| Default values for the package options | .omnipathr_options_defaults |
| All UniProt ACs for one organism | all_uniprot_acs |
| A table with all UniProt records | all_uniprots |
| Inspect the ambiguity of a mapping | ambiguity |
| All ancestors in the ontology tree | ancestors |
| Network interactions with annotations | annotated_network |
| Annotation categories and resources | annotation_categories |
| Retrieves a list of available resources in the annotations database of OmniPath | annotation_resources get_annotation_resources |
| Protein and gene annotations from OmniPath | annotations import_omnipath_annotations |
| Query the Ensembl BioMart web service | biomart_query |
| Downloads all BioPlex interaction datasets | bioplex_all |
| Downloads the BioPlex HCT116 version 1.0 interaction dataset | bioplex_hct116_1 |
| Downloads the BioPlex version 1.0 interaction dataset | bioplex1 |
| Downloads the BioPlex version 2.0 interaction dataset | bioplex2 |
| Downloads the BioPlex version 3.0 interaction dataset | bioplex3 |
| BMA motifs from a sequence of edges | bma_motif_es |
| Prints a BMA motif to the screen from a sequence of nodes, which can be copy/pasted into the BMA canvas | bma_motif_vs |
| Genome scale metabolic model by Wang et al. 2021 | chalmers_gem |
| Metabolite ID translation tables from Chalmers Sysbio | chalmers_gem_id_mapping_table |
| Metabolite identifier type label used in Chalmers Sysbio GEM | chalmers_gem_id_type |
| Metabolites from the Chalmers SysBio GEM (Wang et al., 2021) | chalmers_gem_metabolites |
| Chalmers SysBio GEM in the form of gene-metabolite interactions | chalmers_gem_network |
| GEM matlab file from Chalmers Sysbio (Wang et al., 2021) | chalmers_gem_raw |
| Reactions from the Chalmers SysBio GEM (Wang et al., 2021) | chalmers_gem_reactions |
| Common (English) names of organisms | common_name |
| Get all the molecular complexes for a given gene(s) | complex_genes get_complex_genes |
| Retrieve a list of complex resources available in Omnipath | complex_resources get_complex_resources |
| Protein complexes from OmniPath | complexes import_omnipath_complexes |
| Retrieves the ConsensusPathDB network | consensuspathdb_download |
| Downloads interaction data from ConsensusPathDB | consensuspathdb_raw_table |
| Prior knowledge network (PKN) for COSMOS | cosmos_pkn |
| Curated ligand-receptor interactions | curated_ligand_receptor_interactions |
| Statistics about literature curated ligand-receptor interactions | curated_ligrec_stats |
| Summary of the annotations and intercell database contents | database_summary |
| Create a column with dataset names listed | datasets_one_column |
| All descendants in the ontology tree | descendants |
| Ensembl dataset name from organism | ensembl_dataset |
| Identifier translation table from Ensembl | ensembl_id_mapping_table |
| Ensembl identifier type label | ensembl_id_type |
| Ensembl identifiers of organisms | ensembl_name |
| Organism names and identifiers from Ensembl | ensembl_organisms |
| Table of Ensembl organisms | ensembl_organisms_raw |
| Orthologous gene pairs from Ensembl | ensembl_orthology |
| Converts a network to igraph object unless it is already one | ensure_igraph |
| Enzyme-substrate graph | enzsub_graph |
| Retrieves a list of enzyme-substrate resources available in OmniPath | enzsub_resources get_enzsub_resources |
| Enzyme-substrate (PTM) relationships from OmniPath | enzyme_substrate import_omnipath_enzsub |
| Interactions from the EVEX database | evex_download |
| Show evidences for an interaction | evidences |
| Possible values of an extra attribute | extra_attr_values |
| Extra attribute names in an interaction data frame | extra_attrs |
| New columns from extra attributes | extra_attrs_to_cols |
| Filters OmniPath data by resources | filter_by_resource |
| Filter evidences by dataset, resource and license | filter_evidences |
| Filter interactions by extra attribute values | filter_extra_attrs |
| Filter intercell annotations | filter_intercell |
| Quality filter an intercell network | filter_intercell_network |
| All paths between two groups of vertices | find_all_paths |
