{ "_id": "6a607fd414e95619b75da7b1", "Package": "OmnipathR", "Type": "Package", "Title": "OmniPath web service client and more", "Version": "3.19.1", "Authors@R": "c(\nperson(\ngiven = \"Alberto\",\nfamily = \"Valdeolivas\",\nrole = c(\"aut\"),\nemail = \"alvaldeolivas@gmail.com\",\ncomment = c(ORCID = \"0000-0001-5482-9023\")),\nperson(\ngiven = \"Denes\",\nfamily = \"Turei\",\nrole = c(\"aut\"),\nemail = \"turei.denes@gmail.com\",\ncomment = c(ORCID = \"0000-0002-7249-9379\")),\nperson(\ngiven = \"Attila\",\nfamily = \"Gabor\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-0776-1182\")),\nperson(\ngiven = \"Diego\",\nfamily = \"Mananes\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-7247-6794\")),\nperson(\ngiven = \"Aurelien\",\nfamily = \"Dugourd\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-0714-028X\")),\nperson(\ngiven = \"Zaoqu\",\nfamily = \"Liu\",\nrole = c(\"cre\", \"ctb\"),\nemail = \"liuzaoqu@163.com\",\ncomment = c(ORCID = \"0000-0002-0452-742X\")))", "Author": "Zaoqu Liu [cre, ctb], Alberto Valdeolivas [aut], Denes Turei\n[aut], Attila Gabor [aut], Diego Mananes [aut], Aurelien\nDugourd [aut]", "Maintainer": "Zaoqu Liu ", "Description": "A client for the OmniPath web service\n(https://www.omnipathdb.org) and many other resources. 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"page": "ensembl_dataset", "title": "Ensembl dataset name from organism", "topics": [ "ensembl_dataset" ] }, { "page": "ensembl_id_mapping_table", "title": "Identifier translation table from Ensembl", "topics": [ "ensembl_id_mapping_table" ] }, { "page": "ensembl_id_type", "title": "Ensembl identifier type label", "topics": [ "ensembl_id_type" ] }, { "page": "ensembl_name", "title": "Ensembl identifiers of organisms", "topics": [ "ensembl_name" ] }, { "page": "ensembl_organisms", "title": "Organism names and identifiers from Ensembl", "topics": [ "ensembl_organisms" ] }, { "page": "ensembl_organisms_raw", "title": "Table of Ensembl organisms", "topics": [ "ensembl_organisms_raw" ] }, { "page": "ensembl_orthology", "title": "Orthologous gene pairs from Ensembl", "topics": [ "ensembl_orthology" ] }, { "page": "ensure_igraph", "title": "Converts a network to igraph object unless it is already one", "topics": [ "ensure_igraph" ] }, { "page": "enzsub_graph", "title": "Enzyme-substrate graph", "topics": [ "enzsub_graph" ] }, { "page": "enzsub_resources", "title": "Retrieves a list of enzyme-substrate resources available in OmniPath", "topics": [ "enzsub_resources", "get_enzsub_resources" ] }, { "page": "enzyme_substrate", "title": "Enzyme-substrate (PTM) relationships from OmniPath", "topics": [ "enzyme_substrate", "import_omnipath_enzsub" ] }, { "page": "evex_download", "title": "Interactions from the EVEX database", "topics": [ "evex_download" ] }, { "page": "evidences", "title": "Show evidences for an interaction", "topics": [ "evidences" ] }, { "page": "extra_attr_values", "title": "Possible values of an extra attribute", "topics": [ "extra_attr_values" ] }, { "page": "extra_attrs", "title": "Extra attribute names in an interaction data frame", "topics": [ "extra_attrs" ] }, { "page": "extra_attrs_to_cols", "title": "New columns from extra attributes", "topics": [ "extra_attrs_to_cols" ] }, { "page": "filter_by_resource", "title": "Filters OmniPath data by resources", "topics": [ "filter_by_resource" ] }, { "page": "filter_evidences", "title": "Filter evidences by dataset, resource and license", "topics": [ "filter_evidences" ] }, { "page": "filter_extra_attrs", "title": "Filter interactions by extra attribute values", "topics": [ "filter_extra_attrs" ] }, { "page": "filter_intercell", "title": "Filter intercell annotations", "topics": [ "filter_intercell" ] }, { "page": "filter_intercell_network", "title": "Quality filter an intercell network", "topics": [ "filter_intercell_network" ] }, { "page": "find_all_paths", "title": "All paths between two groups of vertices", "topics": [ "find_all_paths" ] }, { "page": "from_evidences", "title": "Recreate interaction records from evidences columns", "topics": [ "from_evidences" ] }, { "page": "get_db", "title": "Access a built in database", "topics": [ "get_db" ] }, { "page": "get_ontology_db", "title": "Access an ontology database", "topics": [ "get_ontology_db" ] }, { "page": "giant_component", "title": "Giant component of a graph", "topics": [ "giant_component" ] }, { "page": "go_annot_download", "title": "Gene annotations from Gene Ontology", "topics": [ "go_annot_download" ] }, { "page": "go_annot_slim", "title": "GO slim gene annotations", "topics": [ "go_annot_slim" ] }, { "page": "go_ontology_download", "title": "The Gene Ontology tree", "topics": [ "go_ontology_download" ] }, { "page": "graph_interaction", "title": "Interaction data frame from igraph graph object", "topics": [ "graph_interaction" ] }, { "page": "guide2pharma_download", "title": "Downloads interactions from the Guide to Pharmacology database", "topics": [ "guide2pharma_download" ] }, { "page": "harmonizome_download", "title": "Downloads a Harmonizome network dataset", "topics": [ "harmonizome_download" ] }, { "page": "has_extra_attrs", "title": "Tells if an interaction data frame has an extra_attrs column", "topics": [ "has_extra_attrs" ] }, { "page": "hmdb_id_mapping_table", "title": "Identifier translation table from HMDB", "topics": [ "hmdb_id_mapping_table" ] }, { "page": "hmdb_id_type", "title": "HMDB identifier type label", "topics": [ "hmdb_id_type" ] }, { "page": "hmdb_metabolite_fields", "title": "Field names for the HMDB metabolite dataset", "topics": [ "hmdb_metabolite_fields" ] }, { "page": "hmdb_protein_fields", "title": "Field names for the HMDB proteins dataset", "topics": [ "hmdb_protein_fields" ] }, { "page": "hmdb_table", "title": "Download a HMDB XML file and process it into a table", "topics": [ "hmdb_table" ] }, { "page": "homologene_download", "title": "Orthology table for a pair of organisms", "topics": [ "homologene_download" ] }, { "page": "homologene_organisms", "title": "Organisms in NCBI HomoloGene", "topics": [ "homologene_organisms" ] }, { "page": "homologene_raw", "title": "Orthology data from NCBI HomoloGene", "topics": [ "homologene_raw" ] }, { "page": "homologene_uniprot_orthology", "title": "Orthology table with UniProt IDs", "topics": [ "homologene_uniprot_orthology" ] }, { "page": "hpo_download", "title": "Downloads protein annotations from Human Phenotype Ontology", "topics": [ "hpo_download" ] }, { "page": "htridb_download", "title": "Downloads TF-target interactions from HTRIdb", "topics": [ "htridb_download" ] }, { "page": "id_translation_resources", "title": "List available ID translation resources", "topics": [ "id_translation_resources" ] }, { "page": "id_types", "title": "ID types and synonyms in identifier translation", "topics": [ "id_types" ] }, { "page": "inbiomap_download", "title": "Downloads and preprocesses network data from InWeb InBioMap", "topics": [ "inbiomap_download" ] }, { "page": "inbiomap_raw", "title": "Downloads network data from InWeb InBioMap", "topics": [ "inbiomap_raw" ] }, { "page": "interaction_datasets", "title": "Datasets in the OmniPath Interactions database", "topics": [ "interaction_datasets" ] }, { "page": "interaction_graph", "title": "Build Omnipath interaction graph", "topics": [ "interaction_graph" ] }, { "page": "interaction_resources", "title": "Interaction resources available in Omnipath", "topics": [ "get_interaction_resources", "interaction_resources" ] }, { "page": "interaction_types", "title": "Interaction types in the OmniPath Interactions database", "topics": [ "interaction_types" ] }, { "page": "intercell", "title": "Cell-cell communication roles from OmniPath", "topics": [ "import_omnipath_intercell", "intercell" ] }, { "page": "intercell_categories", "title": "Categories in the intercell database of OmniPath", "topics": [ "get_intercell_categories", "intercell_categories" ] }, { "page": "intercell_consensus_filter", "title": "Quality filter for intercell annotations", "topics": [ "intercell_consensus_filter" ] }, { "page": "intercell_generic_categories", "title": "Retrieves a list of the generic categories in the intercell database of OmniPath", "topics": [ "get_intercell_generic_categories", "intercell_generic_categories" ] }, { "page": "intercell_network", "title": "Intercellular communication network", "topics": [ "import_intercell_network", "intercell_network" ] }, { "page": "intercell_resources", "title": "Retrieves a list of intercellular communication resources available in OmniPath", "topics": [ "get_intercell_resources", "intercell_resources" ] }, { "page": "intercell_summary", "title": "Full list of intercell categories and resources", "topics": [ "intercell_summary" ] }, { "page": "is_ontology_id", "title": "Looks like an ontology ID", "topics": [ "is_ontology_id" ] }, { "page": "is_swissprot", "title": "Check for SwissProt IDs", "topics": [ "is_swissprot" ] }, { "page": "is_trembl", "title": "Check for TrEMBL IDs", "topics": [ "is_trembl" ] }, { "page": "is_uniprot", "title": "Looks like a UniProt ID?", "topics": [ "is_uniprot" ] }, { "page": "kegg_api_templates", "title": "List