Index

A

add_constant() (in module spras.interactome) add_directionality_constant() (in module spras.interactome) add_rank_column() (in module spras.util) aggregate_per_algorithm (spras.config.schema.EvaluationAnalysis attribute) (spras.config.schema.MlAnalysis attribute) algorithms (spras.config.schema.RawConfig attribute) all (spras.omicsintegrator1.DummyMode attribute) (spras.omicsintegrator2.DummyMode attribute)

AllPairs (class in spras.allpairs) alpha (spras.rwr.RWRParams attribute) (spras.strwr.ST_RWRParams attribute) Analysis (class in spras.config.schema) analysis (spras.config.schema.RawConfig attribute) average (spras.config.schema.MlLinkage attribute)

B

b (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute)

BowTieBuilder (class in spras.btb)

C

capacity (spras.mincostflow.MinCostFlowParams attribute) CaseInsensitiveEnum (class in spras.config.util) complete (spras.config.schema.MlLinkage attribute) components (spras.config.schema.MlAnalysis attribute) Config (class in spras.config.config) ContainerError containers (spras.config.schema.RawConfig attribute)

contains_node_columns() (spras.dataset.Dataset method) convert_directed_to_undirected() (in module spras.interactome) convert_docker_path() (in module spras.containers) convert_undirected_to_directed() (in module spras.interactome) cosine (spras.config.schema.MlMetric attribute) create_palette() (in module spras.analysis.ml) cytoscape (spras.config.schema.Analysis attribute) CytoscapeAnalysis (class in spras.config.schema)

D

d (spras.omicsintegrator1.OmicsIntegrator1Params attribute) data_dir (spras.config.schema.Dataset attribute) (spras.config.schema.GoldStandard attribute) (spras.evaluation.GoldStandardDict attribute) Dataset (class in spras.config.schema) (class in spras.dataset) dataset_labels (spras.config.schema.GoldStandard attribute) (spras.evaluation.GoldStandardDict attribute) datasets (spras.config.schema.RawConfig attribute) (spras.evaluation.Evaluation attribute) default() (spras.util.NpHashEncoder method) degree() (in module spras.analysis.summary) directed_edge_table (spras.evaluation.Evaluation attribute) dois (spras.allpairs.AllPairs attribute) (spras.btb.BowTieBuilder attribute) (spras.domino.DOMINO attribute) (spras.meo.MEO attribute) (spras.mincostflow.MinCostFlow attribute) (spras.omicsintegrator1.OmicsIntegrator1 attribute) (spras.omicsintegrator2.OmicsIntegrator2 attribute) (spras.pathlinker.PathLinker attribute) (spras.prm.PRM attribute) (spras.responsenet.ResponseNet attribute) (spras.rwr.RWR attribute) (spras.strwr.ST_RWR attribute)

DOMINO (class in spras.domino) DominoParams (class in spras.domino) download_gcs() (in module spras.containers) dummy_mode (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) DummyMode (class in spras.omicsintegrator1) (class in spras.omicsintegrator2) duplicate_edges() (in module spras.util)

E

edge_dummy_function() (spras.evaluation.Evaluation static method) edge_files (spras.config.schema.Dataset attribute) (spras.config.schema.GoldStandard attribute) (spras.evaluation.GoldStandardDict attribute) edge_frequency_node_ensemble() (spras.evaluation.Evaluation static method) Empty (class in spras.config.util) ensemble_network() (in module spras.analysis.ml)

env_to_items() (in module spras.containers) error_code (spras.containers.ContainerError attribute) euclidean (spras.config.schema.MlMetric attribute) Evaluation (class in spras.evaluation) evaluation (spras.config.schema.Analysis attribute) EvaluationAnalysis (class in spras.config.schema) exclude_terms (spras.omicsintegrator1.OmicsIntegrator1Params attribute)

F

file (spras.omicsintegrator1.DummyMode attribute) flow (spras.mincostflow.MinCostFlowParams attribute)

from_file() (spras.dataset.Dataset class method) (spras.evaluation.Evaluation static method)

