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Course Material for "Advanced topics in single-cell transcriptomics"
This repository hosts the course material for the SIB course Advanced topics in single-cell transcriptomics
Teachers:
- Alma Andersson
- Panagiotis Papasaikas
- Rok Roskar
- Mike Smith
- Charlotte Soneson
- Avi Srivastava
- Michael Stadler
Program
| Wednesday, May 27 | |
|---|---|
| 9:00 - 9:30 | Welcome and setup of working environment (C. Soneson)<ul><li>Zoom</li><li>slack workspace</li><li>HackMD document</li><li>Introducing participants (ice breaker)</li></ul> |
| 9:30 - 10:00 | Introduction to Renku (R. Roskar) |
| 10:00 - 10:30 | Introduction to the course (M. Stadler)<ul><li>Course overview, expected background</li><li>Prepare renku workspace</li></ul> |
| 10:30 - 10:45 | Break |
| 10:45 - 11:15 | Combining the best of two worlds: Python + R (introduction, M. Stadler) |
| 11:15 - 11:30 | Break |
| 11:30 - 12:30 | Combining the best of two worlds: Python + R (interactive exercise, M. Stadler) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Python + R (continued) |
| 14:30 - 14:45 | Break |
| 14:45 - 15:30 | Beyond cellranger: Quantification of gene expression (presentation, A. Srivastava) |
| 15:30 - 15:45 | Break |
| 15:45 - 16:45 | Quantification of gene expression (exercises, A. Srivastava) |
| 16:45 - 17:00 | Break |
| 17:00 - 18:00 | Quantification of gene expression (continued) |
| Thursday, May 28 | |
|---|---|
| 9:00 - 10:00 | RNA velocity (presentation, C. Soneson) |
| 10:00 - 10:15 | Break |
| 10:15 - 11:15 | RNA velocity (exercises, C. Soneson) |
| 11:15 - 11:30 | Break |
| 11:30 - 12:30 | RNA velocity (continued) |
| 12:30 - 14:00 | Lunch |
| 14:00 - 15:00 | Spatial transcriptomics (presentation, A. Andersson) |
| 15:00 - 15:15 | Break |
| 15:15 - 16:15 | Spatial transcriptomics (exercises, A. Andersson) |
| 16:15 - 16:30 | Break |
| 16:30 - 17:30 | Spatial transcriptomics (continued) |
| Friday, May 29 | |
|---|---|
| 9:00 - 10:00 | Working with on-disk data formats (presentation, M. Smith) |
| 10:00 - 10:15 | Break |
| 10:15 - 11:15 | Working with on-disk data formats (exercises, M. Smith) |
| 11:15 - 11:30 | Break |
| 11:30 - 12:30 | Working with on-disk data formats (continued) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Deep Generative Networks (presentation and exercises, P. Papasaikas) |
| 14:30 - 14:45 | Break |
| 14:45 - 15:45 | Deep Generative Networks (continued) |
| 15:45 - 16:00 | Break |
| 16:00 - 17:00 | Deep Generative Networks (continued) |
| 17:00 - 17:30 | Wrap-up (feedback form, slack workspace, all) |