| Recreate interaction records from evidences columns | from_evidences |
| Access a built in database | get_db |
| Access an ontology database | get_ontology_db |
| Giant component of a graph | giant_component |
| Gene annotations from Gene Ontology | go_annot_download |
| GO slim gene annotations | go_annot_slim |
| The Gene Ontology tree | go_ontology_download |
| Interaction data frame from igraph graph object | graph_interaction |
| Downloads interactions from the Guide to Pharmacology database | guide2pharma_download |
| Downloads a Harmonizome network dataset | harmonizome_download |
| Tells if an interaction data frame has an extra_attrs column | has_extra_attrs |
| Identifier translation table from HMDB | hmdb_id_mapping_table |
| HMDB identifier type label | hmdb_id_type |
| Field names for the HMDB metabolite dataset | hmdb_metabolite_fields |
| Field names for the HMDB proteins dataset | hmdb_protein_fields |
| Download a HMDB XML file and process it into a table | hmdb_table |
| Orthology table for a pair of organisms | homologene_download |
| Organisms in NCBI HomoloGene | homologene_organisms |
| Orthology data from NCBI HomoloGene | homologene_raw |
| Orthology table with UniProt IDs | homologene_uniprot_orthology |
| Downloads protein annotations from Human Phenotype Ontology | hpo_download |
| Downloads TF-target interactions from HTRIdb | htridb_download |
| List available ID translation resources | id_translation_resources |
| ID types and synonyms in identifier translation | id_types |
| Downloads and preprocesses network data from InWeb InBioMap | inbiomap_download |
| Downloads network data from InWeb InBioMap | inbiomap_raw |
| Datasets in the OmniPath Interactions database | interaction_datasets |
| Build Omnipath interaction graph | interaction_graph |
| Interaction resources available in Omnipath | get_interaction_resources interaction_resources |
| Interaction types in the OmniPath Interactions database | interaction_types |
| Cell-cell communication roles from OmniPath | import_omnipath_intercell intercell |
| Categories in the intercell database of OmniPath | get_intercell_categories intercell_categories |
| Quality filter for intercell annotations | intercell_consensus_filter |
| Retrieves a list of the generic categories in the intercell database of OmniPath | get_intercell_generic_categories intercell_generic_categories |
| Intercellular communication network | import_intercell_network intercell_network |
| Retrieves a list of intercellular communication resources available in OmniPath | get_intercell_resources intercell_resources |
| Full list of intercell categories and resources | intercell_summary |
| Looks like an ontology ID | is_ontology_id |
| Check for SwissProt IDs | is_swissprot |
| Check for TrEMBL IDs | is_trembl |
| Looks like a UniProt ID? | is_uniprot |
| List of templates in the KEGG REST API | kegg_api_templates |
| Convert KEGG identifiers to/from outside identifiers | kegg_conv |
| List of databases (endpoints) in the KEGG REST API | kegg_databases |
| Find adverse drug-drug interactions in KEGG | kegg_ddi |
| Find entries in KEGG with matching query keyword or other query data | kegg_find |
| Information about a KEGG Pathway | kegg_info |
| Find related KEGG entries by using database cross-references | kegg_link |
| Obtain a list of KEGG entry identifiers and associated names | kegg_list |
| Open a KEGG Pathway diagram in the browser | kegg_open |
| List of operations in the KEGG REST API | kegg_operations |
| All 3 letter organism code from KEGG | kegg_organism_codes |
| List of organisms in KEGG | kegg_organisms |
| Protein pathway annotations | kegg_pathway_annotations |
| Download one KEGG pathway | kegg_pathway_download |
| List of KEGG pathways | kegg_pathway_list |
| Download the KEGG Pathways database | kegg_pathways_download |
| Download a pathway diagram as a picture | kegg_picture |
| Interactions from KGML | kegg_process |
| Compile a query for the KEGG REST API | kegg_query |
| Perform a KEGG REST API request | kegg_request |
| Remove prefix from KEGG foreign database identifiers | kegg_rm_prefix |
