Tutorials

Contents:

• A tiny simulation
  • Data generation
  • Run Steamboat
• Ovarian cancer data analysis
  • Load data
  • Train a Steamboat model
  • Metagene interpretation: cell types and states
  • Attention map interpretation: Cell-cell interaction
  • Misc visuals
• Train on mouse brain data
• Interpret the results on mouse brain data
  • Astro-Epen in different regions
  • Head weights
  • Clustering and spatial domain segmentaiton
  • Ligand-receptor analysis
  • Interpretation of global attention
• Spatial perturbation tasks on mouse brain data
  • Spatial perturbation scenario 1: transplanting cells
  • Spatial perturbation scenario 2: changing environment.
• Investigating Global Attention and Prognosis on Colorectal CODEX data
  • Process dataset
  • Train model
  • Global attention interpretation
  • Survival analysis
  • Misc visualization
• Evaluating Spatial Perturbation Prediction on Perturb-FISH Data
• Generalization of Steamboat to Slide-tags Data
  • Load data
  • Train Steamboat model
  • Clustering and evaluation
  • Domain segmentation
  • Infer cell-cell interactions
  • List known L-R pairs
  • Analyze contribution of heads and scales
• Selecting number of heads on Slide-tags Data
  • Load data
  • Train Steamboat model
• Generalization of Steamboat to Visium Data
  • Load data
  • Train Steamboat model
  • Find spatial domains