OmniPath web service client and more
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Documentation for package ‘OmnipathR’ version 3.17.0
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A B C D E F G H I K L M N O P Q R S T U V W Z misc
| OmnipathR-package | The OmnipathR package |
-- A --
| all_interactions | Molecular interactions from OmniPath |
| all_uniprots | A table with all UniProt records |
| all_uniprot_acs | All UniProt ACs for one organism |
| ambiguity | Inspect the ambiguity of a mapping |
| ancestors | All ancestors in the ontology tree |
| annotated_network | Network interactions with annotations |
| annotations | Protein and gene annotations from OmniPath |
| annotation_categories | Annotation categories and resources |
| annotation_resources | Retrieves a list of available resources in the annotations database of OmniPath |
-- B --
| biomart_query | Query the Ensembl BioMart web service |
| bioplex1 | Downloads the BioPlex version 1.0 interaction dataset |
| bioplex2 | Downloads the BioPlex version 2.0 interaction dataset |
| bioplex3 | Downloads the BioPlex version 3.0 interaction dataset |
| bioplex_all | Downloads all BioPlex interaction datasets |
| bioplex_hct116_1 | Downloads the BioPlex HCT116 version 1.0 interaction dataset |
| bma_motif_es | BMA motifs from a sequence of edges |
| bma_motif_vs | Prints a BMA motif to the screen from a sequence of nodes, which can be copy/pasted into the BMA canvas |
-- C --
| chalmers_gem | Genome scale metabolic model by Wang et al. 2021 |
| chalmers_gem_id_mapping_table | Metabolite ID translation tables from Chalmers Sysbio |
| chalmers_gem_id_type | Metabolite identifier type label used in Chalmers Sysbio GEM |
| chalmers_gem_metabolites | Metabolites from the Chalmers SysBio GEM (Wang et al., 2021) |
| chalmers_gem_network | Chalmers SysBio GEM in the form of gene-metabolite interactions |
| chalmers_gem_raw | GEM matlab file from Chalmers Sysbio (Wang et al., 2021) |
| chalmers_gem_reactions | Reactions from the Chalmers SysBio GEM (Wang et al., 2021) |
| collectri | Molecular interactions from OmniPath |
| common_name | Common (English) names of organisms |
| complexes | Protein complexes from OmniPath |
| complex_genes | Get all the molecular complexes for a given gene(s) |
| complex_resources | Retrieve a list of complex resources available in Omnipath |
| config_path | Current config file path of OmnipathR |
| consensuspathdb_download | Retrieves the ConsensusPathDB network |
| consensuspathdb_raw_table | Downloads interaction data from ConsensusPathDB |
| cosmos_pkn | Prior knowledge network (PKN) for COSMOS |
| curated_ligand_receptor_interactions | Curated ligand-receptor interactions |
| curated_ligrec_stats | Statistics about literature curated ligand-receptor interactions |
-- D --
| database_summary | Summary of the annotations and intercell database contents |
| datasets_one_column | Create a column with dataset names listed |
| descendants | All descendants in the ontology tree |
| dorothea | Molecular interactions from OmniPath |
-- E --
| ensembl_dataset | Ensembl dataset name from organism |
| ensembl_id_mapping_table | Identifier translation table from Ensembl |
| ensembl_id_type | Ensembl identifier type label |
| ensembl_name | Ensembl identifiers of organisms |
| ensembl_organisms | Organism names and identifiers from Ensembl |
| ensembl_organisms_raw | Table of Ensembl organisms |
| ensembl_orthology | Orthologous gene pairs from Ensembl |
| ensure_igraph | Converts a network to igraph object unless it is already one |
| enzsub_graph | Enzyme-substrate graph |
| enzsub_resources | Retrieves a list of enzyme-substrate resources available in OmniPath |
| enzyme_substrate | Enzyme-substrate (PTM) relationships from OmniPath |
| evex_download | Interactions from the EVEX database |
| evidences | Show evidences for an interaction |
| extra_attrs | Extra attribute names in an interaction data frame |
| extra_attrs_to_cols | New columns from extra attributes |
| extra_attr_values | Possible values of an extra attribute |
-- F --
| filter_by_resource | Filters OmniPath data by resources |
| filter_evidences | Filter evidences by dataset, resource and license |
| filter_extra_attrs | Filter interactions by extra attribute values |
| filter_intercell | Filter intercell annotations |
| filter_intercell_network | Quality filter an intercell network |
