Index

_

__allowed_edge_types (perturbationx.CausalNetwork attribute) (perturbationx.CausalNetwork.CausalNetwork attribute)

A

add_edge() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) add_edges_from_csv() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) add_edges_from_dsv() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) add_edges_from_pandas() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

add_edges_from_tsv() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) add_mapping() (perturbationx.io.RelationTranslator method) (perturbationx.io.RelationTranslator.RelationTranslator method) (perturbationx.RelationTranslator method) adjacency_permutation_k1() (in module perturbationx.topo_npa.permutation.adjacency_permutation) adjacency_permutation_k2() (in module perturbationx.topo_npa.permutation.adjacency_permutation)

B

build() (perturbationx.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder.NPAResultBuilder method)

C

CausalNetwork (class in perturbationx.CausalNetwork) clear_bypass() (in module perturbationx.vis.cytoscape) coefficient_inference() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.core) color_nodes() (perturbationx.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay.NPAResultDisplay method) color_nodes_by_column() (in module perturbationx.vis.cytoscape) compute_variances() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.statistics) (in module perturbationx.topo_npa.statistics.statistics)

confidence_interval() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.statistics) (in module perturbationx.topo_npa.statistics.statistics) connect_adjacency_components() (in module perturbationx.util) (in module perturbationx.util.connectivity) copy() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) (perturbationx.io.RelationTranslator method) (perturbationx.io.RelationTranslator.RelationTranslator method) (perturbationx.RelationTranslator method) core_covariance_matrix() (in module perturbationx.topo_npa.statistics.variance)

D

datasets() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) display_network() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method)

distributions() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method)

E

edge_to_p4c_format() (in module perturbationx.vis.cytoscape) edges() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) enumerate_nodes() (in module perturbationx.topo_npa.preprocessing.preprocess_network) evaluate_modifications() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.topo_npa) (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

extract_leading_nodes() (perturbationx.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay.NPAResultDisplay method) extract_subgraph() (in module perturbationx.vis.cytoscape)

F

format_dataset() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.preprocessing) (in module perturbationx.topo_npa.preprocessing.preprocessing) from_csv() (perturbationx.CausalNetwork class method) (perturbationx.CausalNetwork.CausalNetwork class method) from_cyjs_json() (perturbationx.CausalNetwork class method) (perturbationx.CausalNetwork.CausalNetwork class method)

from_dsv() (perturbationx.CausalNetwork class method) (perturbationx.CausalNetwork.CausalNetwork class method) from_networkx() (perturbationx.CausalNetwork class method) (perturbationx.CausalNetwork.CausalNetwork class method) from_pandas() (perturbationx.CausalNetwork class method) (perturbationx.CausalNetwork.CausalNetwork class method) from_tsv() (perturbationx.CausalNetwork class method) (perturbationx.CausalNetwork.CausalNetwork class method)

G

generate_adjacencies() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.matrices) generate_boundary_laplacian() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.matrices) generate_core_laplacians() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.matrices) get_adjacencies() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) get_distribution() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) get_laplacians() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) get_leading_nodes() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) get_neighborhood_components() (in module perturbationx.util) (in module perturbationx.util.neighbors)

get_node_subgraph() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) get_osmotic_stress_boundary_path() (in module perturbationx.resources) (in module perturbationx.resources.resources) get_osmotic_stress_core_path() (in module perturbationx.resources) (in module perturbationx.resources.resources) get_osmotic_stress_dataset_paths() (in module perturbationx.resources) (in module perturbationx.resources.resources) get_results() (perturbationx.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay.NPAResultDisplay method) get_shortest_path_components() (in module perturbationx.util) (in module perturbationx.util.shortest_paths) get_style_xml_path() (in module perturbationx.resources) (in module perturbationx.resources.resources) global_info() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method)

H

highlight_leading_nodes() (perturbationx.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay.NPAResultDisplay method)

highlight_subgraph() (in module perturbationx.vis.cytoscape)

I

infer_edge_attributes() (in module perturbationx.topo_npa.preprocessing.preprocess_network) infer_graph_attributes() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.preprocessing) (in module perturbationx.topo_npa.preprocessing.preprocessing) (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

infer_metadata() (in module perturbationx.topo_npa.preprocessing.preprocess_network) infer_node_type() (in module perturbationx.topo_npa.preprocessing.preprocess_network) init_cytoscape() (in module perturbationx.vis.cytoscape) initialize_metadata() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) isolate_subgraph() (in module perturbationx.vis.cytoscape)

L

load_network_data() (in module perturbationx.vis.cytoscape)

M

metadata() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) modify_edge() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) modify_network() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) module perturbationx perturbationx.CausalNetwork perturbationx.io perturbationx.io.network_io perturbationx.io.RelationTranslator perturbationx.resources perturbationx.resources.resources perturbationx.result perturbationx.result.NPAResult perturbationx.result.NPAResultBuilder perturbationx.topo_npa perturbationx.topo_npa.core perturbationx.topo_npa.matrices perturbationx.topo_npa.permutation perturbationx.topo_npa.permutation.adjacency_permutation perturbationx.topo_npa.permutation.permutation perturbationx.topo_npa.preprocessing perturbationx.topo_npa.preprocessing.preprocess_network perturbationx.topo_npa.preprocessing.preprocessing perturbationx.topo_npa.statistics perturbationx.topo_npa.statistics.permutation_tests perturbationx.topo_npa.statistics.statistics perturbationx.topo_npa.statistics.variance perturbationx.topo_npa.topo_npa perturbationx.util perturbationx.util.connectivity perturbationx.util.neighbors perturbationx.util.shortest_paths perturbationx.vis perturbationx.vis.cytoscape perturbationx.vis.NPAResultDisplay

