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) Zoom slack workspace HackMD document Introducing participants (ice breaker)
9:30 - 10:00	Introduction to Renku (R. Roskar)
10:00 - 10:30	Introduction to the course (M. Stadler) Course overview, expected background Prepare renku workspace
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)