Examples

Contents

• Step by step tutorial
  • Prepare
    • The hardware environment used for this tutorial
      • CPU
      • GPU
    • install ONTraC
    • Load Modules
    • create directories
    • validate ONTraC version info
  • Download dataset
  • Input data
    • Input data visualization
  • set up options
  • niche network construction
    • niche network visulization
  • GNN training
    • GNN results visualization
      • spatial niche cluster loadings
      • niche cluster proportions
      • niche cluster connectivities
      • cell type loadings in each niche cluster
  • niche trajectory construction
    • construct niche trajectory
    • niche trajectory based visualization
      • spatial NT scores
      • cell-level NT score distribution for each cell type
      • cell type propotion along cell-level NT score
      • We can reorder niche clusters by their position in trajectory
        • spatial niche cluster loadings
        • niche cluster connectivities
        • cell type loadings in each niche cluster
• Running ONTraC on a simulated dataset
  • Generate the simulated data using Dyngen
  • Running ONTraC
  • Results visualization
• Running ONTraC on a MERFISH dataset
  • Download the data
  • Running ONTraC
  • Results visualization
• Running ONTraC on a Stereo-seq dataset
  • Download the data
  • Running ONTraC
  • Results visualization
• Running ONTraC on a Xenium dataset
  • Download the data
  • Data preparation
  • Running ONTraC
  • Results visualization