| find_all_paths | All paths between two groups of vertices |
| from_evidences | Recreate interaction records from evidences columns |
-- G --
| get_annotation_resources | Retrieves a list of available resources in the annotations database of OmniPath |
| get_complex_genes | Get all the molecular complexes for a given gene(s) |
| get_complex_resources | Retrieve a list of complex resources available in Omnipath |
| get_db | Access a built in database |
| get_enzsub_resources | Retrieves a list of enzyme-substrate resources available in OmniPath |
| get_interaction_resources | Interaction resources available in Omnipath |
| get_intercell_categories | Categories in the intercell database of OmniPath |
| get_intercell_generic_categories | Retrieves a list of the generic categories in the intercell database of OmniPath |
| get_intercell_resources | Retrieves a list of intercellular communication resources available in OmniPath |
| get_ontology_db | Access an ontology database |
| get_resources | Retrieve the available resources for a given query type |
| get_signed_ptms | Causal effect enzyme-PTM interactions |
| giant_component | Giant component of a graph |
| go_annot_download | Gene annotations from Gene Ontology |
| go_annot_slim | GO slim gene annotations |
| go_ontology_download | The Gene Ontology tree |
| graph_interaction | Interaction data frame from igraph graph object |
| guide2pharma_download | Downloads interactions from the Guide to Pharmacology database |
-- H --
| harmonizome_download | Downloads a Harmonizome network dataset |
| has_extra_attrs | Tells if an interaction data frame has an extra_attrs column |
| hmdb_id_mapping_table | Identifier translation table from HMDB |
| hmdb_id_type | HMDB identifier type label |
| hmdb_metabolite_fields | Field names for the HMDB metabolite dataset |
| hmdb_protein_fields | Field names for the HMDB proteins dataset |
| hmdb_table | Download a HMDB XML file and process it into a table |
| homologene_download | Orthology table for a pair of organisms |
| homologene_organisms | Organisms in NCBI HomoloGene |
| homologene_raw | Orthology data from NCBI HomoloGene |
| homologene_uniprot_orthology | Orthology table with UniProt IDs |
| hpo_download | Downloads protein annotations from Human Phenotype Ontology |
| htridb_download | Downloads TF-target interactions from HTRIdb |
-- I --
| id_translation_resources | List available ID translation resources |
| id_types | ID types and synonyms in identifier translation |
| import_all_interactions | Molecular interactions from OmniPath |
| import_dorothea_interactions | Molecular interactions from OmniPath |
| import_intercell_network | Intercellular communication network |
| import_kinaseextra_interactions | Molecular interactions from OmniPath |
| import_ligrecextra_interactions | Molecular interactions from OmniPath |
| import_lncrna_mrna_interactions | Molecular interactions from OmniPath |
| import_mirnatarget_interactions | Molecular interactions from OmniPath |
| import_omnipath_annotations | Protein and gene annotations from OmniPath |
| import_omnipath_complexes | Protein complexes from OmniPath |
| import_omnipath_enzsub | Enzyme-substrate (PTM) relationships from OmniPath |
| import_omnipath_interactions | Molecular interactions from OmniPath |
| import_omnipath_intercell | Cell-cell communication roles from OmniPath |
| import_pathwayextra_interactions | Molecular interactions from OmniPath |
| import_post_translational_interactions | Molecular interactions from OmniPath |
| import_small_molecule_protein_interactions | Molecular interactions from OmniPath |
| import_tf_mirna_interactions | Molecular interactions from OmniPath |
| import_tf_target_interactions | Molecular interactions from OmniPath |
| import_transcriptional_interactions | Molecular interactions from OmniPath |
| inbiomap_download | Downloads and preprocesses network data from InWeb InBioMap |
| inbiomap_raw | Downloads network data from InWeb InBioMap |
| interaction_datasets | Datasets in the OmniPath Interactions database |
| interaction_graph | Build Omnipath interaction graph |
| interaction_resources | Interaction resources available in Omnipath |
| interaction_types | Interaction types in the OmniPath Interactions database |
| intercell | Cell-cell communication roles from OmniPath |
| intercell_categories | Categories in the intercell database of OmniPath |
