SPC analysis

This section contains a pipeline for spatial proximity-based clustering (SPC) to group similar cells into the same clusterbased on both transcriptional similarity and spatial proximity, as well as downstream analyses.

• SPC Pipeline
  • Usage
  • Example workflow:
    • step1: first round of unsupervised clustering to generate cell attributes
    • step2: perform SPC non-continuous segmentation based on the first round leiden clusters
    • step3: second round of unsupervised clustering on spc cells
    • visualization of SPC on deconvolved cells
  • Limited
  • Citation
• Cell-cell connection estimation
• CellCellColocation3D Pipeline
  • Usage
  • Reference
• Meta-Niche
  • For custom usage
  • Further extending
• Digital Lineage Tracing Pipeline
  • Digital Lineage Tracing
    • workflow
      • Step 01
        • example of in.lst
      • Step 02
      • Step 03
      • Step 04
  • Sankey Plot
    • Sankey Plot