Overview#
Welcome to the GSCN Workshop materials! This book contains the workshop materials organized by day:
Each day contains its own set of notebooks and materials for the workshop.
Before the event#
Tech setup#
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.
Syllabus#
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 |
|
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 |
09:30 – 11:30 |
Talk: “Foxa2 pioneers enteroendocrine lineage recruitment from |
|
10:00 – 11:30 |
Option A) Reproduce published figures |
|
Option B) Discuss your own data/analysis |
||
11:30 – 12:00 |
Results / Feedback |