| Kinase-PTM relationships from KinasePhos 3.0 | kinasephos |
| Latin (scientific) names of organisms | latin_name |
| Load a built in database | load_db |
| Build a metabolite-centered MACdb metabolite-cancer association table | macdb_metabolite_cancer_associations |
| List standard GEMs from Metabolic Atlas | metabolic_atlas_list_gems |
| List of original GEMs in Metabolic Atlas | metabolic_atlas_list_models |
| Download and load one or more SBML models from Metabolic Atlas | metabolic_atlas_models |
| Open MetalinksDB as an SQLite3 connection | metalinksdb_sqlite |
| A table from MetalinksDB | metalinksdb_table |
| List tables in MetalinksDB | metalinksdb_tables |
| Load gene annotations from a standard-GEM repository | metatlas_gem_genes |
| Load metabolite annotations from a standard-GEM repository | metatlas_gem_metabolites |
| Load reaction annotations from a standard-GEM repository | metatlas_gem_reactions |
| Load an SBML model from a standard-GEM repository | metatlas_gem_sbml |
| Load a TSV annotation file from a standard-GEM repository | metatlas_gem_tsv |
| NCBI Taxonomy IDs of organisms | ncbi_taxid |
| Construct a NicheNet ligand-target model | nichenet_build_model |
| Expression data from ligand-receptor perturbation experiments used by NicheNet | nichenet_expression_data |
| Builds a NicheNet gene regulatory network | nichenet_gr_network |
| NicheNet gene regulatory network from EVEX | nichenet_gr_network_evex |
| NicheNet gene regulatory network from Harmonizome | nichenet_gr_network_harmonizome |
| NicheNet gene regulatory network from HTRIdb | nichenet_gr_network_htridb |
| Builds gene regulatory network for NicheNet using OmniPath | nichenet_gr_network_omnipath |
| NicheNet gene regulatory network from PathwayCommons | nichenet_gr_network_pathwaycommons |
| NicheNet gene regulatory network from RegNetwork | nichenet_gr_network_regnetwork |
| NicheNet gene regulatory network from ReMap | nichenet_gr_network_remap |
| NicheNet gene regulatory network from TRRUST | nichenet_gr_network_trrust |
| Calls the NicheNet ligand activity analysis | nichenet_ligand_activities |
| Compiles a table with weighted ligand-target links | nichenet_ligand_target_links |
| Creates a NicheNet ligand-target matrix | nichenet_ligand_target_matrix |
| Builds a NicheNet ligand-receptor network | nichenet_lr_network |
| Ligand-receptor network from Guide to Pharmacology | nichenet_lr_network_guide2pharma |
| Builds ligand-receptor network for NicheNet using OmniPath | nichenet_lr_network_omnipath |
| Ligand-receptor network from Ramilowski 2015 | nichenet_lr_network_ramilowski |
| Executes the full NicheNet pipeline | nichenet_main |
| Builds NicheNet network prior knowledge | nichenet_networks |
| Optimizes NicheNet model parameters | nichenet_optimization |
| Removes experiments with orphan ligands | nichenet_remove_orphan_ligands |
| Path to the current NicheNet results directory | nichenet_results_dir |
| Builds a NicheNet signaling network | nichenet_signaling_network |
| Builds signaling network for NicheNet using ConsensusPathDB | nichenet_signaling_network_cpdb |
| NicheNet signaling network from EVEX | nichenet_signaling_network_evex |
| NicheNet signaling network from Harmonizome | nichenet_signaling_network_harmonizome |
| NicheNet signaling network from InWeb InBioMap | nichenet_signaling_network_inbiomap |
| Builds signaling network for NicheNet using OmniPath | nichenet_signaling_network_omnipath |
| NicheNet signaling network from PathwayCommons | nichenet_signaling_network_pathwaycommons |
| NicheNet signaling network from Vinayagam | nichenet_signaling_network_vinayagam |
| Run the NicheNet pipeline with a little dummy network | nichenet_test |
| Workarounds using NicheNet without attaching the package | nichenet_workarounds |
| Generic OBO parser | obo_parser |
| Orthologous Matrix (OMA) codes of organisms | oma_code |
| Organism identifiers from the Orthologous Matrix | oma_organisms |
| Orthologous gene pairs between two organisms | oma_pairwise |
| Orthologous pairs of gene symbols between two organisms | oma_pairwise_genesymbols |
