Index

_

_as_float_array() (in module phylovelo.embedding) (in module phylovelo.pseudo_time) _auto_chunk_size() (VelocityEmbedding method) _bridge_components() (in module phylovelo.pseudo_time) _build_knn_adjacency() (in module phylovelo.pseudo_time) _connected_components() (in module phylovelo.pseudo_time) _d_centered (VelocityEmbedding attribute) _d_mean (VelocityEmbedding attribute) _d_nonzero (VelocityEmbedding attribute) _d_nonzero_values (VelocityEmbedding attribute) _d_norm (VelocityEmbedding attribute) _get_expression_data() (in module phylovelo.pseudo_time)

_get_neighbor_indices() (VelocityEmbedding method) _graph_pseudotime() (in module phylovelo.pseudo_time) _meg_pseudotime_scores() (in module phylovelo.pseudo_time) _neighbor_indices (VelocityEmbedding attribute) _normalize_01() (in module phylovelo.pseudo_time) _normalize_with_bounds() (in module phylovelo.pseudo_time) _positions_for_names() (in module phylovelo.pseudo_time) _prim_edges() (in module phylovelo.pseudo_time) _project_neighbor_block() (VelocityEmbedding method) _sample_cells() (in module phylovelo.pseudo_time) _time_intervals() (in module phylovelo.pseudo_time) _transition_probabilities() (VelocityEmbedding method)

A

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

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

B

base_expr (Gene attribute), [1]

base_expr_calc() (Gene method), [1]

C

calc_meg_pseudotime() (in module phylovelo) (in module phylovelo.pseudo_time) 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) cell_generation (scData attribute), [1] cell_names (scData attribute), [1]

cell_states (scData attribute), [1] cells_genetype (GeneExpr attribute), [1], [2] children (Trie attribute) cid (Cell attribute), [1], [2] combine() (Reaction method), [1], [2] corr_plot() (in module phylovelo) (in module phylovelo.ana_utils) count (scData attribute), [1] (VelocityEmbedding attribute) curr_cells (Gillespie attribute), [1], [2], [3]

D

d (VelocityEmbedding attribute) diff_map (GeneExpr attribute), [1], [2] diffusion() (Gene method), [1]

dimensionality_reduction() (scData method), [1] distance() (Trie method) drift (Gene attribute), [1] drop_duplicate_genes() (scData method), [1]

E

est_z() (in module phylovelo.inference) evolute() (Gillespie method), [1], [2], [3]

expr() (GeneExpr method), [1], [2] expr_rec (GeneExpr attribute), [1], [2]

F

forward_map (GeneExpr attribute), [1], [2]

G

gen (Cell attribute), [1], [2] 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) generation_time (Gillespie attribute), [1], [2], [3] 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

index (Reaction attribute), [1], [2] InfMu (class in phylovelo.inference) insert() (Trie method)

inte (InfMu attribute) is_meg() (in module phylovelo.inference) isend (Trie attribute)

K

kNN (VelocityEmbedding attribute)

L

label_name() (in module phylovelo) (in module phylovelo.ana_utils) latenct_z_inference() (in module phylovelo.inference) latent_z (scData attribute), [1]

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

M

max_cell_num (Gillespie attribute), [1], [2], [3] megs (scData attribute), [1] 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

mu0 (Gene attribute), [1] mullerplot() (in module phylovelo) (in module phylovelo.ana_utils)

N

neighs_log (VelocityEmbedding attribute) Ngene (GeneExpr attribute), [1], [2] normalize_filter() (scData method), [1] Nstates (GeneExpr attribute), [1], [2]

num_diff (Reaction attribute), [1], [2] num_elements (Gillespie attribute), [1], [2], [3] num_lefts (Reaction attribute), [1], [2] num_rights (Reaction attribute), [1], [2]

P

paired_correlation_rows() (in module phylovelo.embedding) parent (Cell attribute), [1], [2] phylo_pseudotime (scData attribute), [1] phylo_tree (scData attribute), [1] 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) project_all() (VelocityEmbedding method) propensity() (Reaction method), [1], [2] pvals (scData attribute), [1]

Q

qvals (scData attribute), [1]

R

rate (Reaction attribute), [1], [2] Reaction (class in phylovelo) (class in phylovelo.gillespie_variable_paras) (class in phylovelo.sim_utils)

reactions (Gillespie attribute), [1], [2], [3] 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) sigma2 (InfMu attribute)

sim_base_expr() (in module phylovelo) (in module phylovelo.sim_utils) slope (InfMu attribute) state (Cell attribute), [1], [2] state_time (GeneExpr attribute), [1], [2]

T

t0 (Gene attribute), [1] tb (Cell attribute), [1], [2] td (Cell attribute), [1], [2]

time_interval() (in module phylovelo.pseudo_time) transit_mat() (VelocityEmbedding method) transit_mat1() (VelocityEmbedding method) Trie (class in phylovelo.elegans_util)

V

v (VelocityEmbedding attribute) variant_gene (GeneExpr attribute), [1], [2] velocity (scData attribute), [1] velocity_embedding() (in module phylovelo) (in module phylovelo.embedding) velocity_embedding_to_grid() (in module phylovelo) (in module phylovelo.ana_utils)

velocity_embeded (scData attribute), [1] 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)

X

x_normed (scData attribute), [1]

Xdr (scData attribute), [1] xdr (VelocityEmbedding attribute)