tHMM
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tHMM
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Index
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A
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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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V
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W
_
__len__() (lineage.LineageTree.LineageTree method)
A
addr (in module lineage.states.stateCommon)
,
[1]
AllGemcitabine (in module lineage.Lineage_collections)
AllLapatinib (in module lineage.Lineage_collections)
Analyze() (in module lineage.Analyze)
Analyze_list() (in module lineage.Analyze)
assign_observs_AU565() (in module lineage.import_lineage)
assign_observs_MCF10A() (in module lineage.import_lineage)
assign_states() (in module lineage.export_states)
assign_times() (lineage.states.StateDistributionGamma.StateDistribution method)
(lineage.states.StateDistributionGaPhs.StateDistribution method)
atonce_estimator() (in module lineage.states.StateDistributionGamma)
B
basic_censor() (in module lineage.states.stateCommon)
bern_estimator() (in module lineage.states.stateCommon)
C
calculate_log_likelihood() (in module lineage.BaumWelch)
calculate_stationary() (in module lineage.BaumWelch)
cell_to_daughters (lineage.LineageTree.LineageTree attribute)
cell_to_daughters() (in module lineage.LineageTree)
cell_to_parent (lineage.LineageTree.LineageTree attribute)
cell_to_parent() (in module lineage.LineageTree)
CellVar (class in lineage.CellVar)
censor_lineage() (lineage.states.StateDistributionGamma.StateDistribution method)
(lineage.states.StateDistributionGaPhs.StateDistribution method)
cheat() (in module lineage.Analyze)
CladeRecursive() (in module lineage.plotTree)
CladeRecursive_MCF10A() (in module lineage.plotTree)
crossval() (in module lineage.crossval)
cs (in module lineage.plotTree)
D
deintegrate() (in module lineage.export_states)
desired_num_states (in module lineage.Lineage_collections)
dist() (lineage.states.StateDistributionGamma.StateDistribution method)
(lineage.states.StateDistributionGaPhs.StateDistribution method)
divide() (lineage.CellVar.CellVar 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.StateDistributionGamma.StateDistribution method)
(lineage.states.StateDistributionGaPhs.StateDistribution method)
draw() (in module lineage.plotTree)
E
E (in module lineage.Lineage_collections)
E2 (in module lineage.Lineage_collections)
E_step
module
egf (in module lineage.Lineage_collections)
endT (lineage.CellVar.Time attribute)
estimate (class in lineage.tHMM)
estimator() (lineage.states.StateDistributionGamma.StateDistribution method)
(lineage.states.StateDistributionGaPhs.StateDistribution method)
exe (in module lineage.crossval)
F
fate_censor() (in module lineage.states.StateDistributionGamma)
(in module lineage.states.StateDistributionGaPhs)
fit_list() (in module lineage.Analyze)
G
gamma_estimator() (in module lineage.states.stateCommon)
gamma_LL() (in module lineage.states.stateCommon)
gammaincc (in module lineage.states.stateCommon)
gammaln (in module lineage.states.stateCommon)
gem04 (in module lineage.Lineage_collections)
gem042 (in module lineage.Lineage_collections)
gem043 (in module lineage.Lineage_collections)
gem05 (in module lineage.Lineage_collections)
gem052 (in module lineage.Lineage_collections)
gem06 (in module lineage.Lineage_collections)
gem062 (in module lineage.Lineage_collections)
Gem10uM (in module lineage.Lineage_collections)
Gem30uM (in module lineage.Lineage_collections)
Gem5uM (in module lineage.Lineage_collections)
gem5uM (in module lineage.Lineage_collections)
gem_10_reps (in module lineage.Lineage_collections)
gem_30_reps (in module lineage.Lineage_collections)
gem_5_reps (in module lineage.Lineage_collections)
gem_cn_reps (in module lineage.Lineage_collections)
gemc33 (in module lineage.Lineage_collections)
gemc332 (in module lineage.Lineage_collections)
