Dynamics (sch.dyn)

The dynamics module provides ODE solvers for simulating Hopfield network dynamics and gene expression trajectories.

Classes

ODESolver(W, bias_vector, gamma, threshold, ...)

ODE solver for Hopfield network dynamics.

ODE-based Simulation

create_solver(adata, cluster[, ...])	Create ODE solver for a specific cluster.
simulate_trajectory(adata, cluster, ...[, ...])	Simulate trajectory from one or more cells' initial states.
simulate_perturbation(adata, perturb_condition)	Simulate gene expression changes after perturbation using direct GRN effects.

CellOracle-style GRN Propagation

These functions implement perturbation simulation using GRN signal propagation, inspired by CellOracle (Kamimoto et al., 2023).

simulate_shift(adata, perturb_condition[, ...])	Simulate gene expression changes after perturbation using direct GRN effects.
calculate_perturbation_effect_scores(adata)	Calculate perturbation effect scores per cluster.
calculate_cell_transition_scores(adata[, ...])	Calculate cell transition scores based on delta_X magnitude.
get_top_affected_genes(adata[, n_genes, ...])	Get the top genes most affected by the perturbation.
compare_perturbations(adata, perturbations)	Compare multiple perturbation conditions.