Workshop Schedule
The planned schedule for the December 2025 Data Lab Virtual Training Workshop “Advanced Single-Cell RNA-Seq” appears below.
Note: All times are EDT (UTC−04:00).
| Time | Topic | Location |
|---|---|---|
| Day 1 | 2025-12-08 | |
| 12:00 PM | Welcome, Introductions and Getting Started (PDF) | Zoom: Main Session |
| 1:00 PM | Introduction/Refresher to Single-cell Analysis with R and Bioconductor | |
| Single-cell analysis with R slides (PDF) | ||
| Single-cell analysis with R instruction notebook | ||
| 3:30 PM | Questions and introduction to the exercises | Zoom: Breakout Rooms |
| 4:00 PM | Exercises and consultation sessions | Slack channel |
| Resources for consultation sessions | ||
| Exercise: Importing CITE-seq data | ||
| Exercise: Cell type assignment This exercise is available in the scRNA-seq module |
||
| 5:00 PM | Adjourn for the day | |
| Day 2 | 2025-12-09 | |
| 12:00 PM | Integrating multiple scRNA-seq samples | Zoom: Main Session |
| Integration slides (PDF) | ||
| Integration instruction notebook | ||
| 3:30 PM | Questions and introduction to the exercises | Zoom: Breakout Rooms |
| 4:00 PM | Exercises and consultation sessions | Slack channel |
| Resources for consultation sessions | ||
| Exercise: Integration | ||
| 5:00 PM | Adjourn for the day | |
| Day 3 | 2025-12-10 | |
| 12:00 PM | Differential expression analysis with scRNA-seq | Zoom: Main Session |
| Differential expression slides (PDF) | ||
| Differential expression instruction notebook | ||
| 3:30 PM | Questions and introduction to the exercises | Zoom: Breakout Rooms |
| 4:00 PM | Exercises and consultation sessions | Slack channel |
| Resources for consultation sessions | ||
| Exercise: Differential Expression | ||
| 5:00 PM | Adjourn for the day | |
| Day 4 | 2025-12-11 | Zoom: Main Session |
| 12:00 PM | Pathway analysis with scRNA-seq | |
| Pathway analysis slides (PDF) | ||
| 12:30 PM | Pathway analysis: Gene Set Enrichment Analysis (GSEA) | |
| GSEA instruction notebook | ||
| 2:00 PM | Pathway analysis: AUCell | |
| AUCell instruction notebook | ||
| 3:30 PM | Questions and introduction to the exercises | Zoom: Breakout Rooms |
| 4:00 PM | Exercises and consultation sessions | Slack channel |
| Resources for consultation sessions | ||
| Exercise: AUCell | ||
| Exercise: Evaluating cluster quality | ||
| 5:00 PM | Adjourn for the day | |
| Day 5 | 2025-12-12 | |
| 12:00 PM | Consultation sessions | Slack channel |
| 2:30 PM | Participant presentations begin | Zoom: Main Session |
| 5:00 PM | Adjourn |