| intercell_consensus_filter | Quality filter for intercell annotations |
| intercell_generic_categories | Retrieves a list of the generic categories in the intercell database of OmniPath |
| intercell_network | Intercellular communication network |
| intercell_resources | Retrieves a list of intercellular communication resources available in OmniPath |
| intercell_summary | Full list of intercell categories and resources |
| is_ontology_id | Looks like an ontology ID |
| is_swissprot | Check for SwissProt IDs |
| is_trembl | Check for TrEMBL IDs |
| is_uniprot | Looks like a UniProt ID? |
-- K --
| kegg_api_templates | List of templates in the KEGG REST API |
| kegg_conv | Convert KEGG identifiers to/from outside identifiers |
| kegg_databases | List of databases (endpoints) in the KEGG REST API |
| kegg_ddi | Find adverse drug-drug interactions in KEGG |
| kegg_find | Find entries in KEGG with matching query keyword or other query data |
| kegg_info | Information about a KEGG Pathway |
| kegg_link | Find related KEGG entries by using database cross-references |
| kegg_list | Obtain a list of KEGG entry identifiers and associated names |
| kegg_open | Open a KEGG Pathway diagram in the browser |
| kegg_operations | List of operations in the KEGG REST API |
| kegg_organisms | List of organisms in KEGG |
| kegg_organism_codes | All 3 letter organism code from KEGG |
| kegg_pathways_download | Download the KEGG Pathways database |
| kegg_pathway_annotations | Protein pathway annotations |
| kegg_pathway_download | Download one KEGG pathway |
| kegg_pathway_list | List of KEGG pathways |
| kegg_picture | Download a pathway diagram as a picture |
| kegg_process | Interactions from KGML |
| kegg_query | Compile a query for the KEGG REST API |
| kegg_request | Perform a KEGG REST API request |
| kegg_rm_prefix | Remove prefix from KEGG foreign database identifiers |
| kinaseextra | Molecular interactions from OmniPath |
-- L --
| latin_name | Latin (scientific) names of organisms |
| ligrecextra | Molecular interactions from OmniPath |
| lncrna_mrna | Molecular interactions from OmniPath |
| load_config | Load the package configuration from a config file |
| load_db | Load a built in database |
| logfile | Path to the current OmnipathR log file |
-- M --
| metalinksdb_sqlite | Open MetalinksDB as an SQLite3 connection |
| metalinksdb_table | A table from MetalinksDB |
| metalinksdb_tables | List tables in MetalinksDB |
| mirna_target | Molecular interactions from OmniPath |
-- N --
| ncbi_taxid | NCBI Taxonomy IDs of organisms |
| nichenet_build_model | Construct a NicheNet ligand-target model |
| nichenet_expression_data | Expression data from ligand-receptor perturbation experiments used by NicheNet |
| nichenet_gr_network | Builds a NicheNet gene regulatory network |
| nichenet_gr_network_evex | NicheNet gene regulatory network from EVEX |
| nichenet_gr_network_harmonizome | NicheNet gene regulatory network from Harmonizome |
| nichenet_gr_network_htridb | NicheNet gene regulatory network from HTRIdb |
| nichenet_gr_network_omnipath | Builds gene regulatory network for NicheNet using OmniPath |
| nichenet_gr_network_pathwaycommons | NicheNet gene regulatory network from PathwayCommons |
| nichenet_gr_network_regnetwork | NicheNet gene regulatory network from RegNetwork |
| nichenet_gr_network_remap | NicheNet gene regulatory network from ReMap |
| nichenet_gr_network_trrust | NicheNet gene regulatory network from TRRUST |
| nichenet_ligand_activities | Calls the NicheNet ligand activity analysis |
| nichenet_ligand_target_links | Compiles a table with weighted ligand-target links |
| nichenet_ligand_target_matrix | Creates a NicheNet ligand-target matrix |
| nichenet_lr_network | Builds a NicheNet ligand-receptor network |
| nichenet_lr_network_guide2pharma | Ligand-receptor network from Guide to Pharmacology |
| nichenet_lr_network_omnipath | Builds ligand-receptor network for NicheNet using OmniPath |
| nichenet_lr_network_ramilowski | Ligand-receptor network from Ramilowski 2015 |
| nichenet_main | Executes the full NicheNet pipeline |
| nichenet_networks | Builds NicheNet network prior knowledge |
| nichenet_optimization | Optimizes NicheNet model parameters |
| nichenet_remove_orphan_ligands | Removes experiments with orphan ligands |
| nichenet_results_dir | Path to the current NicheNet results directory |