gemc34 (in module lineage.Lineage_collections)
gemc342 (in module lineage.Lineage_collections)
gemc35 (in module lineage.Lineage_collections)
gemc352 (in module lineage.Lineage_collections)
gemc401 (in module lineage.Lineage_collections)
gemc402 (in module lineage.Lineage_collections)
gemc403 (in module lineage.Lineage_collections)
gemc404 (in module lineage.Lineage_collections)
gemc405 (in module lineage.Lineage_collections)
gemc406 (in module lineage.Lineage_collections)
gemc407 (in module lineage.Lineage_collections)
gemc408 (in module lineage.Lineage_collections)
gemc409 (in module lineage.Lineage_collections)
gemc410 (in module lineage.Lineage_collections)
gemc411 (in module lineage.Lineage_collections)
gemc412 (in module lineage.Lineage_collections)
gemc413 (in module lineage.Lineage_collections)
gemc414 (in module lineage.Lineage_collections)
gemc415 (in module lineage.Lineage_collections)
Gemcitabine_Control (in module lineage.Lineage_collections)
gemD31 (in module lineage.Lineage_collections)
gemD32 (in module lineage.Lineage_collections)
gemD33 (in module lineage.Lineage_collections)
gemD34 (in module lineage.Lineage_collections)
gemD35 (in module lineage.Lineage_collections)
gemD36 (in module lineage.Lineage_collections)
gemD37 (in module lineage.Lineage_collections)
gemD38 (in module lineage.Lineage_collections)
gen (lineage.CellVar.CellVar attribute)
generate_lineage_list() (in module lineage.LineageTree)
get_all_zetas() (in module M_step)
get_beta() (in module E_step)
get_BIC() (lineage.tHMM.tHMM method)
get_delta_parent_child_prod() (in module lineage.Viterbi)
get_deltas() (in module lineage.Viterbi)
get_Emission_Likelihoods() (in module lineage.LineageTree)
get_gamma() (in module E_step)
get_leaf_Normalizing_Factors() (in module E_step)
get_leaves_idx() (in module lineage.LineageTree)
get_MSD() (in module E_step)
get_root_cell() (lineage.CellVar.CellVar method)
get_sister() (lineage.CellVar.CellVar method)
GFs (in module lineage.Lineage_collections)
H
hgf (in module lineage.Lineage_collections)
hide_observation() (in module lineage.crossval)
I
idx_by_gen (lineage.LineageTree.LineageTree attribute)
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)
isRootParent() (lineage.CellVar.CellVar method)
L
lap01 (in module lineage.Lineage_collections)
lap012 (in module lineage.Lineage_collections)
lap02 (in module lineage.Lineage_collections)
lap03 (in module lineage.Lineage_collections)
Lap250uM (in module lineage.Lineage_collections)
Lapatinib_Control (in module lineage.Lineage_collections)
lapb63 (in module lineage.Lineage_collections)
lapb632 (in module lineage.Lineage_collections)
lapb64 (in module lineage.Lineage_collections)
lapb642 (in module lineage.Lineage_collections)
lapb65 (in module lineage.Lineage_collections)
lapb652 (in module lineage.Lineage_collections)
lapb653 (in module lineage.Lineage_collections)
lapC501 (in module lineage.Lineage_collections)
lapC502 (in module lineage.Lineage_collections)
lapC503 (in module lineage.Lineage_collections)
lapC504 (in module lineage.Lineage_collections)
lapC505 (in module lineage.Lineage_collections)
lapC506 (in module lineage.Lineage_collections)
lapC507 (in module lineage.Lineage_collections)
lapC508 (in module lineage.Lineage_collections)
lapC509 (in module lineage.Lineage_collections)
lapC510 (in module lineage.Lineage_collections)
lapC511 (in module lineage.Lineage_collections)
lapC512 (in module lineage.Lineage_collections)
lapC513 (in module lineage.Lineage_collections)
lapC514 (in module lineage.Lineage_collections)
lapD51 (in module lineage.Lineage_collections)
lapD52 (in module lineage.Lineage_collections)
lapD53 (in module lineage.Lineage_collections)
lapD54 (in module lineage.Lineage_collections)
lapD55 (in module lineage.Lineage_collections)
lapD56 (in module lineage.Lineage_collections)
lapD57 (in module lineage.Lineage_collections)
lapD58 (in module lineage.Lineage_collections)
Lapt25uM (in module lineage.Lineage_collections)
