https://github.com/scverse/202504_workshop_gscn
https://github.com/scverse/202504_workshop_gscn
Last synced: 3 months ago
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- Host: GitHub
- URL: https://github.com/scverse/202504_workshop_gscn
- Owner: scverse
- Created: 2025-03-06T15:08:17.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-04-17T20:38:49.000Z (about 1 year ago)
- Last Synced: 2025-04-18T10:39:27.840Z (about 1 year ago)
- Language: Jupyter Notebook
- Size: 108 MB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 11
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Metadata Files:
- Readme: README.md
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README
# Overview
## 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](https://github.com/scverse/202504_workshop_GSCN/blob/main/misc/pre-workshop/pre_workshop_session.ipynb)). 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](https://scverse.zulipchat.com/#narrow/channel/493335-2025-04.3A-Workshop-GSCN/topic/pre-workshop.20support/with/509718455) 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](https://github.com/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](https://www.tripadvisor.de/Restaurant_Review-g187323-d2456707-Reviews-Porta_Nova-Berlin.html) ([Robert-Koch-Platz 12](https://maps.app.goo.gl/wFXHXyAk1Fdkpf658)) |
| | | |
| **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](https://www.mdc-berlin.de/de/person/dr-med-dr-rer-nat-leif-s-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](www.linkedin.com/in/tancredi-massimo-pentimalli) |
| | 09:30 – 11:30 | Talk: "Foxa2 pioneers enteroendocrine lineage recruitment from
intestinal stem cells" by [Michael Sterr](https://www.helmholtz-munich.de/en/pi-3-20) |
| | 10:00 – 11:30 | Option A) Reproduce published figures |
| | | Option B) Discuss your own data/analysis |
| | 11:30 – 12:00 | Results / Feedback |