Example notebooks

Simulation

• Simulating multi-modal spatial data from dissociated single-cell data
  • Load single-cell reference
  • Simulate spatial data
  • Visualize simulated data

Deconvolution

• Deconvoluting spatialATAC data with Cell2Location
  • Import libraries
  • Read in the data
  • Select HVFs with deconvATAC
  • Run Cell2Location
• Deconvoluting spatialATAC data with RCTD
  • Import libraries
  • Read in & preprocess the data
  • Run RCTD
  • Calculate Metrics