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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)
  • 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)