workflows

[HelenaLC]

(Putting this here for prosperity:) After local discussion, our idea for workflow chapters would be two per part to cover as many different tech/use-cases as possible, specifically:

• seq: Visium, Visium HD (+spatialLIBD)
• img: Xenium, CosMx (single-section or replicated)
• crs:
  • aligned Xenium+Visium (for comparison/integrated analysis)
  • multi-section dataset (for cross-section comparison)

[HelenaLC]

Status:

• seq:
  • Visium (Workflow chapter using Visium breast cancer dataset #42; @estellad)
  • Visium HD (seq - Visium HD workflow #62; open)
• img:
  • Xenium (Workflow chapter using Xenium dataset #43 @estellad)
  • CosMx (img-workflow-cosmx #93; @drighelli, @drisso, @HelenaLC)
• crs:
  • aligned Xenium+Visium (aligned Xenium + Visium workflow #75) (1st draft done by @estellad @HelenaLC)
  • multi-section dataset (open)