pybel-tools
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Getting Started
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Command Line Interface
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Summary
Filters
Selection
Integration
Mutation
Visualization
Query Builder
Workflows
Stability Analysis
Subgraph Expansion Workflow
Unbiased Candidate Mechanism Generation
Heat Diffusion Workflow
Algorithms
Other Utilities
IO Utilities
Document Utilities
Utilities
pybel-tools
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M
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N
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O
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P
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Q
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R
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S
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T
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W
A
append_network() (pybel_tools.query.Query method)
append_pipeline() (pybel_tools.query.Query method)
append_seeding_annotation() (pybel_tools.query.Query method)
append_seeding_induction() (pybel_tools.query.Query method)
append_seeding_neighbors() (pybel_tools.query.Query method)
append_seeding_sample() (pybel_tools.query.Query method)
average_node_annotation() (in module pybel_tools.selection)
B
barh() (in module pybel_tools.utils)
barv() (in module pybel_tools.utils)
build_annotation_dict_all_filter() (in module pybel_tools.filters.edge_filters)
build_annotation_dict_any_filter() (in module pybel_tools.filters.edge_filters)
build_author_inclusion_filter() (in module pybel_tools.filters.edge_filters)
build_delete_node_by_hash() (in module pybel_tools.mutation)
build_edge_data_filter() (in module pybel_tools.filters.edge_filters)
build_expand_node_neighborhood_by_hash() (in module pybel_tools.mutation)
build_node_data_search() (in module pybel_tools.filters.node_filters)
build_node_key_search() (in module pybel_tools.filters.node_filters)
build_pmid_exclusion_filter() (in module pybel_tools.filters.edge_filters)
build_pmid_inclusion_filter() (in module pybel_tools.filters.edge_filters)
build_source_namespace_filter() (in module pybel_tools.filters.edge_filters)
build_target_namespace_filter() (in module pybel_tools.filters.edge_filters)
build_template_environment() (in module pybel_tools.utils)
build_template_renderer() (in module pybel_tools.utils)
C
calculate_average_score_by_annotation() (in module pybel_tools.analysis.heat)
calculate_average_scores_on_graph() (in module pybel_tools.analysis.heat)
calculate_average_scores_on_subgraphs() (in module pybel_tools.analysis.heat)
calculate_betweenness_centality() (in module pybel_tools.utils)
calculate_error_by_annotation() (in module pybel_tools.summary)
calculate_global_tanimoto_set_distances() (in module pybel_tools.utils)
calculate_incorrect_name_dict() (in module pybel_tools.summary)
calculate_score() (pybel_tools.analysis.heat.Runner method)
calculate_single_tanimoto_set_distances() (in module pybel_tools.utils)
calculate_subgraph_edge_overlap() (in module pybel_tools.summary)
calculate_tanimoto_set_distances() (in module pybel_tools.utils)
canonical_circulation() (in module pybel_tools.utils)
collapse_consistent_edges() (in module pybel_tools.mutation)
collapse_equivalencies_by_namespace() (in module pybel_tools.mutation)
collapse_gene_variants() (in module pybel_tools.mutation)
collapse_nodes() (in module pybel_tools.mutation)
collapse_orthologies_by_namespace() (in module pybel_tools.mutation)
collapse_protein_variants() (in module pybel_tools.mutation)
collapse_to_protein_interactions() (in module pybel_tools.mutation)
convert_directory() (in module pybel_tools.ioutils)
convert_path_to_metapath() (in module pybel_tools.selection)
convert_paths() (in module pybel_tools.ioutils)
count_annotation_values() (in module pybel_tools.summary)
count_annotation_values_filtered() (in module pybel_tools.summary)
count_annotations() (in module pybel_tools.summary)
count_author_publications() (in module pybel_tools.summary)
count_authors() (in module pybel_tools.summary)
count_authors_by_annotation() (in module pybel_tools.summary)
count_citation_years() (in module pybel_tools.summary)
count_citations() (in module pybel_tools.summary)
count_citations_by_annotation() (in module pybel_tools.summary)
count_defaultdict() (in module pybel_tools.utils)
count_dict_values() (in module pybel_tools.utils)
count_error_types() (in module pybel_tools.summary)
count_naked_names() (in module pybel_tools.summary)
count_pathologies() (in module pybel_tools.summary)
count_pmids() (in module pybel_tools.summary)
count_possible_predecessors() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