N

new_builder() (perturbationx.NPAResultBuilder class method) (perturbationx.result.NPAResultBuilder class method) (perturbationx.result.NPAResultBuilder.NPAResultBuilder class method) node_attributes() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) node_info() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) nodes() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

NPAResult (class in perturbationx) (class in perturbationx.result.NPAResult) NPAResultBuilder (class in perturbationx) (class in perturbationx.result.NPAResultBuilder) NPAResultDisplay (class in perturbationx) (class in perturbationx.vis.NPAResultDisplay) number_of_edges() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) number_of_nodes() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

P

p_value() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.statistics) (in module perturbationx.topo_npa.statistics.statistics) parse_pandas() (in module perturbationx.io) (in module perturbationx.io.network_io) permute_adjacency() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.permutation) (in module perturbationx.topo_npa.permutation.permutation) permute_edge_list() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.permutation) (in module perturbationx.topo_npa.permutation.permutation) perturbation_amplitude() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.core) perturbation_amplitude_contributions() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.core) perturbation_variance() (in module perturbationx.topo_npa.statistics.variance) perturbationx module perturbationx.CausalNetwork module perturbationx.io module perturbationx.io.network_io module perturbationx.io.RelationTranslator module perturbationx.resources module perturbationx.resources.resources module perturbationx.result module perturbationx.result.NPAResult module perturbationx.result.NPAResultBuilder module perturbationx.topo_npa module perturbationx.topo_npa.core module perturbationx.topo_npa.matrices module

perturbationx.topo_npa.permutation module perturbationx.topo_npa.permutation.adjacency_permutation module perturbationx.topo_npa.permutation.permutation module perturbationx.topo_npa.preprocessing module perturbationx.topo_npa.preprocessing.preprocess_network module perturbationx.topo_npa.preprocessing.preprocessing module perturbationx.topo_npa.statistics module perturbationx.topo_npa.statistics.permutation_tests module perturbationx.topo_npa.statistics.statistics module perturbationx.topo_npa.statistics.variance module perturbationx.topo_npa.topo_npa module perturbationx.util module perturbationx.util.connectivity module perturbationx.util.neighbors module perturbationx.util.shortest_paths module perturbationx.vis module perturbationx.vis.cytoscape module perturbationx.vis.NPAResultDisplay module plot_distribution() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) prune_network_dataset() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.preprocessing) (in module perturbationx.topo_npa.preprocessing.preprocessing)

R

read_dsv() (in module perturbationx.io) (in module perturbationx.io.network_io) RelationTranslator (class in perturbationx) (class in perturbationx.io.RelationTranslator) remove_edge() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) remove_invalid_graph_elements() (in module perturbationx.topo_npa.preprocessing.preprocess_network)

remove_mapping() (perturbationx.io.RelationTranslator method) (perturbationx.io.RelationTranslator.RelationTranslator method) (perturbationx.RelationTranslator method) reset_display() (perturbationx.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay method) (perturbationx.vis.NPAResultDisplay.NPAResultDisplay method) rewire_edges() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

S

set_boundary_display() (in module perturbationx.vis.cytoscape) set_distribution() (perturbationx.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder.NPAResultBuilder method) set_global_attributes() (perturbationx.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder.NPAResultBuilder method)

set_node_attributes() (perturbationx.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder method) (perturbationx.result.NPAResultBuilder.NPAResultBuilder method)

T

test_boundary_permutations() (in module perturbationx.topo_npa.statistics.permutation_tests) test_core_permutations() (in module perturbationx.topo_npa.statistics.permutation_tests) test_permutations() (in module perturbationx.topo_npa) (in module perturbationx.topo_npa.statistics) (in module perturbationx.topo_npa.statistics.statistics) to_csv() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) to_cyjs_json() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) to_dict() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) to_dsv() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) to_edge_list() (in module perturbationx.io) (in module perturbationx.io.network_io) (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

to_json() (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) to_networkx() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) (perturbationx.NPAResult method) (perturbationx.result.NPAResult method) (perturbationx.result.NPAResult.NPAResult method) to_tsv() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) toponpa() (in module perturbationx.topo_npa.topo_npa) (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method) translate() (perturbationx.io.RelationTranslator method) (perturbationx.io.RelationTranslator.RelationTranslator method) (perturbationx.RelationTranslator method)

V

validate_nx_graph() (in module perturbationx.io) (in module perturbationx.io.network_io)

W

wire_edges() (perturbationx.CausalNetwork method) (perturbationx.CausalNetwork.CausalNetwork method)

write_dsv() (in module perturbationx.io) (in module perturbationx.io.network_io)