Index

A

animate() (in module scTimeBench.shared.utils)

AUTO_TRAIN_TEST (scTimeBench.config.RunType attribute)

B

BaseDataset (class in scTimeBench.shared.dataset.base) BaseDatasetPreprocessor (class in scTimeBench.shared.dataset.base) BaseMethod (class in scTimeBench.method_utils.method_runner) BaseMetric (class in scTimeBench.metrics.base)

BaseOTMethod (class in scTimeBench.method_utils.ot_method_runner) BaseTrajectoryInferMethod (class in scTimeBench.trajectory_infer.base) block_interrupts() (in module scTimeBench.shared.utils) BOOSTING (scTimeBench.trajectory_infer.classifier.ClassifierTypes attribute)

C

CELL_TYPE (scTimeBench.shared.constants.ObservationColumns attribute) cell_types_to_one_hot() (scTimeBench.trajectory_infer.ot.OptimalTransport method) CellTypist (class in scTimeBench.trajectory_infer.classifier) cheeky_message() (in module scTimeBench.shared.utils) Classifier (class in scTimeBench.trajectory_infer.classifier) ClassifierTypes (class in scTimeBench.trajectory_infer.classifier)

clear_dataset_cache() (in module scTimeBench.shared.utils) clear_tables() (scTimeBench.database.DatabaseManager method) close() (scTimeBench.database.DatabaseManager method) Config (class in scTimeBench.config) create_dataset_dir() (scTimeBench.shared.dataset.base.BaseDataset method) CsvExportType (class in scTimeBench.config) CsvWriteMode (class in scTimeBench.config)

D

DatabaseManager (class in scTimeBench.database)

E

EMBEDDING (scTimeBench.config.CsvExportType attribute) (scTimeBench.shared.constants.RequiredOutputFiles attribute) embedding_to_csv() (scTimeBench.database.DatabaseManager method) encode() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method)

encode_dataset_dict() (scTimeBench.shared.dataset.base.BaseDataset method) encode_for_classifier() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method) encode_preprocessors() (scTimeBench.shared.dataset.base.BaseDataset method) eval() (scTimeBench.metrics.base.BaseMetric method) EVAL_ONLY (scTimeBench.config.RunType attribute)

F

FROM_ZERO_TO_END_PRED_GEX (scTimeBench.shared.constants.RequiredOutputFiles attribute)

G

generate() (scTimeBench.method_utils.method_runner.BaseMethod method) generate_embedding() (scTimeBench.method_utils.method_runner.BaseMethod method) (scTimeBench.method_utils.ot_method_runner.BaseOTMethod method) generate_next_cell_type() (scTimeBench.method_utils.method_runner.BaseMethod method) (scTimeBench.method_utils.ot_method_runner.BaseOTMethod method) generate_next_tp_embedding() (scTimeBench.method_utils.method_runner.BaseMethod method) (scTimeBench.method_utils.ot_method_runner.BaseOTMethod method) generate_next_tp_gex() (scTimeBench.method_utils.method_runner.BaseMethod method) (scTimeBench.method_utils.ot_method_runner.BaseOTMethod method) generate_pred_graph() (scTimeBench.method_utils.method_runner.BaseMethod method) generate_zero_to_end_pred_gex() (scTimeBench.method_utils.method_runner.BaseMethod method) get_checkpoint_dir() (scTimeBench.shared.dataset.base.BaseDataset method) get_dataset() (in module scTimeBench.shared.utils) get_dataset_dir() (scTimeBench.shared.dataset.base.BaseDataset method)

get_dataset_id() (scTimeBench.database.DatabaseManager method) get_dataset_tag_from_id() (scTimeBench.database.DatabaseManager method) get_evals_per_method() (scTimeBench.database.DatabaseManager method) get_evals_per_metric() (scTimeBench.database.DatabaseManager method) get_kNN_graph() (scTimeBench.trajectory_infer.kNN.kNN method) get_method_output_path() (scTimeBench.database.DatabaseManager method) get_name() (scTimeBench.shared.dataset.base.BaseDataset method) get_ot_labels() (scTimeBench.trajectory_infer.ot.OptimalTransport method) get_parser() (in module scTimeBench.method_utils.method_runner) get_trajectory_infer_method() (scTimeBench.trajectory_infer.base.TrajectoryInferenceMethodFactory method) get_transport_plan() (scTimeBench.method_utils.ot_method_runner.BaseOTMethod method) GEX_PRED (scTimeBench.config.CsvExportType attribute) gex_pred_to_csv() (scTimeBench.database.DatabaseManager method) GRAPH_SIM (scTimeBench.config.CsvExportType attribute) graph_sim_to_csv() (scTimeBench.database.DatabaseManager method)

H

has_eval() (scTimeBench.database.DatabaseManager method)

has_metric() (scTimeBench.database.DatabaseManager method)

I

infer_trajectory() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method) insert_dataset() (scTimeBench.database.DatabaseManager method) insert_dataset_metric() (scTimeBench.database.DatabaseManager method) insert_eval() (scTimeBench.database.DatabaseManager method)

insert_method_output() (scTimeBench.database.DatabaseManager method) insert_metric() (scTimeBench.database.DatabaseManager method) is_log_normalized_to_counts() (in module scTimeBench.shared.utils) is_raw() (in module scTimeBench.shared.utils) iterate_csv_types() (in module scTimeBench.main)

