Contents:

• Run CalicoST on a simulated data
  • Download the data
  • Run CalicoST to infer CNAs and cancer clones assuming spots are purely tumor or purely normal
  • Load the results of CalicoST
• Run CalicoST on prostate cancer dataset
  • Obtain the data
  • Compute allele counts by preprocessing: genotyping and reference-based phasing
  • Estimate tumor proportion per spot
    • Load and visualize inferred tumor proportions
  • Run CalicoST to infer CNAs and cancer clones based on estimated tumor proportions
    • Load CalicoST-generated result tables
    • Visualize CalicoST-generated plots
  • Reconstruct tumor phylogeny and phylogeography