| nichenet_signaling_network | Builds a NicheNet signaling network |
| nichenet_signaling_network_cpdb | Builds signaling network for NicheNet using ConsensusPathDB |
| nichenet_signaling_network_evex | NicheNet signaling network from EVEX |
| nichenet_signaling_network_harmonizome | NicheNet signaling network from Harmonizome |
| nichenet_signaling_network_inbiomap | NicheNet signaling network from InWeb InBioMap |
| nichenet_signaling_network_omnipath | Builds signaling network for NicheNet using OmniPath |
| nichenet_signaling_network_pathwaycommons | NicheNet signaling network from PathwayCommons |
| nichenet_signaling_network_vinayagam | NicheNet signaling network from Vinayagam |
| nichenet_test | Run the NicheNet pipeline with a little dummy network |
| nichenet_workarounds | Workarounds using NicheNet without attaching the package |
-- O --
| obo_parser | Generic OBO parser |
| oma_code | Orthologous Matrix (OMA) codes of organisms |
| oma_organisms | Organism identifiers from the Orthologous Matrix |
| oma_pairwise | Orthologous gene pairs between two organisms |
| oma_pairwise_genesymbols | Orthologous pairs of gene symbols between two organisms |
| oma_pairwise_translated | Orthologous pairs between two organisms for ID types not supported by OMA |
| omnipath | Molecular interactions from OmniPath |
| omnipath-interactions | Molecular interactions from OmniPath |
| OmnipathR | The OmnipathR package |
| omnipath_cache_autoclean | Keeps only the latest versions of complete downloads |
| omnipath_cache_clean | Removes the items from the cache directory which are unknown by the cache database |
| omnipath_cache_clean_db | Removes the cache database entries without existing files |
| omnipath_cache_download_ready | Sets the download status to ready for a cache item |
| omnipath_cache_filter_versions | Filters the versions from one cache record |
| omnipath_cache_get | Retrieves one item from the cache directory |
| omnipath_cache_key | Generates a hash which identifies an element in the cache database |
| omnipath_cache_latest_or_new | The latest or a new version of a cache record |
| omnipath_cache_latest_version | Finds the most recent version in a cache record |
| omnipath_cache_load | Loads an R object from the cache |
| omnipath_cache_move_in | Moves an existing file into the cache |
| omnipath_cache_remove | Removes contents from the cache directory |
| omnipath_cache_save | Saves an R object to the cache |
| omnipath_cache_search | Searches for cache items |
| omnipath_cache_set_ext | Sets the file extension for a cache record |
| omnipath_cache_update_status | Updates the status of an existing cache record |
| omnipath_cache_wipe | Permanently removes all the cache contents |
| omnipath_config_path | Current config file path of OmnipathR |
| omnipath_for_cosmos | OmniPath PPI for the COSMOS PKN |
| omnipath_interactions | Molecular interactions from OmniPath |
| omnipath_load_config | Load the package configuration from a config file |
| omnipath_log | Browse the current OmnipathR log file |
| omnipath_logfile | Path to the current OmnipathR log file |
| omnipath_msg | Dispatch a message to the OmnipathR logger |
| omnipath_query | Download data from the OmniPath web service |
| omnipath_reset_config | Restore the built-in default values of all config parameters of a package |
| omnipath_save_config | Save the current package configuration |
| omnipath_set_cachedir | Change the cache directory |
| omnipath_set_console_loglevel | Sets the log level for the console |
| omnipath_set_logfile_loglevel | Sets the log level for the logfile |
| omnipath_set_loglevel | Sets the log level for the package logger |
| omnipath_show_db | Built in database definitions |
| omnipath_unlock_cache_db | Removes the lock file from the cache directory |
| only_from | Recreate interaction data frame based on certain datasets and resources |
| ontology_ensure_id | Only ontology IDs |
| ontology_ensure_name | Only ontology term names |
| ontology_name_id | Translate between ontology IDs and names |
| organism_for | Make sure the resource supports the organism and it has the ID |
| orthology_translate_column | Translate a column of identifiers by orthologous gene pairs |
-- P --
| pathwaycommons_download | Interactions from PathwayCommons |
| pathwayextra | Molecular interactions from OmniPath |
| pivot_annotations | Converts annotation tables to a wide format |
