PathMe
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Contents:
Command Line Interface
KEGG
Reactome
WikiPathways
Constants
Utils
PathMe
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Index
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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P
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Q
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R
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S
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U
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W
A
add_bel_metadata() (in module pathme.utils)
B
BEL_STATS_COLUMN_NAMES (in module pathme.constants)
BRENDA (in module pathme.constants)
C
CallCounted (class in pathme.utils)
CHEBI (in module pathme.constants)
CHEBI_NAME (in module pathme.constants)
check_multiple() (in module pathme.wikipathways.utils)
CHEMBL (in module pathme.constants)
convert_json() (in module pathme.wikipathways.json_rdf_parser)
convert_to_bel() (in module pathme.reactome.convert_to_bel)
(in module pathme.wikipathways.convert_to_bel)
convert_to_nx() (in module pathme.wikipathways.utils)
D
debug_global_statistics() (in module pathme.wikipathways.utils)
debug_pathway_info() (in module pathme.wikipathways.utils)
download_kgml_files() (in module pathme.kegg.utils)
E
ENSEMBL (in module pathme.constants)
ensure_pathme_folders() (in module pathme.constants)
ENTREZ (in module pathme.constants)
entries_dict_ids_argument() (in module pathme.utils)
entry_result_to_dict() (in module pathme.utils)
evaluate_wikipathways_metadata() (in module pathme.wikipathways.utils)
EXPASY (in module pathme.constants)
F
filter_wikipathways_files() (in module pathme.wikipathways.utils)
G
generate_empty_pathway_graph() (in module pathme.wikipathways.json_rdf_parser)
GET_ALL_COMPLEXES_SPARQL (in module pathme.wikipathways.rdf_sparql)
GET_ALL_DATA_NODES_SPARQL (in module pathme.wikipathways.rdf_sparql)
GET_ALL_DIRECTED_INTERACTIONS_SPARQL (in module pathme.wikipathways.rdf_sparql)
GET_ALL_PATHWAY_COMPONENTS (in module pathme.reactome.rdf_sparql)
GET_ALL_PATHWAYS (in module pathme.reactome.rdf_sparql)
get_all_reactions() (in module pathme.kegg.kegg_xml_parser)
get_all_relationships() (in module pathme.kegg.kegg_xml_parser)
GET_ALL_TYPES (in module pathme.reactome.rdf_sparql)
get_bel_stats() (in module pathme.utils)
get_bel_types() (in module pathme.utils)
get_complex_components() (in module pathme.kegg.kegg_xml_parser)
get_data_dir() (in module pathme.constants)
GET_ENTITY_METADATA (in module pathme.reactome.rdf_sparql)
get_entity_nodes() (in module pathme.kegg.kegg_xml_parser)
GET_ENTRIES_SUBTYPES_SPARQL (in module pathme.wikipathways.rdf_sparql)
get_entry_attribute_value() (in module pathme.wikipathways.json_rdf_parser)
get_entry_statitics() (in module pathme.utils)
get_entry_type() (in module pathme.wikipathways.json_rdf_parser)
get_file_name_from_url() (in module pathme.wikipathways.utils)
get_genes_from_pickles() (in module pathme.utils)
get_genes_in_graph() (in module pathme.utils)
get_hgnc_node_info() (in module pathme.reactome.utils)
GET_INTERACTION_PARTICIPANTS_AND_TYPE (in module pathme.reactome.rdf_sparql)
get_kegg_genes_from_pickles() (in module pathme.utils)
get_kegg_pathway_ids() (in module pathme.kegg.utils)
get_kegg_statistics() (in module pathme.kegg.utils)
GET_PATHWAY_INFO_SPARQL (in module pathme.wikipathways.rdf_sparql)
get_pathway_statitics() (in module pathme.utils)
get_reaction_pathway_edges() (in module pathme.kegg.kegg_xml_parser)
get_reactome_statistics() (in module pathme.reactome.rdf_sparql)
get_valid_gene_identifier() (in module pathme.wikipathways.utils)
