Index

Symbols

--batch_effect CLI-Parser-Documentation command line option --batch_effect_var CLI-Parser-Documentation command line option --cell_types CLI-Parser-Documentation command line option --cell_types_colnames CLI-Parser-Documentation command line option --cell_types_delim CLI-Parser-Documentation command line option --creation CLI-Parser-Documentation command line option --emulation CLI-Parser-Documentation command line option --exprs CLI-Parser-Documentation command line option --exprs_colnames CLI-Parser-Documentation command line option --exprs_delim CLI-Parser-Documentation command line option --help CLI-Parser-Documentation command line option --make_new_dir CLI-Parser-Documentation command line option

--n_batches CLI-Parser-Documentation command line option --n_cells CLI-Parser-Documentation command line option --n_markers CLI-Parser-Documentation command line option --n_trees CLI-Parser-Documentation command line option --n_types CLI-Parser-Documentation command line option --out_dir CLI-Parser-Documentation command line option --temporal_effect CLI-Parser-Documentation command line option --temporal_effect_var CLI-Parser-Documentation command line option --trajectory CLI-Parser-Documentation command line option --version CLI-Parser-Documentation command line option -h CLI-Parser-Documentation command line option -o CLI-Parser-Documentation command line option

B

brownian_bridge_function() (in module cytomulate.utilities)

C

CLI-Parser-Documentation command line option --batch_effect --batch_effect_var --cell_types --cell_types_colnames --cell_types_delim --creation --emulation --exprs --exprs_colnames --exprs_delim --help --make_new_dir --n_batches --n_cells --n_markers --n_trees --n_types --out_dir --temporal_effect --temporal_effect_var --trajectory --version -h -o

CreationCellGraph (class in cytomulate.creation.cell_graph) CreationCellType (class in cytomulate.creation.cell_type) CreationCytofData (class in cytomulate.creation.cytof_data) cytomulate.__main__ module

E

EmulationCellGraph (class in cytomulate.emulation.cell_graph) EmulationCellType (class in cytomulate.emulation.cell_type)

EmulationCytofData (class in cytomulate.emulation.cytof_data) estimate_noise_model() (in module cytomulate.utilities)

F

fit() (cytomulate.emulation.cell_type.EmulationCellType method)

G

GeneralCellGraph (class in cytomulate.cell_graph_general) GeneralCellType (class in cytomulate.cell_type_general) GeneralCytofData (class in cytomulate.cytof_data_general) generate_cell_abundances() (cytomulate.cytof_data_general.GeneralCytofData method) (cytomulate.emulation.cytof_data.EmulationCytofData method) generate_cell_graph() (cytomulate.creation.cytof_data.CreationCytofData method) (cytomulate.emulation.cytof_data.EmulationCytofData method)

generate_local_batch_effects() (cytomulate.cytof_data_general.GeneralCytofData method) generate_marker_expression_patterns() (cytomulate.creation.cell_type.CreationCellType method) generate_marker_expressions() (cytomulate.creation.cell_type.CreationCellType method) generate_model() (cytomulate.creation.cell_type.CreationCellType method) generate_overall_batch_effects() (cytomulate.cytof_data_general.GeneralCytofData method) generate_temporal_effects() (cytomulate.cytof_data_general.GeneralCytofData method) generate_trajectories() (cytomulate.cell_graph_general.GeneralCellGraph method)

I

initialize_cell_types() (cytomulate.creation.cytof_data.CreationCytofData method) (cytomulate.emulation.cytof_data.EmulationCytofData method)

initialize_graph() (cytomulate.creation.cell_graph.CreationCellGraph method) (cytomulate.emulation.cell_graph.EmulationCellGraph method)

M

module cytomulate.__main__

P

polynomial_function() (in module cytomulate.utilities)

prune_graph() (cytomulate.emulation.cell_graph.EmulationCellGraph method)

S

sample() (cytomulate.cytof_data_general.GeneralCytofData method) sample_cell() (cytomulate.cell_type_general.GeneralCellType method) sample_graph() (cytomulate.cell_graph_general.GeneralCellGraph method)

sample_one_batch() (cytomulate.cytof_data_general.GeneralCytofData method) sample_to_pycytodata() (cytomulate.cytof_data_general.GeneralCytofData method) spline_function() (in module cytomulate.utilities)

T

trajectories() (in module cytomulate.utilities)

U

univariate_noise_model() (in module cytomulate.utilities)

V

visualize_graph() (cytomulate.cell_graph_general.GeneralCellGraph method)