Day 5

All day

On the last day, you hopefully have the tools to get started with work on your own datasets. We are available for all questions and support. Alternatively, or if you do not have your own project data yet, you are welcome to choose one of the challenges below (or come up with your own!).

• Option 1: Doublet detection in PBMCs
• Option 2: Trajectory inference in the bone marrow
• Option 3: Try playing with a CITE-Seq dataset using a public tutorial
  • Seurat’s WNN tutorial
  • muon’s WNN tutorial (scanpy-compatible python multiomics package)
• Option 4: Download and analyze the mystery dataset
  • Analyze the dataset according to the workflow we have practiced, paying attention to the following questions:
    • What species and tissue is represented in this dataset?
    • How many cells are in there?
    • Which cell types can you identify?
    • Look at the mitochondrial fraction of reads in this dataset. Is this in line with your expectations for this tissue? What could be special about this dataset?