K

kNN (class in scTimeBench.trajectory_infer.kNN)

kNNStrategy (class in scTimeBench.trajectory_infer.kNN)

L

load_data() (scTimeBench.shared.dataset.base.BaseDataset method)

load_output_file() (in module scTimeBench.shared.utils) load_test_dataset() (in module scTimeBench.shared.utils)

M

main() (in module scTimeBench.main) (in module scTimeBench.method_utils.method_runner) MAJORITY_VOTE (scTimeBench.trajectory_infer.kNN.kNNStrategy attribute) MERGE (scTimeBench.config.CsvWriteMode attribute) MethodManager (class in scTimeBench.metrics.method_manager) module scTimeBench.config scTimeBench.database scTimeBench.main scTimeBench.method_utils.method_runner scTimeBench.method_utils.ot_method_runner scTimeBench.metrics.base scTimeBench.metrics.method_manager scTimeBench.shared.constants scTimeBench.shared.dataset.base scTimeBench.shared.helpers scTimeBench.shared.utils scTimeBench.trajectory_infer.base scTimeBench.trajectory_infer.classifier scTimeBench.trajectory_infer.kNN scTimeBench.trajectory_infer.ot

N

NEXT_CELLTYPE (scTimeBench.shared.constants.RequiredOutputFiles attribute)

NEXT_TIMEPOINT_EMBEDDING (scTimeBench.shared.constants.RequiredOutputFiles attribute) NEXT_TIMEPOINT_GENE_EXPRESSION (scTimeBench.shared.constants.RequiredOutputFiles attribute)

O

ObservationColumns (class in scTimeBench.shared.constants)

OptimalTransport (class in scTimeBench.trajectory_infer.ot)

P

parse_cell_lineage() (in module scTimeBench.shared.helpers) parse_equivalence() (in module scTimeBench.shared.helpers) plot() (in module scTimeBench.main) PRED_GRAPH (scTimeBench.shared.constants.RequiredOutputFiles attribute) predict_next_tp() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method)

PREPROCESS (scTimeBench.config.RunType attribute) preprocess() (scTimeBench.shared.dataset.base.BaseDatasetPreprocessor method) print_all() (scTimeBench.database.DatabaseManager method) print_available() (in module scTimeBench.main) process_yaml() (in module scTimeBench.method_utils.method_runner)

R

RANDOM_FOREST (scTimeBench.trajectory_infer.classifier.ClassifierTypes attribute) register_dataset() (in module scTimeBench.shared.dataset.base) register_dataset_preprocessor() (in module scTimeBench.shared.dataset.base) register_metric() (in module scTimeBench.metrics.base) register_trajectory_inference_method() (in module scTimeBench.trajectory_infer.base) RequiredOutputFiles (class in scTimeBench.shared.constants)

requires_caching() (scTimeBench.shared.dataset.base.BaseDataset method) (scTimeBench.shared.dataset.base.BaseDatasetPreprocessor method) restore_interrupts() (in module scTimeBench.shared.utils) return_all() (scTimeBench.database.DatabaseManager method) run_metrics() (in module scTimeBench.main) RunType (class in scTimeBench.config)

S

scTimeBench.config module scTimeBench.database module scTimeBench.main module scTimeBench.method_utils.method_runner module scTimeBench.method_utils.ot_method_runner module scTimeBench.metrics.base module scTimeBench.metrics.method_manager module scTimeBench.shared.constants module scTimeBench.shared.dataset.base module

scTimeBench.shared.helpers module scTimeBench.shared.utils module scTimeBench.trajectory_infer.base module scTimeBench.trajectory_infer.classifier module scTimeBench.trajectory_infer.kNN module scTimeBench.trajectory_infer.ot module SEPARATE (scTimeBench.config.CsvWriteMode attribute) skip_metric() (in module scTimeBench.metrics.base) soft_labels_to_cell_types() (scTimeBench.trajectory_infer.ot.OptimalTransport method) supports_gex() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method) (scTimeBench.trajectory_infer.ot.OptimalTransport method)

T

TIMEPOINT (scTimeBench.shared.constants.ObservationColumns attribute) to_csv() (in module scTimeBench.main) train() (scTimeBench.method_utils.method_runner.BaseMethod method) (scTimeBench.method_utils.ot_method_runner.BaseOTMethod method)

train_and_predict() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method) train_and_predict_k_fold_cv() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method) train_and_test() (scTimeBench.metrics.method_manager.MethodManager method) TRAIN_ONLY (scTimeBench.config.RunType attribute) TrajectoryInferenceMethodFactory (class in scTimeBench.trajectory_infer.base)

U

uses_gene_expr() (scTimeBench.trajectory_infer.base.BaseTrajectoryInferMethod method)

V

view_evals_by_method() (in module scTimeBench.main)

view_evals_by_metric() (in module scTimeBench.main)

W

WEIGHTED_AVERAGE (scTimeBench.trajectory_infer.kNN.kNNStrategy attribute)