Index

A

add_constant() (in module spras.interactome) add_directionality_constant() (in module spras.interactome)

add_rank_column() (in module spras.util) AllPairs (class in spras.allpairs)

C

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

D

Dataset (class in spras.dataset) default() (spras.util.NpHashEncoder method) degree() (in module spras.analysis.summary) dois (spras.allpairs.AllPairs 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)

DOMINO (class in spras.domino) download_gcs() (in module spras.containers) duplicate_edges() (in module spras.util)

E

edge_frequency_node_ensemble() (spras.evaluation.Evaluation static method) ensemble_network() (in module spras.analysis.ml)

env_to_items() (in module spras.containers) Evaluation (class in spras.evaluation)

F

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

G

generate_inputs() (spras.allpairs.AllPairs 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 method) (spras.pathlinker.PathLinker static method) (spras.prm.PRM 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_required_inputs() (in module spras.runner)

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_params_sha1_base32() (in module spras.util)

J

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

L

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

M

make_required_dirs() (in module spras.util) MEO (class in spras.meo) merge_gold_standard_input() (spras.evaluation.Evaluation static method) merge_input() (in module spras.runner) MinCostFlow (class in spras.mincostflow) module spras spras.allpairs spras.analysis spras.analysis.cytoscape spras.analysis.ml spras.analysis.summary spras.config spras.containers spras.dataset spras.domino spras.evaluation spras.interactome spras.meo spras.mincostflow spras.omicsintegrator1 spras.omicsintegrator2 spras.pathlinker spras.prm spras.runner spras.util

N

NODE_ID (spras.dataset.Dataset attribute) (spras.evaluation.Evaluation attribute)

node_precision_and_recall() (spras.evaluation.Evaluation static method) NpHashEncoder (class in spras.util)

O

OmicsIntegrator1 (class in spras.omicsintegrator1)

OmicsIntegrator2 (class in spras.omicsintegrator2)

P

parse_output() (in module spras.runner) (spras.allpairs.AllPairs 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) PathLinker (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)

R

raw_pathway_df() (in module spras.util) reinsert_direction_col_directed() (in module spras.interactome) reinsert_direction_col_mixed() (in module spras.interactome) reinsert_direction_col_undirected() (in module spras.interactome) required_inputs (spras.allpairs.AllPairs 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) run() (in module spras.runner) (spras.allpairs.AllPairs 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)

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)

S

spras module spras.allpairs module spras.analysis module spras.analysis.cytoscape module spras.analysis.ml module spras.analysis.summary module spras.config module spras.containers module spras.dataset module spras.domino module spras.evaluation module

spras.interactome module spras.meo module spras.mincostflow module spras.omicsintegrator1 module spras.omicsintegrator2 module spras.pathlinker module spras.prm module spras.runner module spras.util module summarize_networks() (in module spras.analysis.ml) (in module spras.analysis.summary)

T

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

U

upload_gcs() (in module spras.containers)

V

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

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

W

warning_threshold (spras.dataset.Dataset attribute)

write_conf() (in module spras.omicsintegrator1) write_properties() (in module spras.meo)