Index

_

__len__() (lineage.LineageTree.LineageTree method) _addr_gammaincc (in module lineage.states.stateCommon) _addr_gammaln (in module lineage.states.stateCommon) _addr_psi (in module lineage.states.stateCommon) _build_cellvar_list() (lineage.LineageTree.LineageTree method)

_gamma_logpdf() (in module lineage.states.StateDistributionCR) _gamma_logsf() (in module lineage.states.StateDistributionCR) _output_lineage (lineage.LineageTree.LineageTree attribute) _state_weights() (in module lineage.compare_emissions) _sync() (lineage.states.StateDistributionCR.StateDistributionPhase method)

A

AllGemcitabine (in module lineage.Lineage_collections) AllLapatinib (in module lineage.Lineage_collections) Analyze_list() (in module lineage.Analyze) arr_type (in module lineage.states.stateCommon) assign_observs_AU565() (in module lineage.import_lineage)

assign_observs_MCF10A() (in module lineage.import_lineage) assign_states() (in module lineage.export_states) atonce_estimator (lineage.states.StateDistributionCR.StateDistribution attribute) (lineage.states.StateDistributionCR.StateDistributionPhase attribute) atonce_estimator() (in module lineage.states.StateDistributionCR) (in module lineage.states.StateDistributionGamma)

B

bern_estimator() (in module lineage.states.stateCommon)

build() (in module lineage.compare_emissions)

C

calculate_log_likelihood() (in module lineage.BaumWelch) calculate_stationary() (in module lineage.BaumWelch) cell_to_daughters (lineage.LineageTree.LineageTree property) CellVar (class in lineage.CellVar) censor_lineage_array() (lineage.states.StateDistributionCR.StateDistribution method) (lineage.states.StateDistributionCR.StateDistributionPhase method) (lineage.states.StateDistributionGamma.StateDistribution method) (lineage.states.StateDistributionGaPhs.StateDistribution method)

censor_lineage_gamma() (in module lineage.states.stateCommon) censor_lineage_gaphs() (in module lineage.states.stateCommon) cheat() (in module lineage.Analyze) CladeRecursive() (in module lineage.plotTree) CladeRecursive_MCF10A() (in module lineage.plotTree) coarse_logpdf() (in module lineage.compare_emissions) crossval() (in module lineage.crossval) cs (in module lineage.plotTree)

D

death_clock (lineage.states.StateDistributionCR.StateDistribution property) death_time_LL() (in module lineage.compare_emissions) deintegrate() (in module lineage.export_states) desired_num_states (in module lineage.Lineage_collections) dist() (lineage.states.StateDistributionCR.StateDistribution method) (lineage.states.StateDistributionCR.StateDistributionPhase method) (lineage.states.StateDistributionGamma.StateDistribution method) (lineage.states.StateDistributionGaPhs.StateDistribution method) div_clock (lineage.states.StateDistributionCR.StateDistribution property) divide() (lineage.CellVar.CellVar method) division_probability() (lineage.states.StateDistributionCR.StateDistribution method)

do_E_step() (in module lineage.BaumWelch) do_M_E_step() (in module lineage.BaumWelch) do_M_E_step_atonce() (in module lineage.BaumWelch) do_M_pi_step() (in module lineage.BaumWelch) do_M_step() (in module lineage.BaumWelch) do_M_T_step() (in module lineage.BaumWelch) dof() (lineage.states.StateDistributionCR.StateDistribution method) (lineage.states.StateDistributionCR.StateDistributionPhase method) (lineage.states.StateDistributionGamma.StateDistribution method) (lineage.states.StateDistributionGaPhs.StateDistribution method) draw() (in module lineage.plotTree)

E

E (in module lineage.Lineage_collections) (lineage.LineageTree.LineageTree attribute) E2 (in module lineage.Lineage_collections) edges (lineage.LineageTree.LineageTree property) egf (in module lineage.Lineage_collections) endT (lineage.CellVar.Time attribute) estimate (class in lineage.tHMM) (lineage.tHMM.tHMM attribute)

estimator() (lineage.states.StateDistributionCR.StateDistribution method) (lineage.states.StateDistributionCR.StateDistributionPhase method) (lineage.states.StateDistributionGamma.StateDistribution method) (lineage.states.StateDistributionGaPhs.StateDistribution method) event_masks() (in module lineage.states.StateDistributionCR) exe (in module lineage.crossval) exponential_estimator() (in module lineage.states.StateDistributionCR)

