Topic outline

  • Advance topics in single-cell transcriptomics

    Streamed from Basel and other places, 27 - 29 May 2020

    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact training@sib.swiss


  • Program

    • Course material


      Wednesday, May 27

      9:00 - 10:30

      Welcome and Introduction (all)


      • Course overview, expected background
        (R/python, single cell analysis workflow links, M. Stadler)

      • Introducing participants (“ice breaker”, polls, …, C. Soneson)

      • Setup of working environment

        • Slack workspace

        • Zoom (M. Stadler, C. Soneson, P. Papasaikas)

        • Renkulab (TBD)

      10:30 - 10:45

      Break

      10:45 - 11:30

      Combining the best of two worlds: Python + R
      (interactive exercise, M. Stadler)

      11:30 - 11:45

      Break

      11:45 - 12:30

      Combining the best of two worlds: Python + R (continued)

      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)