| Orthologous pairs between two organisms for ID types not supported by OMA | oma_pairwise_translated |
| Keeps only the latest versions of complete downloads | omnipath_cache_autoclean |
| Removes the items from the cache directory which are unknown by the cache database | omnipath_cache_clean |
| Removes the cache database entries without existing files | omnipath_cache_clean_db |
| Sets the download status to ready for a cache item | omnipath_cache_download_ready |
| Filters the versions from one cache record | omnipath_cache_filter_versions |
| Retrieves one item from the cache directory | omnipath_cache_get |
| Generates a hash which identifies an element in the cache database | omnipath_cache_key |
| The latest or a new version of a cache record | omnipath_cache_latest_or_new |
| Finds the most recent version in a cache record | omnipath_cache_latest_version |
| Loads an R object from the cache | omnipath_cache_load |
| Moves an existing file into the cache | omnipath_cache_move_in |
| Removes contents from the cache directory | omnipath_cache_remove |
| Saves an R object to the cache | omnipath_cache_save |
| Searches for cache items | omnipath_cache_search |
| Sets the file extension for a cache record | omnipath_cache_set_ext |
| Updates the status of an existing cache record | omnipath_cache_update_status |
| Permanently removes all the cache contents | omnipath_cache_wipe |
| Current config file path of OmnipathR | config_path omnipath_config_path |
| OmniPath PPI for the COSMOS PKN | omnipath_for_cosmos |
| Load the package configuration from a config file | load_config omnipath_load_config |
| Browse the current OmnipathR log file | omnipath_log read_log |
| Path to the current OmnipathR log file | logfile omnipath_logfile |
| Dispatch a message to the OmnipathR logger | omnipath_msg |
| Download data from the OmniPath web service | omnipath_query |
| Save the current package configuration | omnipath_save_config save_config |
| Change the cache directory | omnipath_set_cachedir |
| Sets the log level for the console | omnipath_set_console_loglevel |
| Sets the log level for the logfile | omnipath_set_logfile_loglevel |
| Sets the log level for the package logger | omnipath_set_loglevel set_loglevel |
| Built in database definitions | omnipath_show_db |
| Removes the lock file from the cache directory | omnipath_unlock_cache_db |
| Molecular interactions from OmniPath | all_interactions collectri dorothea import_all_interactions import_dorothea_interactions import_kinaseextra_interactions import_ligrecextra_interactions import_lncrna_mrna_interactions import_mirnatarget_interactions import_omnipath_interactions import_pathwayextra_interactions import_post_translational_interactions import_small_molecule_protein_interactions import_tf_mirna_interactions import_tf_target_interactions import_transcriptional_interactions kinaseextra ligrecextra lncrna_mrna mirna_target omnipath omnipath-interactions omnipath_interactions pathwayextra post_translational small_molecule tf_mirna tf_target transcriptional |
| The OmnipathR package | OmnipathR-package OmnipathR |
| Recreate interaction data frame based on certain datasets and resources | only_from |
| Only ontology IDs | ontology_ensure_id |
| Only ontology term names | ontology_ensure_name |
| Translate between ontology IDs and names | ontology_name_id |
| Make sure the resource supports the organism and it has the ID | organism_for |
| Translate a column of identifiers by orthologous gene pairs | orthology_translate_column |
| Interactions from PathwayCommons | pathwaycommons_download |
| Converts annotation tables to a wide format | pivot_annotations |
| Interactions from PrePPI | preppi_download |
| Filter PrePPI interactions by scores | preppi_filter |
| Prints BMA motifs to the screen from a sequence of edges | print_bma_motif_es |
| Prints BMA motifs to the screen from a sequence of nodes | print_bma_motif_vs |
| Print OmniPath interactions | print_interactions |
| Prints network paths in an edge sequence | print_path_es |
| Print networks paths given by node sequence | print_path_vs |
