In addition to the actual workshop, we offer two pre-workshop sessions designed to help participants with any issues installing software required for the workshop. During these, we also encourage participants to ask questions about basic Python/Jupyter Notebook usages (the notebook discussed in these sessions can be found here). The two sessions take place on:
- Wednesday (02.04.2025), 15:00 - 17:00 CET
- Thursday (03.04.2025), 15:30 - 17:30 CET
The Zoom links to these events can be found in the mail sent on Sunday, 30.03.2025. If you have any other questions, please direct them to the 2025-04: Workshop GSCN > pre-workshop support Zulip channel.
Note: Schedule subject to minor adjustments.
| Date | Time | Activity |
|---|---|---|
| Monday, 07.04.2025 | 09:00 – 09:15 | Welcome & Introduction to the Workshop |
| 09:15 – 10:00 | Talk: "An in-depth look at AnnData" by Ilan Gold | |
| 10:00 – 11:30 | 1) Basic pre-processing of scRNA-seq data | |
| 2) Batch effect correction | ||
| 3) Downstream analysis | ||
| 11:30 - 12:00 | Hands-on coding & Troubleshooting | |
| 12:00 – 13:00 | Lunch | |
| 13:00 – 13:30 | Intro to "Trajectory analysis" | |
| 13:30 – 13:40 | Break | |
| 13:40 – 15:20 | Trajectory analysis | |
| 15:20 – 15:40 | Break | |
| 15:40 – 17:30 | Trajectory analysis | |
| 19:00 - tbd | Dinner at Porta Nova (Robert-Koch-Platz 12) | |
| Tuesday, 08.04.2025 | 09:00 – 09:30 | Recap and Q&A, tech setup for spatial workshop |
| 09:30 – 10:00 | Talk: "Clonal dynamics and mitochondrial genetics through the lens of single-cell multi-omics" by Leif Ludwig |
|
| 10:00 – 11:30 | 1) Ligand-receptor interaction analysis | |
| 2) Differential cellular abundance | ||
| 11:30 - 12:00 | Hands-on coding & Troubleshooting | |
| 12:00 – 13:00 | Lunch | |
| 13:00 – 13:30 | Intro to "Spatial Omics" | |
| 13:30 – 13:40 | Break | |
| 13:40 – 15:20 | Spatial preprocessing & analysis | |
| 15:20 – 15:40 | Break | |
| 15:40 – 17:30 | Spatial preprocessing & analysis | |
| 20:00 - tbd | Dinner (self-organised) | |
| Wednesday, 09.042025 | 09:00 – 09:30 | Talk: “Spatiotemporal dynamics of tumor development in a novel triple-negative breast cancer model" by Tancredi Massimo Pentimalli |
| 09:30 – 11:30 | Talk: "Foxa2 pioneers enteroendocrine lineage recruitment from intestinal stem cells" by Michael Sterr |
|
| 10:00 – 11:30 | Option A) Reproduce published figures | |
| Option B) Discuss your own data/analysis | ||
| 11:30 – 12:00 | Results / Feedback |