Index

_

__init__() (scHopfield.dynamics.ODESolver method)

C

calculate_cell_transition_scores() (in module scHopfield.dynamics) calculate_perturbation_effect_scores() (in module scHopfield.dynamics) celltype_correlation() (in module scHopfield.tools) compare_perturbations() (in module scHopfield.dynamics) compute_eigenanalysis() (in module scHopfield.tools) compute_energies() (in module scHopfield.tools) compute_jacobian_elements() (in module scHopfield.tools)

compute_jacobian_stats() (in module scHopfield.tools) compute_jacobians() (in module scHopfield.tools) compute_network_centrality() (in module scHopfield.tools) compute_reconstructed_velocity() (in module scHopfield.tools) compute_rotational_part() (in module scHopfield.tools) compute_sigmoid() (in module scHopfield.preprocessing) compute_umap() (in module scHopfield.tools) create_solver() (in module scHopfield.dynamics)

D

decompose_bias_energy() (in module scHopfield.tools)

decompose_degradation_energy() (in module scHopfield.tools) decompose_interaction_energy() (in module scHopfield.tools)

E

energy_embedding() (in module scHopfield.tools)

energy_gene_correlation() (in module scHopfield.tools)

F

fit_all_sigmoids() (in module scHopfield.preprocessing)

fit_interactions() (in module scHopfield.inference) future_celltype_correlation() (in module scHopfield.tools)

G

get_correlation_table() (in module scHopfield.tools) get_eigenanalysis_table() (in module scHopfield.tools) get_network_links() (in module scHopfield.tools)

get_top_affected_genes() (in module scHopfield.dynamics) get_top_eigenvector_genes() (in module scHopfield.tools) get_top_genes_table() (in module scHopfield.tools)

L

load_embedding() (in module scHopfield.tools)

load_jacobians() (in module scHopfield.tools)

N

network_correlations() (in module scHopfield.tools)

O

ODESolver (class in scHopfield.dynamics)

P

plot_centrality_comparison() (in module scHopfield.plotting) plot_centrality_scatter() (in module scHopfield.plotting) plot_correlations_grid() (in module scHopfield.plotting) plot_eigenanalysis_grid() (in module scHopfield.plotting) plot_eigenvalue_spectrum() (in module scHopfield.plotting) plot_eigenvector_components() (in module scHopfield.plotting) plot_energy_boxplots() (in module scHopfield.plotting) plot_energy_components() (in module scHopfield.plotting) plot_energy_landscape() (in module scHopfield.plotting) plot_energy_scatters() (in module scHopfield.plotting) plot_gene_centrality() (in module scHopfield.plotting) plot_gene_correlation_scatter() (in module scHopfield.plotting) plot_gene_response() (in module scHopfield.plotting) plot_grn_network() (in module scHopfield.plotting)

plot_grn_subset() (in module scHopfield.plotting) plot_interaction_matrix() (in module scHopfield.plotting) plot_jacobian_eigenvalue_boxplots() (in module scHopfield.plotting) plot_jacobian_eigenvalue_spectrum() (in module scHopfield.plotting) plot_jacobian_element_grid() (in module scHopfield.plotting) plot_jacobian_stats_boxplots() (in module scHopfield.plotting) plot_network_centrality_rank() (in module scHopfield.plotting) plot_perturbation_effect_heatmap() (in module scHopfield.plotting) plot_perturbation_magnitude() (in module scHopfield.plotting) plot_reference_flow() (in module scHopfield.plotting) plot_sigmoid_fit() (in module scHopfield.plotting) plot_simulation_comparison() (in module scHopfield.plotting) plot_top_affected_genes_bar() (in module scHopfield.plotting) plot_trajectory() (in module scHopfield.plotting)

S

save_embedding() (in module scHopfield.tools) save_jacobians() (in module scHopfield.tools)

simulate_perturbation() (in module scHopfield.dynamics) simulate_shift() (in module scHopfield.dynamics) simulate_trajectory() (in module scHopfield.dynamics)

V

validate_velocity() (in module scHopfield.tools)

visualize_perturbation_flow() (in module scHopfield.plotting)