| Open one or more PubMed articles | pubmed_open |
| OmniPath query parameters | query_info |
| Downloads ligand-receptor interactions from Ramilowski et al. 2015 | ramilowski_download |
| Pairwise ID translation table from RaMP database | ramp_id_mapping_table |
| RaMP identifier type label | ramp_id_type |
| Download and open RaMP database SQLite | ramp_sqlite |
| Return table from RaMP database | ramp_table |
| List tables in RaMP database | ramp_tables |
| Reactome ChEBI mappings | reactome_chebi |
| Reactome ChEBI pathway mapping | reactome_chebi_pathways |
| Reactome pathway relations | reactome_pathway_relations |
| Reactome pathways | reactome_pathways |
| Metabolites from Recon-3D | recon3d_compartments recon3d_genes recon3d_metabolites recon3d_reactions |
| Recon-3D from JSON | recon3d_raw |
| Recon3D model from BiGG | recon3d_raw_matlab |
| Recon-3D model from Virtual Metabolic Human | recon3d_raw_vmh |
| Transcription factor effects from RegNetwork | regnetwork_directions |
| Interactions from RegNetwork | regnetwork_download |
| Table from a nested list of ontology relations | relations_list_to_table |
| Graph from a table of ontology relations | relations_table_to_graph |
| Nested list from a table of ontology relations | relations_table_to_list |
| Downloads TF-target interactions from ReMap | remap_dorothea_download |
| Downloads TF-target interactions from ReMap | remap_filtered |
| Downloads TF-target interactions from ReMap | remap_tf_target_download |
| Restore the built-in default values of all config parameters of a package | omnipath_reset_config reset_config |
| OmniPath resource information | resource_info |
| Retrieve the available resources for a given query type | get_resources resources |
| Name of the column with the resources | resources_colname |
| Collect resource names from a data frame | resources_in |
| Visualize node neighborhood with SigmaJS | show_network |
| Causal effect enzyme-PTM interactions | get_signed_ptms signed_ptms |
| Simplify an intercell network | simplify_intercell_network |
| Retrieve a static table from OmniPath | static_table |
| List the static tables available from OmniPath | static_tables |
| Retrieve the STITCH actions dataset | stitch_actions |
| Retrieve the STITCH links dataset | stitch_links |
| Chemical-protein interactions from STITCH | stitch_network |
| Remove the prefixes from STITCH identifiers | stitch_remove_prefixes |
| Extract a custom subnetwork from a large network | subnetwork |
| Reverse the direction of ontology relations | swap_relations |
| Retain only SwissProt IDs | swissprots_only |
| Downloads the list of transcription factors from TF census | tfcensus_download |
| Translate gene, protein and small molecule identifiers | translate_ids |
| Translate gene, protein and small molecule identifiers from multiple columns | translate_ids_multi |
| Retain only TrEMBL IDs | trembls_only |
| Downloads TF-target interactions from TRRUST | trrust_download |
| Creates an ID translation table from UniProt data | uniprot_full_id_mapping_table |
| TrEMBL to SwissProt by gene names | uniprot_genesymbol_cleanup |
| ID translation data from UniProt ID Mapping | uniprot_id_mapping_table |
| UniProt identifier type label | uniprot_id_type |
| ID types available in the UniProt ID Mapping service | uniprot_idmapping_id_types |
| UniProt taxonomy data | uniprot_organisms |
| Unique intercellular interactions | unique_intercell_network |
| Separate evidences by direction and effect sign | unnest_evidences |
| UniProt Uploadlists identifier type label | uploadlists_id_type |
| Protein-protein interactions from Vinayagam 2011 | vinayagam_download |
| All nodes of a subtree starting from the selected nodes | walk_ontology_tree |
| WikiPathways metabolites per pathway (GPML) | wikipathways_metabolites |
| WikiPathways metabolites via SPARQL | wikipathways_metabolites_sparql |
| List WikiPathways pathways | wikipathways_pathways |
| Interaction records having certain extra attributes | with_extra_attrs |
| Interactions having references | with_references |
| Retrieves data from Zenodo | zenodo_download |
