Tutorials

• MESA Ecospatial Tutorials (Murine Spleen, CODEX)
  • Read Data
  • Customise colour palette
  • Selecting the scale for spatial tessellation
  • Perform Ecospatial Analysis on one sample
    • Calculate MDI
    • Diversity Heatmap Related Analysis
  • Perform Ecospatial Analysis on all samples
    • Calculate MDI
    • Calculate GDI
    • Calculate DPI
    • Calculate Global Cell Frequency & Cell Co-Occurrence
    • Calculate Cell Frequency and Cell Co-Occurrence in hot/coldspots
    • Process Cell Co-Occurrence Dataframe
    • Cell Co-Occurrence Circle Plot
• MESA Ecospatial Tutorials (Colorectal Cancer, CODEX)
  • Read Data
  • Customise colour palette
  • Selecting the scale for spatial tessellation
  • Perform Ecospatial Analysis on one sample
    • Diversity Heatmap Related Analysis
  • Perform Ecospatial Analysis on all samples
    • Calculate MDI
    • Calculate GDI
    • Calculate DPI
    • Calculate Global Cell Frequency & Cell Co-Occurrence
    • Calculate Cell Frequency and Cell Co-Occurrence in hot/coldspots
    • Process Cell Co-Occurrence Dataframe
    • Cell Co-Occurrence Circle Plot
• MESA Ecospatial Tutorials (hepatocellular carcinoma, CosMx)
  • Helper functions
  • Read Data
  • Perform Ecospatial Analysis on one sample
  • Perform Ecospatial Analysis on all samples
    • Calculate Global Cell Frequency & Cell Co-Occurrence
    • Calculate Cell Frequency and Cell Co-Occurrence in hot/coldspots
    • Process Cell Co-Occurrence Dataframe
    • Cell Co-Occurrence Circle Plot
• MESA Multiomics Tutorials
  • Prepare Data for Multiomics Integration
  • Multiomics Integration
    • Step I: preparations
    • Step II: finding initial pivots
    • Step III: finding refined pivots
    • Step IV: propagation
  • Neighborhood Characterization
    • Cellular Composition-based Neighborhoods
    • MESA’s Local Average Protein Expression-based Neighborhoods
    • MESA’s Local Average mRNA Expression-based Neighborhoods
    • Neighborhood Heatmap
• Using MESA in R
  • Loading Packages
  • Read and prepare data
  • Calculate MDI
  • Perform statistical test and plot results