Index

A

animate_gene_expression() (scegot.scEGOT method), [1]

animatie_interpolated_distribution() (scegot.scEGOT method), [1] apply_umap() (scegot.scEGOT method), [1]

B

bures_wasserstein_distance() (scegot.scEGOT method), [1]

C

calculate_cell_velocities() (scegot.scEGOT method), [1] calculate_grns() (scegot.scEGOT method), [1] calculate_mut_st() (scegot.scEGOT method), [1] calculate_normalized_solutions() (scegot.scEGOT method), [1]

calculate_solution() (scegot.scEGOT method), [1] calculate_solutions() (scegot.scEGOT method), [1] calculate_waddington_potential() (scegot.scEGOT method), [1] CellStateGraph (class in scegot), [1] create_separated_data() (scegot.scEGOT method), [1]

E

egot() (scegot.scEGOT method), [1]

F

fit_gmm() (scegot.scEGOT method), [1]

fit_predict_gmm() (scegot.scEGOT method), [1]

G

gaussian_mixture_density() (scegot.scEGOT method), [1] generate_cluster_names_with_day() (scegot.scEGOT method), [1]

get_gaussian_map() (scegot.scEGOT method), [1] get_gmm_means() (scegot.scEGOT method), [1] get_positive_gmm_mean_gene_values_per_cluster() (scegot.scEGOT method), [1]

I

integrate_data() (in module scegot), [1]

is_notebook() (in module scegot), [1]

M

make_cell_state_graph() (scegot.scEGOT method), [1] make_cell_state_graph_object() (scegot.scEGOT method), [1] make_interpolation_data() (scegot.scEGOT method), [1]

merge_cluster_names_by_pathway() (scegot.scEGOT method), [1] module sce scegot, [1], [2]

P

plot_cell_state_graph() (scegot.CellStateGraph method), [1] (scegot.scEGOT method), [1] plot_cell_velocity() (scegot.scEGOT method), [1] plot_fold_change() (scegot.scEGOT method), [1] plot_gene_expression_2d() (scegot.scEGOT method), [1] plot_gene_expression_3d() (scegot.scEGOT method), [1] plot_gmm_predictions() (scegot.scEGOT method), [1] plot_grn_graph() (scegot.scEGOT method), [1] plot_interpolation_of_cell_velocity() (scegot.scEGOT method), [1] plot_pathway_gene_expressions() (scegot.scEGOT method), [1]

plot_pathway_mean_var() (scegot.scEGOT method), [1] plot_pathway_single_gene_2d() (scegot.scEGOT method), [1] plot_pathway_single_gene_3d() (scegot.scEGOT method), [1] plot_simple_cell_state_graph() (scegot.CellStateGraph method), [1] (scegot.scEGOT method), [1] plot_true_and_interpolation_distributions() (scegot.scEGOT method), [1] plot_waddington_potential() (scegot.scEGOT method), [1] plot_waddington_potential_surface() (scegot.scEGOT method), [1] predict_gmm_label() (scegot.scEGOT method), [1] predict_gmm_labels() (scegot.scEGOT method), [1] preprocess() (scegot.scEGOT method), [1]

R

replace_gmm_labels() (scegot.scEGOT method), [1]

reverse_graph() (scegot.CellStateGraph method), [1]

S

sce module scegot module, [1], [2]

scEGOT (class in scegot), [1] set_cluster_names() (scegot.CellStateGraph method), [1]

U

update_cluster_names() (scegot.CellStateGraph method), [1]