G

g (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) gamma (spras.responsenet.ResponseNetParams attribute) generate_inputs() (spras.allpairs.AllPairs static method) (spras.btb.BowTieBuilder static method) (spras.domino.DOMINO static method) (spras.meo.MEO static method) (spras.mincostflow.MinCostFlow static method) (spras.omicsintegrator1.OmicsIntegrator1 static method) (spras.omicsintegrator2.OmicsIntegrator2 static method) (spras.pathlinker.PathLinker static method) (spras.prm.PRM static method) (spras.responsenet.ResponseNet static method) (spras.rwr.RWR static method) (spras.strwr.ST_RWR static method)

get_algorithm() (in module spras.runner) get_interactome() (spras.dataset.Dataset method) get_node_columns() (spras.dataset.Dataset method) get_other_files() (spras.dataset.Dataset method) get_params_generic() (spras.prm.PRM class method) get_required_inputs() (in module spras.runner) gold_standards (spras.config.schema.RawConfig attribute) GoldStandard (class in spras.config.schema) GoldStandardDict (class in spras.evaluation)

H

hac_horizontal() (in module spras.analysis.ml) hac_vertical() (in module spras.analysis.ml) has_direction() (in module spras.interactome)

hash_filename() (in module spras.util) hash_length (spras.config.schema.RawConfig attribute) hash_params_sha1_base32() (in module spras.util)

I

include (spras.config.schema.CytoscapeAnalysis attribute) (spras.config.schema.EvaluationAnalysis attribute) (spras.config.schema.MlAnalysis attribute) (spras.config.schema.SummaryAnalysis attribute)

indent() (in module spras.logging) init_from_file() (in module spras.config.config) init_global() (in module spras.config.config)

J

jaccard_similarity_eval() (in module spras.analysis.ml)

K

k (spras.pathlinker.PathLinkerParams attribute)

kde (spras.config.schema.MlAnalysis attribute)

L

label (spras.config.schema.Dataset attribute) (spras.config.schema.GoldStandard attribute) (spras.evaluation.Evaluation attribute) (spras.evaluation.GoldStandardDict attribute) label_validator() (in module spras.config.schema)

labels (spras.config.schema.MlAnalysis attribute) linkage (spras.config.schema.MlAnalysis attribute) load_files_from_dict() (spras.dataset.Dataset method) local_search (spras.meo.MEOParams attribute) Locations (class in spras.config.schema) locations (spras.config.schema.ReconstructionSettings attribute)

M

make_required_dirs() (in module spras.util) manhattan (spras.config.schema.MlMetric attribute) max_path_length (spras.meo.MEOParams attribute) MEO (class in spras.meo) MEOParams (class in spras.meo) merge_gold_standard_input() (spras.evaluation.Evaluation static method) merge_input() (in module spras.runner) metric (spras.config.schema.MlAnalysis attribute) MinCostFlow (class in spras.mincostflow) MinCostFlowParams (class in spras.mincostflow) mixed_edge_table (spras.evaluation.Evaluation attribute) ml (spras.config.schema.Analysis attribute) MlAnalysis (class in spras.config.schema) MlLinkage (class in spras.config.schema) MlMetric (class in spras.config.schema) model_config (spras.config.schema.Analysis attribute) (spras.config.schema.CytoscapeAnalysis attribute) (spras.config.schema.Dataset attribute) (spras.config.schema.EvaluationAnalysis attribute) (spras.config.schema.GoldStandard attribute) (spras.config.schema.Locations attribute) (spras.config.schema.MlAnalysis attribute) (spras.config.schema.RawConfig attribute) (spras.config.schema.ReconstructionSettings attribute) (spras.config.schema.SummaryAnalysis attribute) (spras.config.util.Empty attribute) (spras.domino.DominoParams attribute) (spras.meo.MEOParams attribute) (spras.mincostflow.MinCostFlowParams attribute) (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) (spras.pathlinker.PathLinkerParams attribute) (spras.responsenet.ResponseNetParams attribute) (spras.rwr.RWRParams attribute) (spras.strwr.ST_RWRParams attribute)