F

fate_logloss() (in module lineage.compare_emissions) fE (lineage.tHMM.estimate attribute) (lineage.tHMM.tHMM attribute) fit_clocks() (in module lineage.states.StateDistributionCR) fit_list() (in module lineage.Analyze)

fixed_death_shape (lineage.states.StateDistributionCR.StateDistribution attribute) fpi (lineage.tHMM.estimate attribute) (lineage.tHMM.tHMM attribute) fT (lineage.tHMM.estimate attribute) (lineage.tHMM.tHMM attribute)

G

G1 (lineage.plotTree.PhaseClade attribute) (lineage.states.StateDistributionCR.StateDistributionPhase attribute) (lineage.states.StateDistributionGaPhs.StateDistribution attribute) G1lw (lineage.plotTree.PhaseClade attribute) G2 (lineage.plotTree.PhaseClade attribute) (lineage.states.StateDistributionCR.StateDistributionPhase attribute) (lineage.states.StateDistributionGaPhs.StateDistribution attribute) G2lw (lineage.plotTree.PhaseClade attribute) gamma_estimator() (in module lineage.states.stateCommon) gamma_LL() (in module lineage.states.stateCommon) gamma_LL_grad() (in module lineage.states.stateCommon) gamma_mle_closed_form() (in module lineage.states.stateCommon)

gammaincc (in module lineage.states.stateCommon) gammaln (in module lineage.states.stateCommon) gem5uM (in module lineage.Lineage_collections) gen (lineage.CellVar.CellVar attribute) get_all_zetas() (in module lineage.HMM.M_step) get_beta_and_NF() (in module lineage.HMM.E_step) get_BIC() (lineage.tHMM.tHMM method) get_deltas() (in module lineage.Viterbi) get_Emission_Likelihoods() (in module lineage.LineageTree) get_gamma() (in module lineage.HMM.E_step) get_MSD() (in module lineage.HMM.E_step) GFs (in module lineage.Lineage_collections)

H

heldout_LL() (in module lineage.compare_emissions)

hgf (in module lineage.Lineage_collections) hide_observation() (in module lineage.crossval)

I

import_AU565() (in module lineage.import_lineage) import_exp_data() (in module lineage.LineageInputOutput)

import_MCF10A() (in module lineage.import_lineage) isLeaf() (lineage.CellVar.CellVar method) isLeafBecauseTerminal() (lineage.CellVar.CellVar method)

L

leaves_idx (lineage.LineageTree.LineageTree attribute) left (lineage.CellVar.CellVar attribute) lineage module lineage.Analyze module lineage.BaumWelch module lineage.CellVar module lineage.compare_emissions module lineage.crossval module lineage.export_states module lineage.HMM module lineage.HMM.E_step module lineage.HMM.M_step module lineage.import_lineage module lineage.Lineage_collections module lineage.LineageInputOutput module lineage.LineageTree module

lineage.plotTree module lineage.states module lineage.states.stateCommon module lineage.states.StateDistributionCR module lineage.states.StateDistributionGamma module lineage.states.StateDistributionGaPhs module lineage.tests module lineage.tests.conftest module lineage.tHMM module lineage.Viterbi module lineage_to_tree() (in module lineage.LineageTree) LineageTree (class in lineage.LineageTree) load_condition() (in module lineage.Lineage_collections) load_conditions() (in module lineage.Lineage_collections) load_replicate_groups() (in module lineage.Lineage_collections) log_score() (lineage.tHMM.tHMM method) log_T_score() (in module lineage.tHMM) logpdf() (lineage.states.StateDistributionCR.StateDistribution method) (lineage.states.StateDistributionCR.StateDistributionPhase method) (lineage.states.StateDistributionGamma.StateDistribution method) (lineage.states.StateDistributionGaPhs.StateDistribution method)

