LineageOT
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LineageOT
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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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J
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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
A
add_conditional_means_and_variances() (in module lineageot.inference)
add_division_times_from_vertex_times() (in module lineageot.inference)
add_inverse_times_to_edges() (in module lineageot.inference)
add_leaf_barcodes() (in module lineageot.inference)
add_leaf_times() (in module lineageot.inference)
add_leaf_x() (in module lineageot.inference)
add_node_times_from_dict() (in module lineageot.inference)
add_node_times_from_division_times() (in module lineageot.inference)
add_nodes_at_time() (in module lineageot.inference)
add_samples_to_clone_tree() (in module lineageot.inference)
add_times() (in module lineageot.inference)
add_times_to_edges() (in module lineageot.inference)
annotate_tree() (in module lineageot.inference)
B
barcode_distances() (in module lineageot.inference)
C
Cell (class in lineageot.simulation)
center() (in module lineageot.simulation)
compute_leaf_times() (in module lineageot.inference)
compute_new_distances() (in module lineageot.inference)
compute_q_matrix() (in module lineageot.inference)
compute_tree_distances() (in module lineageot.inference)
convergent_flow() (in module lineageot.simulation)
convert_data_to_arrays() (in module lineageot.simulation)
convert_newick_to_networkx() (in module lineageot.inference)
coupling_to_coupling_cost_matrix() (in module lineageot.evaluation)
coupling_W2() (in module lineageot.evaluation)
cvxopt_qp_from_numpy() (in module lineageot.inference)
D
deepcopy() (lineageot.simulation.Cell method)
distances_to_joined_node() (in module lineageot.inference)
E
estimate_division_time() (in module lineageot.inference)
evolve_b() (in module lineageot.simulation)
evolve_cell() (in module lineageot.simulation)
evolve_x() (in module lineageot.simulation)
expand_coupling() (in module lineageot.evaluation)
expand_coupling_independent() (in module lineageot.evaluation)
extract_ancestor_data_arrays() (in module lineageot.inference)
extract_data_arrays() (in module lineageot.inference)
F
find_parent_clone() (in module lineageot.inference)
fit_lineage_coupling() (in module lineageot.core)
fit_tree() (in module lineageot.core)
flatten_list_of_lists() (in module lineageot.simulation)
G
get_ancestor_data() (in module lineageot.inference)
get_components() (in module lineageot.inference)
get_internal_nodes() (in module lineageot.inference)
get_leaf_descendants() (in module lineageot.inference)
get_leaves() (in module lineageot.inference)
get_lineage_distances_across_time() (in module lineageot.inference)
get_parent_clone_of_leaf() (in module lineageot.inference)
get_true_coupling() (in module lineageot.inference)
J
join_nodes() (in module lineageot.inference)
L
l2_difference() (in module lineageot.evaluation)
lineageot.core
module
lineageot.evaluation
module
lineageot.inference
module
lineageot.simulation
module
list_tree_to_digraph() (in module lineageot.inference)
M
make_clone_reference_tree() (in module lineageot.inference)
make_tree_from_clones() (in module lineageot.inference)
make_tree_from_nonnested_clones() (in module lineageot.inference)
mask_barcode() (in module lineageot.simulation)
mismatched_clusters_flow() (in module lineageot.simulation)
module
lineageot.core
lineageot.evaluation
lineageot.inference
lineageot.simulation
mutate_barcode() (in module lineageot.simulation)
N
neighbor_join() (in module lineageot.inference)
NeighborJoinNode (class in lineageot.inference)
normalize_columns() (in module lineageot.evaluation)
O
OT_cost() (in module lineageot.inference)
P
pairwise_squared_distances() (in module lineageot.evaluation)
partial_convergent_flow() (in module lineageot.simulation)
pick_joined_nodes() (in module lineageot.inference)
plot2D_samples_mat() (in module lineageot.evaluation)
plot_metrics() (in module lineageot.evaluation)
print_metrics() (in module lineageot.evaluation)
R
rate_estimator() (in module lineageot.inference)
read_newick() (in module lineageot.core)
recursive_add_barcodes() (in module lineageot.inference)
recursive_list_tree_to_digraph() (in module lineageot.inference)
remove_node_and_descendants() (in module lineageot.inference)
remove_times() (in module lineageot.inference)
reproducible_poisson() (in module lineageot.simulation)
resample_cells() (in module lineageot.inference)
reset_seed() (lineageot.simulation.Cell method)
robinson_foulds() (in module lineageot.inference)
S
sample_barcode() (in module lineageot.simulation)
sample_cell() (in module lineageot.simulation)
sample_coordinates_from_coupling() (in module lineageot.evaluation)
sample_descendants() (in module lineageot.simulation)
sample_division_time() (in module lineageot.simulation)
sample_indices_from_coupling() (in module lineageot.evaluation)
sample_interpolant() (in module lineageot.evaluation)
sample_pop() (in module lineageot.simulation)
sample_population_descendants() (in module lineageot.simulation)
sample_x0() (in module lineageot.simulation)
save_coupling_as_tmap() (in module lineageot.core)
scaled_Hamming_distance() (in module lineageot.inference)
scaled_l2_difference() (in module lineageot.evaluation)
SimulationParameters (class in lineageot.simulation)
single_bifurcation_flow() (in module lineageot.simulation)
split_edge() (in module lineageot.inference)
split_targets_between_daughters() (in module lineageot.simulation)
squeeze_coupling() (in module lineageot.evaluation)
squeeze_coupling_by_late_cluster() (in module lineageot.evaluation)
subsample_list() (in module lineageot.simulation)
subsample_pop() (in module lineageot.simulation)
subtree_to_ete3() (in module lineageot.inference)
T
tree_accuracy() (in module lineageot.inference)
tree_discrepancy() (in module lineageot.inference)
tree_to_ete3() (in module lineageot.inference)
truncate_tree() (in module lineageot.inference)
tv() (in module lineageot.evaluation)
V
vector_field() (in module lineageot.simulation)
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