count_possible_successors() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
count_relations() (in module pybel_tools.summary)
count_sources() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
count_subgraph_sizes() (in module pybel_tools.summary)
count_targets() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
count_top_centrality() (in module pybel_tools.summary)
count_unique_authors() (in module pybel_tools.summary)
count_unique_citations() (in module pybel_tools.summary)
count_unique_relations() (in module pybel_tools.summary)
create_timeline() (in module pybel_tools.summary)
D
data_contains_key_builder() (in module pybel_tools.filters.node_filters)
data_missing_key_builder() (in module pybel_tools.filters.node_filters)
done_chomping() (pybel_tools.analysis.heat.Runner method)
dump() (pybel_tools.query.Query method)
dumps() (pybel_tools.query.Query method)
E
Effect (class in pybel_tools.analysis.sst)
enrich_complexes() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
enrich_composites() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
enrich_grouping() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
enrich_internal_unqualified_edges() (in module pybel_tools.mutation)
enrich_protein_and_rna_origins() (in module pybel_tools.mutation)
enrich_pubmed_citations() (in module pybel_tools.mutation)
enrich_reactions() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
enrich_unqualified() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
enrich_variants() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
epicom_on_graph() (in module pybel_tools.analysis.epicom.algorithm)
exclude_pathology_filter() (in module pybel_tools.filters.node_filters)
expand_internal() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
expand_internal_causal() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
expand_periphery() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
export_namespace() (in module pybel_tools.definition_utils)
export_namespaces() (in module pybel_tools.definition_utils)
F
from_json() (pybel_tools.query.Query static method)
function_exclusion_filter_builder() (in module pybel_tools.filters.node_filters)
function_inclusion_filter_builder() (in module pybel_tools.filters.node_filters)
function_namespace_inclusion_builder() (in module pybel_tools.filters.node_filters)
G
generate_bioprocess_mechanisms() (in module pybel_tools.generation)
generate_mechanism() (in module pybel_tools.generation)
get_activities() (in module pybel_tools.summary)
get_annotations() (in module pybel_tools.summary)
get_annotations_containing_keyword() (in module pybel_tools.summary)
get_authors() (in module pybel_tools.summary)
get_authors_by_keyword() (in module pybel_tools.summary)
get_causal_central_nodes() (in module pybel_tools.summary)
get_causal_in_edges() (in module pybel_tools.summary)
get_causal_out_edges() (in module pybel_tools.summary)
get_causal_sink_nodes() (in module pybel_tools.summary)
get_causal_source_nodes() (in module pybel_tools.summary)
get_causal_subgraph() (in module pybel_tools.selection)
get_chaotic_pairs() (in module pybel_tools.analysis.stability)
get_chaotic_triplets() (in module pybel_tools.analysis.stability)
get_circulations() (in module pybel_tools.utils)
get_citation_years() (in module pybel_tools.summary)
get_consistent_edges() (in module pybel_tools.summary)
get_contradiction_summary() (in module pybel_tools.analysis.stability)
get_contradictory_pairs() (in module pybel_tools.summary)
get_correlation_graph() (in module pybel_tools.analysis.stability)
get_correlation_triangles() (in module pybel_tools.analysis.stability)
get_dampened_pairs() (in module pybel_tools.analysis.stability)
get_dampened_triplets() (in module pybel_tools.analysis.stability)
get_decrease_mismatch_triplets() (in module pybel_tools.analysis.stability)
get_degradations() (in module pybel_tools.summary)
get_edge_relations() (in module pybel_tools.summary)
get_evidences_by_pmid() (in module pybel_tools.summary)
get_final_score() (pybel_tools.analysis.heat.Runner method)
get_incorrect_names() (in module pybel_tools.summary)
get_incorrect_names_by_namespace() (in module pybel_tools.summary)
get_increase_mismatch_triplets() (in module pybel_tools.analysis.stability)
get_jens_unstable() (in module pybel_tools.analysis.stability)
get_leaves_by_type() (in module pybel_tools.selection)
get_merged_namespace_names() (in module pybel_tools.definition_utils)
get_modifications_count() (in module pybel_tools.summary)
get_most_common_errors() (in module pybel_tools.summary)
get_multi_causal_downstream() (in module pybel_tools.selection)
get_multi_causal_upstream() (in module pybel_tools.selection)
get_mutually_unstable_correlation_triples() (in module pybel_tools.analysis.stability)
