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


  • 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)