Using PROSSTT

Here we will go through the four steps of simulation creation in PROSSTT and explain the various alternatives available in each one.

Contents:

• Generate tree
  • Manual definition
  • From a Newick-formatted string
  • Automatic tree generation
• Simulate average gene expression along tree
  • Contribution coefficients
  • Expression programs
  • Getting average gene expression along tree
• Sample cells from tree
  • Sample whole tree
  • Sample pseudotime series
  • Sample density
  • Combinations and manual sampling
• Simulate UMI counts