dynamo.sim.Simulator

dynamo.sim.Simulator(motif='neurongenesis', seed_num=19491001, clip=None, cell_num=5000)[source]

Simulate the gene expression dynamics via deterministic ODE model

Parameters:

  • motif (str (default: 'neurongenesis')) – str (default: “neurongenesis”) Name of the network motif that will be used in the simulation. Can be one of {“neurongenesis”, “toggle”, “two_genes”, “Ying”, “mixture_of_gaussian”, “four_attractors”}. The last three models are equivalent.

  • clip (Optional[bool] (default: None)) – Whether to clip data points that are negative.

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

Return type:

AnnData

Returns:

An Annodata object containing the simulated data.