Day 3

Morning

• Lecture: Dimensionality reduction 2 (UMAP) and graph-based clustering
• Lecture: Cell type annotation
• Practical work: Dimensionality reduction, clustering, cell type annotation
  • (uses the same notebook as the Day 2 exercises)
  • Automated cell type annotation will be performed with celltypist

Afternoon

• Practical work: Cell states - looking for stressed cells
  • stressed cells exercises - python
  • stressed cells exercises - R
• Practical work: Producing a “publication ready” figure of all results obtained to here (see here for general instructions and here for additional tips and tricks for R users)