| post_translational | Molecular interactions from OmniPath |
| preppi_download | Interactions from PrePPI |
| preppi_filter | Filter PrePPI interactions by scores |
| print_bma_motif_es | Prints BMA motifs to the screen from a sequence of edges |
| print_bma_motif_vs | Prints BMA motifs to the screen from a sequence of nodes |
| print_interactions | Print OmniPath interactions |
| print_path_es | Prints network paths in an edge sequence |
| print_path_vs | Print networks paths given by node sequence |
| pubmed_open | Open one or more PubMed articles |
-- Q --
| query_info | OmniPath query parameters |
-- R --
| ramilowski_download | Downloads ligand-receptor interactions from Ramilowski et al. 2015 |
| ramp_id_mapping_table | Pairwise ID translation table from RaMP database |
| ramp_id_type | RaMP identifier type label |
| ramp_sqlite | Download and open RaMP database SQLite |
| ramp_table | Return table from RaMP database |
| ramp_tables | List tables in RaMP database |
| read_log | Browse the current OmnipathR log file |
| regnetwork_directions | Transcription factor effects from RegNetwork |
| regnetwork_download | Interactions from RegNetwork |
| relations_list_to_table | Table from a nested list of ontology relations |
| relations_table_to_graph | Graph from a table of ontology relations |
| relations_table_to_list | Nested list from a table of ontology relations |
| remap_dorothea_download | Downloads TF-target interactions from ReMap |
| remap_filtered | Downloads TF-target interactions from ReMap |
| remap_tf_target_download | Downloads TF-target interactions from ReMap |
| reset_config | Restore the built-in default values of all config parameters of a package |
| resources | Retrieve the available resources for a given query type |
| resources_colname | Name of the column with the resources |
| resources_in | Collect resource names from a data frame |
| resource_info | OmniPath resource information |
-- S --
| save_config | Save the current package configuration |
| set_loglevel | Sets the log level for the package logger |
| show_network | Visualize node neighborhood with SigmaJS |
| signed_ptms | Causal effect enzyme-PTM interactions |
| simplify_intercell_network | Simplify an intercell network |
| small_molecule | Molecular interactions from OmniPath |
| static_table | Retrieve a static table from OmniPath |
| static_tables | List the static tables available from OmniPath |
| stitch_actions | Retrieve the STITCH actions dataset |
| stitch_links | Retrieve the STITCH links dataset |
| stitch_network | Chemical-protein interactions from STITCH |
| stitch_remove_prefixes | Remove the prefixes from STITCH identifiers |
| subnetwork | Extract a custom subnetwork from a large network |
| swap_relations | Reverse the direction of ontology relations |
| swissprots_only | Retain only SwissProt IDs |
-- T --
| tfcensus_download | Downloads the list of transcription factors from TF census |
| tf_mirna | Molecular interactions from OmniPath |
| tf_target | Molecular interactions from OmniPath |
| transcriptional | Molecular interactions from OmniPath |
| translate_ids | Translate gene, protein and small molecule identifiers |
| translate_ids_multi | Translate gene, protein and small molecule identifiers from multiple columns |
| trembls_only | Retain only TrEMBL IDs |
| trrust_download | Downloads TF-target interactions from TRRUST |
-- U --
| uniprot_full_id_mapping_table | Creates an ID translation table from UniProt data |
| uniprot_genesymbol_cleanup | TrEMBL to SwissProt by gene names |
| uniprot_idmapping_id_types | ID types available in the UniProt ID Mapping service |
| uniprot_id_mapping_table | ID translation data from UniProt ID Mapping |
| uniprot_id_type | UniProt identifier type label |
| unique_intercell_network | Unique intercellular interactions |
| unnest_evidences | Separate evidences by direction and effect sign |
| uploadlists_id_type | UniProt Uploadlists identifier type label |
-- V --
| vinayagam_download | Protein-protein interactions from Vinayagam 2011 |
-- W --
| walk_ontology_tree | All nodes of a subtree starting from the selected nodes |
| with_extra_attrs | Interaction records having certain extra attributes |
| with_references | Interactions having references |
-- Z --
| zenodo_download | Retrieves data from Zenodo |
-- misc --
| .omnipathr_options_defaults | Default values for the package options |