Index

A

add_lineage_noise() (in module phylovelo) (in module phylovelo.sim_utils)

add_reaction() (Gillespie method), [1], [2], [3]

B

base_expr_calc() (Gene method), [1]

C

calc_phylo_pseudotime() (in module phylovelo) (in module phylovelo.pseudo_time) Cell (class in phylovelo) (class in phylovelo.gillespie_variable_paras) (class in phylovelo.sim_utils)

combine() (Reaction method), [1], [2] corr_plot() (in module phylovelo) (in module phylovelo.ana_utils)

D

diffusion() (Gene method), [1] dimensionality_reduction() (scData method), [1]

distance() (Trie method) drop_duplicate_genes() (scData method), [1]

E

est_z() (in module phylovelo.inference)

evolute() (Gillespie method), [1], [2], [3] expr() (GeneExpr method), [1], [2]

G

Gene (class in phylovelo) (class in phylovelo.gene_expr) GeneExpr (class in phylovelo), [1] (class in phylovelo.gene_expr) generate_genes() (GeneExpr method), [1], [2] generate_grid() (in module phylovelo) (in module phylovelo.ana_utils) get_annotation() (in module phylovelo) (in module phylovelo.sim_utils) get_count() (in module phylovelo) (in module phylovelo.sim_utils) get_count_from_base_expr() (in module phylovelo) (in module phylovelo.sim_utils)

get_descendant() (Trie method) get_mu() (InfMu method) get_nearest_neighbor() (in module phylovelo.pseudo_time) get_neighbors() (Trie method) (VelocityEmbedding method) get_weight() (in module phylovelo) (in module phylovelo.ana_utils) Gillespie (class in phylovelo), [1] (class in phylovelo.gillespie_variable_paras) (class in phylovelo.sim_utils) graph_dict() (in module phylovelo.pseudo_time)

I

InfMu (class in phylovelo.inference)

insert() (Trie method) is_meg() (in module phylovelo.inference)

L

label_name() (in module phylovelo) (in module phylovelo.ana_utils) latenct_z_inference() (in module phylovelo.inference) loadtree() (in module phylovelo) (in module phylovelo.ana_utils)

logNormalize() (in module phylovelo) (in module phylovelo.ana_utils) lrtest() (in module phylovelo.inference)

M

mle_nb() (in module phylovelo.inference) mle_norm() (in module phylovelo.inference) mle_zinb() (in module phylovelo.inference) mle_zinorm() (in module phylovelo.inference) module phylovelo phylovelo.ana_utils phylovelo.data_struct phylovelo.elegans_util phylovelo.embedding phylovelo.gene_expr phylovelo.gillespie_variable_paras phylovelo.inference phylovelo.pseudo_time phylovelo.sim_utils

mullerplot() (in module phylovelo) (in module phylovelo.ana_utils)

N

normalize_filter() (scData method), [1]

P

paired_correlation_rows() (in module phylovelo.embedding) phylovelo module phylovelo.ana_utils module phylovelo.data_struct module phylovelo.elegans_util module phylovelo.embedding module phylovelo.gene_expr module

phylovelo.gillespie_variable_paras module phylovelo.inference module phylovelo.pseudo_time module phylovelo.sim_utils module plot_tree() (in module phylovelo) (in module phylovelo.ana_utils), [1] prim() (in module phylovelo.pseudo_time) project() (VelocityEmbedding method) propensity() (Reaction method), [1], [2]

R

Reaction (class in phylovelo) (class in phylovelo.gillespie_variable_paras) (class in phylovelo.sim_utils)

reconstruct() (in module phylovelo) (in module phylovelo.sim_utils) rho() (VelocityEmbedding method)

S

scData (class in phylovelo) (class in phylovelo.data_struct)

search() (Trie method) sim_base_expr() (in module phylovelo) (in module phylovelo.sim_utils)

T

time_interval() (in module phylovelo.pseudo_time) transit_mat() (VelocityEmbedding method)

transit_mat1() (VelocityEmbedding method) Trie (class in phylovelo.elegans_util)

V

velocity_embedding() (in module phylovelo) (in module phylovelo.embedding) velocity_embedding_to_grid() (in module phylovelo) (in module phylovelo.ana_utils)

velocity_inference() (in module phylovelo) (in module phylovelo.inference) velocity_plot() (in module phylovelo) (in module phylovelo.ana_utils) VelocityEmbedding (class in phylovelo.embedding)

W

wirte_lineage_info() (in module phylovelo) (in module phylovelo.sim_utils)