Tutorials

• Deconvolution and decomposition of mouse cortex with Spotiphy
  • Contents
  • Install and load packages
  • Load Visium data, scRNA data, and the HE staining image.
  • Select marker genes for the deconvolution
  • Deconvolution: Estimate cell abundance in spatial spots
  • Segmentation: Estimate cell number in each spatial spot
  • Decomposition: Decompose the expression of each spatial spot into single-cell level
  • Generate pseudo single-cell resolution image