Index

A

adjacency (cosifer.collections.graph.Graph attribute) alpha (cosifer.inferencers.tigress.TIGRESS attribute)

apply_filter() (cosifer.collections.interaction_table.InteractionTable method) Aracne (class in cosifer.inferencers.aracne)

B

benjamini_hochberg_correction() (in module cosifer.utils.stats)

benjamini_yekutieli_correction() (in module cosifer.utils.stats) bonferroni_correction() (in module cosifer.utils.stats)

C

CLR (class in cosifer.inferencers.clr) combine() (cosifer.combiners.network_combiner.NetworkCombiner method) combine_tables (cosifer.combiners.cit.CombineInteractionTables attribute) combine_tables() (in module cosifer.combiners.cit) combined_df_to_interaction_table() (in module cosifer.combiners.core) CombineInteractionTables (class in cosifer.combiners.cit) compute_snf() (in module cosifer.combiners.snf) concatenate_intensities() (in module cosifer.combiners.core) confidence_threshold (cosifer.inferencers.correlation.Correlation attribute) (cosifer.inferencers.funchisq.FunChisq attribute) correction (cosifer.inferencers.correlation.Correlation attribute) (cosifer.inferencers.funchisq.FunChisq attribute) Correlation (class in cosifer.inferencers.correlation) cosifer (module) cosifer.collections (module) cosifer.collections.graph (module) cosifer.collections.interaction_table (module) cosifer.combiners (module) cosifer.combiners.cit (module) cosifer.combiners.core (module) cosifer.combiners.network_combiner (module) cosifer.combiners.snf (module)

cosifer.combiners.summa (module) cosifer.handlers (module) cosifer.handlers.file_handler (module) cosifer.handlers.fs_handler (module) cosifer.handlers.network_handler (module) cosifer.inferencers (module) cosifer.inferencers.aracne (module) cosifer.inferencers.clr (module) cosifer.inferencers.correlation (module) cosifer.inferencers.funchisq (module) cosifer.inferencers.genie3 (module) cosifer.inferencers.glasso (module) cosifer.inferencers.jrf (module) cosifer.inferencers.mrnet (module) cosifer.inferencers.network_inferencer (module) cosifer.inferencers.tigress (module) cosifer.pipelines (module) cosifer.pipelines.pipeline_cli (module) cosifer.pipelines.pipeline_gui (module) cosifer.utils (module) cosifer.utils.data (module) cosifer.utils.stats (module) cosifer.utils.vector_quantization (module)

D

df (cosifer.collections.interaction_table.InteractionTable attribute) directed_to_undirected_interactions() (in module cosifer.collections.interaction_table) disc (cosifer.inferencers.aracne.Aracne attribute) (cosifer.inferencers.clr.CLR attribute) (cosifer.inferencers.mrnet.MRNET attribute)

dump() (cosifer.handlers.file_handler.FileHandler method) (cosifer.handlers.fs_handler.FileSystemHandler method) (cosifer.handlers.network_handler.NetworkHandler method)

E

estimator (cosifer.inferencers.aracne.Aracne attribute) (cosifer.inferencers.clr.CLR attribute) (cosifer.inferencers.mrnet.MRNET attribute)

exist() (cosifer.handlers.file_handler.FileHandler method) (cosifer.handlers.fs_handler.FileSystemHandler method)

F

FileHandler (class in cosifer.handlers.file_handler) filepath (cosifer.handlers.fs_handler.FileSystemHandler attribute), [1] (cosifer.handlers.network_handler.NetworkHandler attribute), [1]

FileSystemHandler (class in cosifer.handlers.fs_handler) fill_na_ranks() (in module cosifer.combiners.summa) from_precision_matrix_partial_correlations() (in module cosifer.utils.stats) FunChisq (class in cosifer.inferencers.funchisq)

G

GENIE3 (class in cosifer.inferencers.genie3) get_df_dict() (cosifer.collections.interaction_table.InteractionTable method) get_interaction_tables() (in module cosifer.pipelines.pipeline_cli) get_scaled_adjacency() (cosifer.collections.graph.Graph method) get_scaled_ranks() (in module cosifer.combiners.cit)

get_synthetic_data() (in module cosifer.utils.data) Glasso (class in cosifer.inferencers.glasso) Graph (class in cosifer.collections.graph) graph (cosifer.combiners.cit.CombineInteractionTables attribute) (cosifer.handlers.network_handler.NetworkHandler attribute), [1] (cosifer.inferencers.network_inferencer.NetworkInferencer attribute), [1]

H

hard_mean_scaled_ranks_table() (in module cosifer.combiners.cit)

hard_mean_table() (in module cosifer.combiners.cit)

I

indices_to_labels (cosifer.collections.graph.Graph attribute), [1] infer_network() (cosifer.inferencers.network_inferencer.NetworkInferencer method) interaction_symbol (cosifer.combiners.cit.CombineInteractionTables attribute) (cosifer.combiners.snf.SNF attribute) (cosifer.combiners.summa.Summa attribute)

interaction_table_from_dict() (in module cosifer.collections.interaction_table) interaction_table_from_edge_list() (in module cosifer.collections.interaction_table) interaction_table_from_gzip() (in module cosifer.collections.interaction_table) interaction_table_to_edge_list() (in module cosifer.collections.interaction_table) InteractionTable (class in cosifer.collections.interaction_table)

J

JointRandomForest (class in cosifer.inferencers.jrf)