Lapt50uM (in module lineage.Lineage_collections)
leaves_idx (lineage.LineageTree.LineageTree attribute)
left (lineage.CellVar.CellVar attribute)
len_gm_10 (in module lineage.Lineage_collections)
len_gm_30 (in module lineage.Lineage_collections)
len_gm_5 (in module lineage.Lineage_collections)
len_gm_cntr (in module lineage.Lineage_collections)
len_lp_25 (in module lineage.Lineage_collections)
len_lp_250 (in module lineage.Lineage_collections)
len_lp_50 (in module lineage.Lineage_collections)
len_lp_cntr (in module lineage.Lineage_collections)
lineage
module
lineage.Analyze
module
lineage.BaumWelch
module
lineage.CellVar
module
lineage.crossval
module
lineage.export_states
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.StateDistributionGamma
module
lineage.states.StateDistributionGaPhs
module
lineage.tests
module
lineage.tHMM
module
lineage.Viterbi
module
LineageTree (class in lineage.LineageTree)
log_score() (lineage.tHMM.tHMM method)
log_T_score() (in module lineage.tHMM)
logpdf() (lineage.states.StateDistributionGamma.StateDistribution method)
(lineage.states.StateDistributionGaPhs.StateDistribution method)
lpt_250_reps (in module lineage.Lineage_collections)
lpt_25_reps (in module lineage.Lineage_collections)
lpt_50_reps (in module lineage.Lineage_collections)
lpt_cn_reps (in module lineage.Lineage_collections)
M
M_step
module
max_gen() (in module lineage.LineageTree)
MCF10A() (in module lineage.import_lineage)
module
E_step
lineage
lineage.Analyze
lineage.BaumWelch
lineage.CellVar
lineage.crossval
lineage.export_states
lineage.import_lineage
lineage.Lineage_collections
lineage.LineageInputOutput
lineage.LineageTree
lineage.plotTree
lineage.states
lineage.states.stateCommon
lineage.states.StateDistributionGamma
lineage.states.StateDistributionGaPhs
lineage.tests
lineage.tHMM
lineage.Viterbi
M_step
N
np_apply_along_axis() (in module E_step)
O
obs (lineage.CellVar.CellVar attribute)
observed (lineage.CellVar.CellVar attribute)
osm (in module lineage.Lineage_collections)
output_assign_obs() (in module lineage.LineageTree)
output_lineage (lineage.LineageTree.LineageTree attribute)
output_LL() (in module lineage.crossval)
P
palbD11 (in module lineage.Lineage_collections)
palbD12 (in module lineage.Lineage_collections)
palbD13 (in module lineage.Lineage_collections)
palbD14 (in module lineage.Lineage_collections)
palbD15 (in module lineage.Lineage_collections)
palbD16 (in module lineage.Lineage_collections)
Palbo250uM (in module lineage.Lineage_collections)
parent (lineage.CellVar.CellVar attribute)
pbs (in module lineage.Lineage_collections)
permute_states() (in module lineage.Analyze)
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)
R
rand_init() (lineage.LineageTree.LineageTree class method)
Results() (in module lineage.Analyze)
right (lineage.CellVar.CellVar attribute)
run_Analyze_over() (in module lineage.Analyze)
rvs() (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.StateDistributionGamma)
(class in lineage.states.StateDistributionGaPhs)
sum_nonleaf_gammas() (in module M_step)
T
T (lineage.LineageTree.LineageTree attribute)
Tax2uM (in module lineage.Lineage_collections)
Tax7uM (in module lineage.Lineage_collections)
taxb40 (in module lineage.Lineage_collections)
taxb402 (in module lineage.Lineage_collections)
taxb41 (in module lineage.Lineage_collections)
taxb412 (in module lineage.Lineage_collections)
taxb42 (in module lineage.Lineage_collections)
taxb422 (in module lineage.Lineage_collections)
taxD301 (in module lineage.Lineage_collections)
taxD302 (in module lineage.Lineage_collections)
tHMM (class in lineage.tHMM)
Time (class in lineage.CellVar)
time_censor() (in module lineage.states.StateDistributionGamma)
(in module lineage.states.StateDistributionGaPhs)
transition_time (lineage.CellVar.Time attribute)
tryRecursion() (in module lineage.LineageInputOutput)
V
Viterbi() (in module lineage.Viterbi)
W
write_onExcel() (in module lineage.export_states)
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