get_naked_names() (in module pybel_tools.summary)
get_names_including_errors() (in module pybel_tools.summary)
get_names_including_errors_by_namespace() (in module pybel_tools.summary)
get_namespaces_with_incorrect_names() (in module pybel_tools.summary)
get_neurommsig_score() (in module pybel_tools.analysis.neurommsig.algorithm)
get_neurommsig_scores() (in module pybel_tools.analysis.neurommsig.algorithm)
get_neurommsig_scores_prestratified() (in module pybel_tools.analysis.neurommsig.algorithm)
get_nodes_in_all_shortest_paths() (in module pybel_tools.selection)
get_path_effect() (in module pybel_tools.analysis.sst)
get_paths_recursive() (in module pybel_tools.ioutils)
get_peripheral_predecessor_edges() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
get_peripheral_successor_edges() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
get_pmid_by_keyword() (in module pybel_tools.summary)
get_random_edge() (pybel_tools.analysis.heat.Runner method)
get_random_subgraph() (in module pybel_tools.selection)
get_random_walk_spanning_tree() (in module pybel_tools.analysis.sst)
get_regulatory_pairs() (in module pybel_tools.analysis.stability)
get_remaining_graph() (pybel_tools.analysis.heat.Runner method)
get_separate_unstable_correlation_triples() (in module pybel_tools.analysis.stability)
get_shortest_directed_path_between_subgraphs() (in module pybel_tools.selection)
get_shortest_undirected_path_between_subgraphs() (in module pybel_tools.selection)
get_subgraph() (in module pybel_tools.selection)
get_subgraph_by_all_shortest_paths() (in module pybel_tools.selection)
get_subgraph_by_annotation_value() (in module pybel_tools.selection)
get_subgraph_by_annotations() (in module pybel_tools.selection)
get_subgraph_by_authors() (in module pybel_tools.selection)
get_subgraph_by_induction() (in module pybel_tools.selection)
get_subgraph_by_neighborhood() (in module pybel_tools.selection)
get_subgraph_by_node_filter() (in module pybel_tools.selection)
get_subgraph_by_node_search() (in module pybel_tools.selection)
get_subgraph_by_pubmed() (in module pybel_tools.selection)
get_subgraph_by_second_neighbors() (in module pybel_tools.selection)
get_subgraph_edges() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
get_subgraph_peripheral_nodes() (in module pybel_tools.mutation)
(in module pybel_tools.mutation.expansion)
get_translocated() (in module pybel_tools.summary)
get_triangles() (in module pybel_tools.analysis.stability)
get_undefined_annotations() (in module pybel_tools.summary)
get_undefined_namespace_names() (in module pybel_tools.summary)
get_undefined_namespaces() (in module pybel_tools.summary)
get_unused_annotations() (in module pybel_tools.summary)
get_unused_list_annotation_values() (in module pybel_tools.summary)
get_unweighted_sources() (in module pybel_tools.generation)
get_version() (in module pybel_tools.utils)
get_walks_exhaustive (in module pybel_tools.selection)
graph_edge_data_iter() (in module pybel_tools.utils)
group_errors() (in module pybel_tools.summary)
group_nodes_by_annotation() (in module pybel_tools.selection)
group_nodes_by_annotation_filtered() (in module pybel_tools.selection)
H
has_leaves() (pybel_tools.analysis.heat.Runner method)
has_pathology_causal() (in module pybel_tools.filters.edge_filters)
highlight_edges() (in module pybel_tools.mutation)
highlight_nodes() (in module pybel_tools.mutation)
highlight_subgraph() (in module pybel_tools.mutation)
I
in_out_ratio() (pybel_tools.analysis.heat.Runner method)
include_pathology_filter() (in module pybel_tools.filters.node_filters)
infer_missing_backwards_edge() (in module pybel_tools.mutation)
infer_missing_two_way_edges() (in module pybel_tools.mutation)
info_json() (in module pybel_tools.summary)
info_list() (in module pybel_tools.summary)
info_str() (in module pybel_tools.summary)
is_causal_central() (in module pybel_tools.summary)
is_causal_relation() (in module pybel_tools.summary)
is_causal_sink() (in module pybel_tools.summary)
is_causal_source() (in module pybel_tools.summary)
is_edge_highlighted() (in module pybel_tools.mutation)
is_node_highlighted() (in module pybel_tools.mutation)
is_unweighted_source() (in module pybel_tools.generation)
iter_leaves() (pybel_tools.analysis.heat.Runner method)
J
jens_transformation_alpha() (in module pybel_tools.analysis.stability)
jens_transformation_beta() (in module pybel_tools.analysis.stability)
L
lint_directory() (in module pybel_tools.document_utils)
lint_file() (in module pybel_tools.document_utils)
load() (pybel_tools.query.Query static method)
load_differential_gene_expression() (in module pybel_tools.integration)
loads() (pybel_tools.query.Query static method)
M
match_simple_metapath() (in module pybel_tools.selection)
