Analyse and interpret single-cell RNA-seq (scRNA-seq) data with Bioconductor: quality control, normalisation, dimensionality reduction, clustering, cell-type annotation, and working at scale. We’ll combine short talks with hands-on exercises using reproducible RStudio Projects and the SingleCellExperiment ecosystem.
Pre-requisites: Familiarity with R and Bioconductor. Familiarity with bulk RNA-seq concepts is helpful but not required.
Instructors: Robert Ivánek, Mireia Ramos, Kevin Rue-Albrecht
Dates: Monday and Tuesday, 15–16 September 2025
Venue: School of Medicine and Life Sciences, Universitat Pompeu Fabra (UPF), Barcelona.
Room: 232
Coffee Break and Lunch:
- Day 1 (Monday): Served on floor -1
- Day 2 (Tuesday): Served in the lobby in front of the cafeteria
All participants are expected to follow the Bioconductor Code of Conduct.
Subject to change.
| Time | Session | Instructor(s) |
|---|---|---|
| 08:30–09:00 | Setup help | All |
| 09:00–09:15 | Welcome | Robert C & Maria |
| 09:15–10:30 | Introduction to Bioconductor & SCE | Kevin |
| 10:30–11:00 | Coffee break | |
| 11:00–13:00 | Exploratory data analysis & quality control | Kevin |
| 13:00–14:00 | Lunch | |
| 14:00–15:30 | Exploratory data analysis (continued) | Kevin |
| 15:30–15:45 | Comfort break | |
| 15:45–16:45 | Cell-type annotation | Robert |
| 16:45–17:00 | Wrap-up and Q&A | All |
| Time | Session | Instructor(s) |
|---|---|---|
| 08:30–09:00 | Helpdesk | All |
| 09:00–09:15 | Recap and Q&A | Robert & Kevin |
| 09:15–10:30 | Multi-sample analyses | Robert |
| 10:30–11:00 | Coffee break | |
| 11:00–13:00 | Multi-sample analyses (continued) | Robert |
| 13:00–14:00 | Lunch | |
| 14:00–15:30 | Working with large data | Kevin |
| 15:30–15:45 | Comfort break | |
| 15:45–16:45 | Accessing Human Cell Atlas data | Mireia |
| 16:45–17:00 | Wrap-up and feedback | All |
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