Index

A

add_genes() (prosstt.tree.Tree method) adjust_to_parent() (in module prosstt.sim_utils)

as_dictionary() (prosstt.tree.Tree method) assign_branches() (in module prosstt.sim_utils)

B

belongs_to() (in module prosstt.sim_utils) bfs_finder() (in module prosstt.sim_utils) bifurc_adjust() (in module prosstt.sim_utils)

branch_points (prosstt.tree.Tree attribute) branch_times() (prosstt.tree.Tree method) branches (prosstt.tree.Tree attribute) breadth_first_branches() (in module prosstt.sim_utils)

C

calc_relat_means() (in module prosstt.sim_utils) calc_scalings() (in module prosstt.sim_utils)

cover_whole_tree() (in module prosstt.simulation) create_groups() (in module prosstt.sim_utils)

D

def_genes (prosstt.tree.Tree attribute) def_time (prosstt.tree.Tree attribute) default_density() (prosstt.tree.Tree method) default_gene_expression() (prosstt.tree.Tree method)

density (prosstt.tree.Tree attribute) diffusion() (in module prosstt.simulation) diverging_parallel() (in module prosstt.sim_utils) draw_counts() (in module prosstt.simulation) draw_times() (in module prosstt.simulation)

F

find_parallel() (in module prosstt.sim_utils) flat_order() (in module prosstt.sim_utils)

from_newick() (prosstt.tree.Tree class method) from_random_topology() (prosstt.tree.Tree class method)

G

G (prosstt.tree.Tree attribute) gen_random_topology() (prosstt.tree.Tree static method) generate_negbin_params() (in module prosstt.count_model) get_max_time() (prosstt.tree.Tree method)

get_parallel_branches() (prosstt.tree.Tree method) get_pr_amp() (in module prosstt.count_model) get_pr_umi() (in module prosstt.count_model) get_pr_umi_atom() (in module prosstt.count_model)

L

lognegbin() (in module prosstt.count_model)

M

max_relat_exp() (in module prosstt.sim_utils) means (prosstt.tree.Tree attribute)

modules (prosstt.tree.Tree attribute) morph_stack() (prosstt.tree.Tree method) my_negbin (class in prosstt.count_model)

N

negbin() (in module prosstt.count_model)

num_branches (prosstt.tree.Tree attribute)

P

parse_newick() (in module prosstt.tree_utils) paths() (prosstt.tree.Tree method) pearson_between_programs() (in module prosstt.sim_utils) pick_branch() (in module prosstt.sim_utils) pick_branches() (in module prosstt.sim_utils) populate_timezone() (prosstt.tree.Tree method) print_progress() (in module prosstt.sim_utils)

process_timeseries_input() (in module prosstt.sim_utils) prosstt (module) prosstt.count_model (module) prosstt.sim_utils (module) prosstt.simulation (module) prosstt.tree (module) prosstt.tree_utils (module)

R

random_partition() (in module prosstt.sim_utils)

root (prosstt.tree.Tree attribute)

S

sample_density() (in module prosstt.simulation) sample_pseudotime_series() (in module prosstt.simulation) sample_whole_tree() (in module prosstt.simulation) sample_whole_tree_restricted() (in module prosstt.simulation) set_density() (prosstt.tree.Tree method)

sim_expr_branch() (in module prosstt.simulation) simulate_base_gene_exp() (in module prosstt.sim_utils) simulate_coefficients() (in module prosstt.simulation) simulate_lineage() (in module prosstt.simulation) sum_negbin (class in prosstt.count_model)

T

test_correlation() (in module prosstt.sim_utils) time (prosstt.tree.Tree attribute)

topology (prosstt.tree.Tree attribute) Tree (class in prosstt.tree)