K

k (cosifer.inferencers.genie3.GENIE3 attribute) (cosifer.inferencers.tigress.TIGRESS attribute) k_max (cosifer.inferencers.funchisq.FunChisq attribute) k_means_bic() (in module cosifer.utils.vector_quantization)

k_means_optimized_with_bic() (in module cosifer.utils.vector_quantization) k_means_vector_quantization() (in module cosifer.utils.vector_quantization) k_min (cosifer.inferencers.funchisq.FunChisq attribute) k_step (cosifer.inferencers.funchisq.FunChisq attribute)

L

labels (cosifer.collections.interaction_table.InteractionTable attribute) labels_to_indices (cosifer.collections.graph.Graph attribute), [1]

load() (cosifer.handlers.file_handler.FileHandler method) (cosifer.handlers.fs_handler.FileSystemHandler method) (cosifer.handlers.network_handler.NetworkHandler method)

M

max_scaled_ranks_table() (in module cosifer.combiners.cit) max_table() (in module cosifer.combiners.cit) mean_scaled_ranks_table() (in module cosifer.combiners.cit) mean_table() (in module cosifer.combiners.cit) median_scaled_ranks_table() (in module cosifer.combiners.cit) median_table() (in module cosifer.combiners.cit) merger (cosifer.inferencers.jrf.JointRandomForest attribute) method (cosifer.inferencers.aracne.Aracne attribute) (cosifer.inferencers.clr.CLR attribute) (cosifer.inferencers.correlation.Correlation attribute), [1] (cosifer.inferencers.funchisq.FunChisq attribute) (cosifer.inferencers.genie3.GENIE3 attribute) (cosifer.inferencers.glasso.Glasso attribute) (cosifer.inferencers.jrf.JointRandomForest attribute) (cosifer.inferencers.mrnet.MRNET attribute) (cosifer.inferencers.tigress.TIGRESS attribute)

method_selection() (in module cosifer.pipelines.pipeline_cli) (in module cosifer.pipelines.pipeline_gui) min_scaled_ranks_table() (in module cosifer.combiners.cit) min_table() (in module cosifer.combiners.cit) MRNET (class in cosifer.inferencers.mrnet) mtry (cosifer.inferencers.jrf.JointRandomForest attribute)

N

n (cosifer.collections.graph.Graph attribute), [1] n_bootstrap (cosifer.inferencers.tigress.TIGRESS attribute) n_cores (cosifer.inferencers.genie3.GENIE3 attribute) (cosifer.inferencers.tigress.TIGRESS attribute) n_step_lars (cosifer.inferencers.tigress.TIGRESS attribute) n_trees (cosifer.inferencers.genie3.GENIE3 attribute)

name (cosifer.combiners.cit.CombineInteractionTables attribute) (cosifer.combiners.snf.SNF attribute) (cosifer.combiners.summa.Summa attribute) NetworkCombiner (class in cosifer.combiners.network_combiner) NetworkHandler (class in cosifer.handlers.network_handler) NetworkInferencer (class in cosifer.inferencers.network_inferencer) ntree (cosifer.inferencers.jrf.JointRandomForest attribute)

P

parameters (cosifer.handlers.network_handler.NetworkHandler attribute) process_group() (in module cosifer.collections.interaction_table)

process_index() (in module cosifer.collections.interaction_table) process_index_with_weights() (in module cosifer.collections.interaction_table)

R

read_data() (in module cosifer.utils.data) read_gmt() (in module cosifer.utils.data) regulators (cosifer.inferencers.genie3.GENIE3 attribute) run() (in module cosifer.pipelines.pipeline_cli) (in module cosifer.pipelines.pipeline_gui)

run_combiner() (in module cosifer.pipelines.pipeline_cli) (in module cosifer.pipelines.pipeline_gui) run_inference() (in module cosifer.pipelines.pipeline_cli) (in module cosifer.pipelines.pipeline_gui)

S

scale_graph() (in module cosifer.utils.data) scoring (cosifer.inferencers.tigress.TIGRESS attribute) set_adjacency_from_numpy() (cosifer.collections.graph.Graph method) set_adjacency_from_pandas() (cosifer.collections.graph.Graph method) set_adjacency_from_sparse() (cosifer.collections.graph.Graph method)

set_labels() (cosifer.collections.graph.Graph method) SNF (class in cosifer.combiners.snf) sort_interaction_entities() (in module cosifer.inferencers.funchisq) Summa (class in cosifer.combiners.summa) summa_object (cosifer.combiners.summa.Summa attribute), [1] summa_scores_table() (in module cosifer.combiners.summa)

T

targets (cosifer.inferencers.genie3.GENIE3 attribute) tf_list (cosifer.inferencers.tigress.TIGRESS attribute) TIGRESS (class in cosifer.inferencers.tigress) to_edge_list() (cosifer.collections.interaction_table.InteractionTable method) to_graph() (cosifer.collections.interaction_table.InteractionTable method)

to_interaction_table() (cosifer.collections.graph.Graph method) trained (cosifer.combiners.network_combiner.NetworkCombiner attribute) (cosifer.handlers.network_handler.NetworkHandler attribute), [1] (cosifer.inferencers.network_inferencer.NetworkInferencer attribute), [1] tree_method (cosifer.inferencers.genie3.GENIE3 attribute)

U

undirected (cosifer.collections.graph.Graph attribute) (cosifer.inferencers.funchisq.FunChisq attribute)

use_parallel (cosifer.inferencers.tigress.TIGRESS attribute)

V

verbose (cosifer.inferencers.genie3.GENIE3 attribute) (cosifer.inferencers.tigress.TIGRESS attribute)