dynamo.sim.Simulator

dynamo.sim.Simulator(motif='neurogenesis', seed_num=19491001, clip=True, cell_num=5000)[source]

Simulate the gene expression dynamics via deterministic ODE model

Parameters

  • motif (str (default: "neurogenesis")) – Name of the network motif that will be used in the simulation.

  • clip (bool (default: True)) – Whether to clip data points that are negative.

  • cell_num (int (default: 5000)) – Number of cells to simulate.

Returns

adata – an Annodata object containing the simulated data.

Return type

AnnData