M

MCF10A() (in module lineage.import_lineage) MODELS (in module lineage.compare_emissions) module lineage lineage.Analyze lineage.BaumWelch lineage.CellVar lineage.compare_emissions lineage.crossval lineage.export_states lineage.HMM lineage.HMM.E_step lineage.HMM.M_step lineage.import_lineage lineage.Lineage_collections lineage.LineageInputOutput lineage.LineageTree lineage.plotTree lineage.states lineage.states.stateCommon lineage.states.StateDistributionCR lineage.states.StateDistributionGamma lineage.states.StateDistributionGaPhs lineage.tests lineage.tests.conftest lineage.tHMM lineage.Viterbi

N

non_leaves_idx (lineage.LineageTree.LineageTree property)

num_states (lineage.tHMM.estimate attribute) (lineage.tHMM.tHMM attribute)

O

obs (lineage.CellVar.CellVar attribute) (lineage.LineageTree.LineageTree attribute) observed (lineage.CellVar.CellVar attribute)

osm (in module lineage.Lineage_collections) outcome_mass() (in module lineage.compare_emissions) output_lineage (lineage.LineageTree.LineageTree property) output_LL() (in module lineage.crossval)

P

Palbo250uM (in module lineage.Lineage_collections) params (lineage.states.StateDistributionCR.StateDistribution attribute) (lineage.states.StateDistributionCR.StateDistributionPhase attribute) (lineage.states.StateDistributionGamma.StateDistribution attribute) (lineage.states.StateDistributionGaPhs.StateDistribution attribute) parent (lineage.CellVar.CellVar attribute) pava_increasing() (in module lineage.states.stateCommon) pbs (in module lineage.Lineage_collections) permute_states() (in module lineage.Analyze)

PHASE_COLS (in module lineage.compare_emissions) PhaseClade (class in lineage.plotTree) pi (lineage.LineageTree.LineageTree attribute) plot_lineage_samples() (in module lineage.plotTree) plot_networkx() (in module lineage.plotTree) plotLineage() (in module lineage.plotTree) plotLineage_MCF10A() (in module lineage.plotTree) popout_single_lineages() (in module lineage.Lineage_collections) predict() (lineage.tHMM.tHMM method) psi (in module lineage.states.stateCommon)

R

rand_init() (lineage.LineageTree.LineageTree class method) Results() (in module lineage.Analyze) right (lineage.CellVar.CellVar attribute) run() (in module lineage.compare_emissions)

run_Analyze_over() (in module lineage.Analyze) rvs() (lineage.states.StateDistributionCR.StateDistribution method) (lineage.states.StateDistributionCR.StateDistributionPhase method) (lineage.states.StateDistributionGamma.StateDistribution method) (lineage.states.StateDistributionGaPhs.StateDistribution method)

S

startT (lineage.CellVar.Time attribute) state (lineage.CellVar.CellVar attribute) stateColors (in module lineage.plotTree) StateDistribution (class in lineage.states.StateDistributionCR) (class in lineage.states.StateDistributionGamma) (class in lineage.states.StateDistributionGaPhs)

StateDistributionPhase (class in lineage.states.StateDistributionCR) states (lineage.LineageTree.LineageTree attribute) sum_nonleaf_gammas() (in module lineage.HMM.M_step)

T

T (lineage.LineageTree.LineageTree attribute) Tax2uM (in module lineage.Lineage_collections) Tax7uM (in module lineage.Lineage_collections) tHMM (class in lineage.tHMM) Time (class in lineage.CellVar) time (lineage.CellVar.CellVar attribute)

TIME_FLOOR (in module lineage.compare_emissions) (in module lineage.states.StateDistributionCR) transition_time (lineage.CellVar.Time attribute) tree (lineage.LineageTree.LineageTree attribute) trigamma() (in module lineage.states.stateCommon) tryRecursion() (in module lineage.LineageInputOutput)

V

Viterbi() (in module lineage.Viterbi)

W

write_onExcel() (in module lineage.export_states)

X

X (lineage.tHMM.tHMM attribute)