding the application process, please contact your Event Organiser, Toke Labiyi.
Posters
If selected for this course, you will be asked to submit your poster upon registration. We expect the posters to act as a talking point between you, other attendees, 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 group.
Registration fees
Payment must be completed within 14 days of receiving your acceptance email. Failure to do so may result in your place being offered to someone else on the waitlist.
Your registration fee includes:
- access to the full five-day course programme
- access to a bespoke online course handbook
- secure community space on Slack
- virtual machine to work on that is accessed via the internet
- dedicated online support team
- certificate on completion of the course
Academia | £250.00 |
Industry* | £350.00 |
* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your Event Organiser for more information.
Financial assistance
Financial assistance is available to a limited number of participants attending this course. For full details, please refer to our dedicated support page for information on available fee waivers, travel grants, and financial assistance.
Accessibility
The EMBL-EBI Training team is committed to making our events inclusive and accessible to all participants. Please read our dedicated support page to find out how we may be able to support you with any accessibility requirements.
Event terms and conditions
By applying and registering for events hosted by EMBL-EBI Training, you are adhering to our terms and conditions. We recommend that you read through these before submitting your details.
Course materials
The materials for the 2026 course are available for you to browse. These provide a snapshot of the content that will be covered in the 2027 course..