merge_namespaces() (in module pybel_tools.definition_utils)
min_tanimoto_set_similarity() (in module pybel_tools.utils)
multi_run_epicom() (in module pybel_tools.analysis.epicom.algorithm)
multirun() (in module pybel_tools.analysis.heat)
N
namespace_inclusion_builder() (in module pybel_tools.filters.node_filters)
node_exclusion_filter_builder() (in module pybel_tools.filters.node_filters)
node_has_label() (in module pybel_tools.filters.node_filters)
node_inclusion_filter_builder() (in module pybel_tools.filters.node_filters)
node_missing_label() (in module pybel_tools.filters.node_filters)
O
overlay_data() (in module pybel_tools.integration)
overlay_type_data() (in module pybel_tools.integration)
P
pair_has_contradiction() (in module pybel_tools.summary)
pair_is_consistent() (in module pybel_tools.summary)
pairwise() (in module pybel_tools.utils)
parse_authors() (in module pybel_tools.mutation)
plot_summary() (in module pybel_tools.summary)
plot_summary_axes() (in module pybel_tools.summary)
prepare_c3() (in module pybel_tools.utils)
prepare_c3_time_series() (in module pybel_tools.utils)
print_summary() (in module pybel_tools.summary)
prune_mechanism_by_data() (in module pybel_tools.generation)
pybel_tools (module)
pybel_tools.analysis.epicom.algorithm (module)
pybel_tools.analysis.heat (module)
pybel_tools.analysis.neurommsig.algorithm (module)
pybel_tools.analysis.rcr (module)
pybel_tools.analysis.sst (module)
pybel_tools.analysis.stability (module)
pybel_tools.definition_utils (module)
pybel_tools.document_utils (module)
pybel_tools.filters (module)
pybel_tools.filters.edge_filters (module)
pybel_tools.filters.node_filters (module)
pybel_tools.generation (module)
pybel_tools.integration (module)
pybel_tools.ioutils (module)
pybel_tools.mutation (module)
pybel_tools.mutation.expansion (module)
pybel_tools.query (module)
pybel_tools.selection (module)
pybel_tools.summary (module)
pybel_tools.utils (module)
pybel_tools.visualization (module)
Q
Query (class in pybel_tools.query)
QueryMissingNetworksError
R
random_by_edges() (in module pybel_tools.mutation)
random_by_nodes() (in module pybel_tools.mutation)
rank_causalr_hypothesis() (in module pybel_tools.analysis.sst)
rank_edges() (in module pybel_tools.analysis.sst)
rank_subgraph_by_node_filter() (in module pybel_tools.summary)
relation_set_has_contradictions() (in module pybel_tools.summary)
remove_highlight_edges() (in module pybel_tools.mutation)
remove_highlight_nodes() (in module pybel_tools.mutation)
remove_highlight_subgraph() (in module pybel_tools.mutation)
remove_inconsistent_edges() (in module pybel_tools.mutation)
remove_random_edge() (pybel_tools.analysis.heat.Runner method)
remove_random_edge_until_has_leaves() (pybel_tools.analysis.heat.Runner method)
remove_unweighted_leaves() (in module pybel_tools.generation)
remove_unweighted_sources() (in module pybel_tools.generation)
RESULT_LABELS (in module pybel_tools.analysis.heat)
rewire_variants_to_genes() (in module pybel_tools.mutation)
run() (pybel_tools.analysis.heat.Runner method)
(pybel_tools.query.Query method)
run_cna() (in module pybel_tools.analysis.sst)
run_epicom() (in module pybel_tools.analysis.epicom.algorithm)
run_rcr() (in module pybel_tools.analysis.rcr)
run_with_graph_transformation() (pybel_tools.analysis.heat.Runner method)
Runner (class in pybel_tools.analysis.heat)
S
safe_add_edge() (in module pybel_tools.utils)
score_leaves() (pybel_tools.analysis.heat.Runner method)
search_node_hgnc_names() (in module pybel_tools.selection)
search_node_names() (in module pybel_tools.selection)
search_node_namespace_names() (in module pybel_tools.selection)
serialize_authors() (in module pybel_tools.mutation)
set_percentage() (in module pybel_tools.utils)
shuffle_node_data() (in module pybel_tools.mutation)
shuffle_relations() (in module pybel_tools.mutation)
subgraphs_to_pickles() (in module pybel_tools.ioutils)
summarize_edge_filter() (in module pybel_tools.filters.edge_filters)
summarize_node_filter() (in module pybel_tools.filters.node_filters)
summarize_stability() (in module pybel_tools.analysis.stability)
summarize_subgraph_edge_overlap() (in module pybel_tools.summary)
summarize_subgraph_node_overlap() (in module pybel_tools.summary)
T
tanimoto_set_similarity() (in module pybel_tools.utils)
to_json() (pybel_tools.query.Query method)
U
unscored_nodes_iter() (pybel_tools.analysis.heat.Runner method)
upload_recursive() (in module pybel_tools.ioutils)
W
workflow() (in module pybel_tools.analysis.heat)
workflow_aggregate() (in module pybel_tools.analysis.heat)
workflow_all() (in module pybel_tools.analysis.heat)
workflow_all_aggregate() (in module pybel_tools.analysis.heat)
write_boilerplate() (in module pybel_tools.document_utils)
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