pybel-tools
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Getting Started
Installation
Command Line Interface
Graph Tools
Summary
Filters
Selection
Integration
Mutation
Algorithms
Reverse Causal Reasoning
CausalR
SPIA
NeuroMMSig
EpiCom
Workflows
Stability Analysis
Subgraph Expansion Workflow
Unbiased Candidate Mechanism Generation
Heat Diffusion Workflow
Assemblers
HTML Assembler
Ideogram Assembler
Other Utilities
Document Utilities
Utilities
pybel-tools
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Index
Symbols
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B
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C
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Symbols
--author <author>
pybel-tools-namespace-write command line option
--authors <authors>
pybel-tools-document-boilerplate command line option
--contact <contact>
pybel-tools-namespace-write command line option
--copyright <copyright>
pybel-tools-document-boilerplate command line option
--description <description>
pybel-tools-namespace-write command line option
--disclaimer <disclaimer>
pybel-tools-document-boilerplate command line option
--keyword <keyword>
pybel-tools-annotation-convert-to-namespace command line option
--license <license>
pybel-tools-namespace-write command line option
--licenses <licenses>
pybel-tools-document-boilerplate command line option
--output <output>
pybel-tools-document-boilerplate command line option
pybel-tools-namespace-write command line option
--species <species>
pybel-tools-namespace-write command line option
--values <values>
pybel-tools-namespace-write command line option
--version
pybel-tools command line option
--version <version>
pybel-tools-document-boilerplate command line option
pybel-tools-namespace-write command line option
-c, --connection <connection>
pybel-tools-document-serialize-namespaces command line option
pybel-tools-io command line option
-d, --directory <directory>
pybel-tools-document-serialize-namespaces command line option
-f, --file <file>
pybel-tools-annotation-convert-to-namespace command line option
pybel-tools-namespace-convert-to-annotation command line option
-o, --output <output>
pybel-tools-annotation-convert-to-namespace command line option
pybel-tools-io-get-pmids command line option
pybel-tools-namespace-convert-to-annotation command line option
-p, --path <path>
pybel-tools-document-serialize-namespaces command line option
A
average_node_annotation() (in module pybel_tools.selection)
B
barh() (in module pybel_tools.utils)
barv() (in module pybel_tools.utils)
bel_to_spia_matrices() (in module pybel_tools.analysis.spia)
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)
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)
CITATION
pybel-tools-namespace-write command line option
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)
CONTACT
pybel-tools-document-boilerplate command line option
convert_path_to_metapath() (in module pybel_tools.selection)
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_confidences() (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_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)
DESCRIPTION
pybel-tools-document-boilerplate command line option
DOMAIN
pybel-tools-namespace-write command line option
done_chomping() (pybel_tools.analysis.heat.Runner method)
E
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_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)
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
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_largest_component() (in module pybel_tools.selection)
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_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_nodes_in_all_shortest_paths() (in module pybel_tools.selection)
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_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_by_node_filter() (in module pybel_tools.selection)
get_subgraph_by_node_search() (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)
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)
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)
K
KEYWORD
pybel-tools-namespace-write command line option
L
lint_directory() (in module pybel_tools.document_utils)
lint_file() (in module pybel_tools.document_utils)
load_differential_gene_expression() (in module pybel_tools.integration)
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)
multirun() (in module pybel_tools.analysis.heat)
N
NAME
pybel-tools-document-boilerplate command line option
pybel-tools-namespace-write command line option
NAMESPACES
pybel-tools-document-serialize-namespaces command line option
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_is_consistent() (in module pybel_tools.summary)
pairwise() (in module pybel_tools.utils)
path
pybel-tools-io-get-pmids command line option
plot_summary() (in module pybel_tools.summary)
plot_summary_axes() (in module pybel_tools.summary)
PMIDS
pybel-tools-document-boilerplate command line option
prepare_c3() (in module pybel_tools.utils)
prepare_c3_time_series() (in module pybel_tools.utils)
prune_mechanism_by_data() (in module pybel_tools.generation)
pybel-tools command line option
--version
pybel-tools-annotation-convert-to-namespace command line option
--keyword <keyword>
-f, --file <file>
-o, --output <output>
pybel-tools-document-boilerplate command line option
--authors <authors>
--copyright <copyright>
--disclaimer <disclaimer>
--licenses <licenses>
--output <output>
--version <version>
CONTACT
DESCRIPTION
NAME
PMIDS
pybel-tools-document-serialize-namespaces command line option
-c, --connection <connection>
-d, --directory <directory>
-p, --path <path>
NAMESPACES
pybel-tools-io command line option
-c, --connection <connection>
pybel-tools-io-get-pmids command line option
-o, --output <output>
path
pybel-tools-namespace-convert-to-annotation command line option
-f, --file <file>
-o, --output <output>
pybel-tools-namespace-write command line option
--author <author>
--contact <contact>
--description <description>
--license <license>
--output <output>
--species <species>
--values <values>
--version <version>
CITATION
DOMAIN
KEYWORD
NAME
pybel_tools (module)
pybel_tools.analysis.causalr (module)
pybel_tools.analysis.epicom (module)
pybel_tools.analysis.heat (module)
pybel_tools.analysis.neurommsig.algorithm (module)
pybel_tools.analysis.rcr (module)
pybel_tools.analysis.spia (module)
pybel_tools.analysis.stability (module)
pybel_tools.assembler.html (module)
pybel_tools.assembler.ideogram (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.mutation (module)
pybel_tools.mutation.expansion (module)
pybel_tools.selection (module)
pybel_tools.summary (module)
pybel_tools.utils (module)
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.causalr)
rank_subgraph_by_node_filter() (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)
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)
set_percentage() (in module pybel_tools.utils)
shuffle_node_data() (in module pybel_tools.mutation)
shuffle_relations() (in module pybel_tools.mutation)
spia_matrices_to_excel() (in module pybel_tools.analysis.spia)
spia_matrices_to_tsvs() (in module pybel_tools.analysis.spia)
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_html() (in module pybel_tools.assembler.html)
(in module pybel_tools.assembler.ideogram)
to_jupyter() (in module pybel_tools.assembler.ideogram)
U
unscored_nodes_iter() (pybel_tools.analysis.heat.Runner method)
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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