module spras spras.allpairs spras.analysis spras.analysis.cytoscape spras.analysis.ml spras.analysis.summary spras.btb spras.config spras.config.config spras.config.schema spras.config.util spras.containers spras.dataset spras.domino spras.evaluation spras.interactome spras.logging spras.meo spras.mincostflow spras.omicsintegrator1 spras.omicsintegrator2 spras.pathlinker spras.prm spras.responsenet spras.runner spras.rwr spras.strwr spras.util module_threshold (spras.domino.DominoParams attribute) mu (spras.omicsintegrator1.OmicsIntegrator1Params attribute) mu_squared (spras.omicsintegrator1.OmicsIntegrator1Params attribute)

N

node_files (spras.config.schema.Dataset attribute) (spras.config.schema.GoldStandard attribute) (spras.evaluation.GoldStandardDict attribute) NODE_ID (spras.dataset.Dataset attribute) (spras.evaluation.Evaluation attribute) node_precision_and_recall() (spras.evaluation.Evaluation static method)

node_table (spras.evaluation.Evaluation attribute) noise (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) noisy_edges (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) NpHashEncoder (class in spras.util)

O

OmicsIntegrator1 (class in spras.omicsintegrator1) OmicsIntegrator1Params (class in spras.omicsintegrator1) OmicsIntegrator2 (class in spras.omicsintegrator2)

OmicsIntegrator2Params (class in spras.omicsintegrator2) other_files (spras.config.schema.Dataset attribute) others (spras.omicsintegrator1.DummyMode attribute) (spras.omicsintegrator2.DummyMode attribute)

P

parse_output() (in module spras.runner) (spras.allpairs.AllPairs static method) (spras.btb.BowTieBuilder static method) (spras.domino.DOMINO static method) (spras.meo.MEO static method) (spras.mincostflow.MinCostFlow static method) (spras.omicsintegrator1.OmicsIntegrator1 static method) (spras.omicsintegrator2.OmicsIntegrator2 static method) (spras.pathlinker.PathLinker static method) (spras.prm.PRM static method) (spras.responsenet.ResponseNet static method) (spras.rwr.RWR static method) (spras.strwr.ST_RWR static method) PathLinker (class in spras.pathlinker) PathLinkerParams (class in spras.pathlinker) pca() (in module spras.analysis.ml)

pca_chosen_pathway() (spras.evaluation.Evaluation static method) plot_dendrogram() (in module spras.analysis.ml) post_domino_id_transform() (in module spras.domino) pre_domino_id_transform() (in module spras.domino) precision_and_recall_pca_chosen_pathway() (spras.evaluation.Evaluation static method) precision_and_recall_per_pathway() (spras.evaluation.Evaluation static method) precision_recall_curve_node_ensemble() (spras.evaluation.Evaluation static method) prepare_dsub_cmd() (in module spras.containers) prepare_inputs() (in module spras.runner) prepare_path_docker() (in module spras.containers) prepare_volume() (in module spras.containers) PRM (class in spras.prm) process_algorithms() (spras.config.config.Config method) process_analysis() (spras.config.config.Config method) process_config() (spras.config.config.Config method) process_datasets() (spras.config.config.Config method)