get_valid_node_parameters() (in module pathme.reactome.utils)
get_wp_statistics() (in module pathme.wikipathways.rdf_sparql)
get_xml_types() (in module pathme.kegg.kegg_xml_parser)
H
HGNC (in module pathme.constants)
HGNC_SYMBOL (in module pathme.constants)
I
import_xml_etree() (in module pathme.kegg.kegg_xml_parser)
INTERPRO (in module pathme.constants)
iterate_wikipathways_paths() (in module pathme.wikipathways.utils)
J
jaccard_similarity() (in module pathme.utils)
K
KEGG (in module pathme.constants)
KEGG_CITATION (in module pathme.constants)
KEGG_ID (in module pathme.constants)
KEGG_KGML_URL (in module pathme.constants)
KEGG_MODIFICATIONS (in module pathme.constants)
KEGG_NAME (in module pathme.constants)
KEGG_STATS_COLUMN_NAMES (in module pathme.constants)
kegg_to_bel() (in module pathme.kegg.convert_to_bel)
kegg_to_pickles() (in module pathme.kegg.convert_to_bel)
KEGG_TYPE (in module pathme.constants)
L
log (in module pathme.kegg.kegg_xml_parser)
(in module pathme.reactome.rdf_sparql)
(in module pathme.reactome.utils)
M
make_downloader() (in module pathme.utils)
match_attribute() (in module pathme.wikipathways.json_rdf_parser)
match_attribute_label() (in module pathme.wikipathways.json_rdf_parser)
match_entry() (in module pathme.wikipathways.json_rdf_parser)
match_entry_type() (in module pathme.wikipathways.json_rdf_parser)
merge_two_dicts() (in module pathme.wikipathways.utils)
MIRBASE (in module pathme.constants)
P
parse_attribute_values() (in module pathme.wikipathways.json_rdf_parser)
parse_attributes() (in module pathme.wikipathways.json_rdf_parser)
parse_entries() (in module pathme.wikipathways.json_rdf_parser)
parse_id_uri() (in module pathme.utils)
(in module pathme.wikipathways.json_rdf_parser)
parse_namespace_uri() (in module pathme.utils)
(in module pathme.wikipathways.json_rdf_parser)
parse_pathway() (in module pathme.wikipathways.json_rdf_parser)
parse_rdf() (in module pathme.utils)
pathme (module)
pathme.constants (module)
pathme.kegg.convert_to_bel (module)
pathme.kegg.kegg_xml_parser (module)
pathme.kegg.utils (module)
pathme.reactome.convert_to_bel (module)
pathme.reactome.rdf_sparql (module)
pathme.reactome.utils (module)
pathme.utils (module)
pathme.wikipathways.convert_to_bel (module)
pathme.wikipathways.json_rdf_parser (module)
pathme.wikipathways.rdf_sparql (module)
pathme.wikipathways.utils (module)
PFAM (in module pathme.constants)
PREFIXES (in module pathme.reactome.rdf_sparql)
(in module pathme.wikipathways.rdf_sparql)
process_multiple_proteins() (in module pathme.reactome.utils)
PUBCHEM (in module pathme.constants)
Q
query_result_to_dict() (in module pathme.utils)
R
RDF_REACTOME (in module pathme.constants)
RDF_WIKIPATHWAYS (in module pathme.constants)
rdf_wikipathways_to_bel() (in module pathme.wikipathways.rdf_sparql)
REACTOME (in module pathme.constants)
REACTOME_CITATION (in module pathme.constants)
reactome_pathway_to_bel() (in module pathme.reactome.rdf_sparql)
reactome_to_bel() (in module pathme.reactome.rdf_sparql)
S
set_entry_attribute() (in module pathme.wikipathways.json_rdf_parser)
set_interaction() (in module pathme.wikipathways.json_rdf_parser)
statistics_to_df() (in module pathme.utils)
summarize_helper() (in module pathme.utils)
U
UNIPROT (in module pathme.constants)
untar_file() (in module pathme.reactome.utils)
unzip_file() (in module pathme.wikipathways.utils)
W
WIKIPATHWAYS (in module pathme.constants)
wikipathways_to_bel() (in module pathme.wikipathways.rdf_sparql)
wikipathways_to_pickles() (in module pathme.wikipathways.rdf_sparql)
WIKIPEDIA (in module pathme.constants)
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