This workshop is organised into a number of semi-independant modules;

  1. Setup : Load a preprocessed dataset, and libraries needed for the analysis.
  2. Explore : Inspect the dataset - what does it look like?
  3. Differential Expression: By Celltype : What genes are expressed differently between conditions, in different celltypes.
  4. Differential Expression: By Niche : Define different tissue niches by regional gene expressesion; Then identify genes that change in these regions by condition.
  5. Differential Expression: By localisation: What genes are expressed differently when a celltype is localised in different tissue niches?
  6. Celltype co-occurances : Do celltypes co-localise with other celltypes, in a manner than changes with condition?