R

r (spras.omicsintegrator1.OmicsIntegrator1Params attribute) rand_restarts (spras.meo.MEOParams attribute) random_terminals (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) raw_pathway_df() (in module spras.util) RawConfig (class in spras.config.schema) reconstruction_dir (spras.config.schema.Locations attribute) reconstruction_settings (spras.config.schema.RawConfig attribute) ReconstructionSettings (class in spras.config.schema) reinsert_direction_col_directed() (in module spras.interactome) reinsert_direction_col_mixed() (in module spras.interactome) reinsert_direction_col_undirected() (in module spras.interactome) remove_empty_pathways (spras.config.schema.MlAnalysis attribute) required_inputs (spras.allpairs.AllPairs attribute) (spras.btb.BowTieBuilder attribute) (spras.domino.DOMINO attribute) (spras.meo.MEO attribute) (spras.mincostflow.MinCostFlow attribute) (spras.omicsintegrator1.OmicsIntegrator1 attribute) (spras.omicsintegrator2.OmicsIntegrator2 attribute) (spras.pathlinker.PathLinker attribute) (spras.prm.PRM attribute) (spras.responsenet.ResponseNet attribute) (spras.rwr.RWR attribute) (spras.strwr.ST_RWR attribute)

ResponseNet (class in spras.responsenet) ResponseNetParams (class in spras.responsenet) run() (in module spras.runner) (spras.allpairs.AllPairs static method) (spras.btb.BowTieBuilder static method) (spras.domino.DOMINO static method) (spras.meo.MEO static method) (spras.mincostflow.MinCostFlow static method) (spras.omicsintegrator1.OmicsIntegrator1 static method) (spras.omicsintegrator2.OmicsIntegrator2 static method) (spras.pathlinker.PathLinker static method) (spras.prm.PRM static method) (spras.responsenet.ResponseNet static method) (spras.rwr.RWR static method) (spras.strwr.ST_RWR static method) run_container() (in module spras.containers) run_container_and_log() (in module spras.containers) run_container_docker() (in module spras.containers) run_container_dsub() (in module spras.containers) run_container_singularity() (in module spras.containers) run_cytoscape() (in module spras.analysis.cytoscape) run_typeless() (spras.prm.PRM class method) RWR (class in spras.rwr) RWRParams (class in spras.rwr)

S

seed (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) shuffled_prizes (spras.omicsintegrator1.OmicsIntegrator1Params attribute) single (spras.config.schema.MlLinkage attribute) slice_threshold (spras.domino.DominoParams attribute) sort_and_deduplicate_undirected() (in module spras.interactome) spras module spras.allpairs module spras.analysis module spras.analysis.cytoscape module spras.analysis.ml module spras.analysis.summary module spras.btb module spras.config module spras.config.config module spras.config.schema module spras.config.util module spras.containers module spras.dataset module spras.domino module spras.evaluation module

spras.interactome module spras.logging module spras.meo module spras.mincostflow module spras.omicsintegrator1 module spras.omicsintegrator2 module spras.pathlinker module spras.prm module spras.responsenet module spras.runner module spras.rwr module spras.strwr module spras.util module ST_RWR (class in spras.strwr) ST_RWRParams (class in spras.strwr) stderr (spras.containers.ContainerError attribute) stdout (spras.containers.ContainerError attribute) streams_contain() (spras.containers.ContainerError method) summarize_networks() (in module spras.analysis.ml) (in module spras.analysis.summary) summary (spras.config.schema.Analysis attribute) SummaryAnalysis (class in spras.config.schema)

T

terminals (spras.omicsintegrator1.DummyMode attribute) (spras.omicsintegrator2.DummyMode attribute) threshold (spras.rwr.RWRParams attribute) (spras.strwr.ST_RWRParams attribute)

to_file() (spras.dataset.Dataset method) (spras.evaluation.Evaluation method)

U

undirected_edge_table (spras.evaluation.Evaluation attribute)

upload_gcs() (in module spras.containers)

V

validate_df() (in module spras.analysis.ml) validate_required_inputs() (spras.prm.PRM class method)

validate_required_run_args() (spras.prm.PRM class method) visualize_precision_and_recall_plot() (spras.evaluation.Evaluation static method)

W

w (spras.omicsintegrator1.OmicsIntegrator1Params attribute) (spras.omicsintegrator2.OmicsIntegrator2Params attribute) ward (spras.config.schema.MlLinkage attribute)

warning_threshold (spras.dataset.Dataset attribute) write_conf() (in module spras.omicsintegrator1) write_properties() (in module spras.meo)