of templates in the KEGG REST API", "topics": [ "kegg_api_templates" ] }, { "page": "kegg_conv", "title": "Convert KEGG identifiers to/from outside identifiers", "topics": [ "kegg_conv" ] }, { "page": "kegg_databases", "title": "List of databases (endpoints) in the KEGG REST API", "topics": [ "kegg_databases" ] }, { "page": "kegg_ddi", "title": "Find adverse drug-drug interactions in KEGG", "topics": [ "kegg_ddi" ] }, { "page": "kegg_find", "title": "Find entries in KEGG with matching query keyword or other query data", "topics": [ "kegg_find" ] }, { "page": "kegg_info", "title": "Information about a KEGG Pathway", "topics": [ "kegg_info" ] }, { "page": "kegg_link", "title": "Find related KEGG entries by using database cross-references", "topics": [ "kegg_link" ] }, { "page": "kegg_list", "title": "Obtain a list of KEGG entry identifiers and associated names", "topics": [ "kegg_list" ] }, { "page": "kegg_open", "title": "Open a KEGG Pathway diagram in the browser", "topics": [ "kegg_open" ] }, { "page": "kegg_operations", "title": "List of operations in the KEGG REST API", "topics": [ "kegg_operations" ] }, { "page": "kegg_organism_codes", "title": "All 3 letter organism code from KEGG", "topics": [ "kegg_organism_codes" ] }, { "page": "kegg_organisms", "title": "List of organisms in KEGG", "topics": [ "kegg_organisms" ] }, { "page": "kegg_pathway_annotations", "title": "Protein pathway annotations", "topics": [ "kegg_pathway_annotations" ] }, { "page": "kegg_pathway_download", "title": "Download one KEGG pathway", "topics": [ "kegg_pathway_download" ] }, { "page": "kegg_pathway_list", "title": "List of KEGG pathways", "topics": [ "kegg_pathway_list" ] }, { "page": "kegg_pathways_download", "title": "Download the KEGG Pathways database", "topics": [ "kegg_pathways_download" ] }, { "page": "kegg_picture", "title": "Download a pathway diagram as a picture", "topics": [ "kegg_picture" ] }, { "page": "kegg_process", "title": "Interactions from KGML", "topics": [ "kegg_process" ] }, { "page": "kegg_query", "title": "Compile a query for the KEGG REST API", "topics": [ "kegg_query" ] }, { "page": "kegg_request", "title": "Perform a KEGG REST API request", "topics": [ "kegg_request" ] }, { "page": "kegg_rm_prefix", "title": "Remove prefix from KEGG foreign database identifiers", "topics": [ "kegg_rm_prefix" ] }, { "page": "kinasephos", "title": "Kinase-PTM relationships from KinasePhos 3.0", "topics": [ "kinasephos" ] }, { "page": "latin_name", "title": "Latin (scientific) names of organisms", "topics": [ "latin_name" ] }, { "page": "load_db", "title": "Load a built in database", "topics": [ "load_db" ] }, { "page": "metalinksdb_sqlite", "title": "Open MetalinksDB as an SQLite3 connection", "topics": [ "metalinksdb_sqlite" ] }, { "page": "metalinksdb_table", "title": "A table from MetalinksDB", "topics": [ "metalinksdb_table" ] }, { "page": "metalinksdb_tables", "title": "List tables in MetalinksDB", "topics": [ "metalinksdb_tables" ] }, { "page": "ncbi_taxid", "title": "NCBI Taxonomy IDs of organisms", "topics": [ "ncbi_taxid" ] }, { "page": "nichenet_build_model", "title": "Construct a NicheNet ligand-target model", "topics": [ "nichenet_build_model" ] }, { "page": "nichenet_expression_data", "title": "Expression data from ligand-receptor perturbation experiments used by NicheNet", "topics": [ "nichenet_expression_data" ] }, { "page": "nichenet_gr_network", "title": "Builds a NicheNet gene regulatory network", "topics": [ "nichenet_gr_network" ] }, { "page": "nichenet_gr_network_evex", "title": "NicheNet gene regulatory network from EVEX", "topics": [ "nichenet_gr_network_evex" ] }, { "page": "nichenet_gr_network_harmonizome", "title": "NicheNet gene regulatory network from Harmonizome", "topics": [ "nichenet_gr_network_harmonizome" ] }, { "page": "nichenet_gr_network_htridb", "title": "NicheNet gene regulatory network from HTRIdb", "topics": [ "nichenet_gr_network_htridb" ] }, { "page": "nichenet_gr_network_omnipath", "title": "Builds gene regulatory network for NicheNet using OmniPath", "topics": [ "nichenet_gr_network_omnipath" ] }, { "page": "nichenet_gr_network_pathwaycommons", "title": "NicheNet gene regulatory network from PathwayCommons", "topics": [ "nichenet_gr_network_pathwaycommons" ] }, { "page": "nichenet_gr_network_regnetwork", "title": "NicheNet gene regulatory network from RegNetwork", "topics": [ "nichenet_gr_network_regnetwork" ] }, { "page": "nichenet_gr_network_remap", "title": "NicheNet gene regulatory network from ReMap", "topics": [ "nichenet_gr_network_remap" ] }, { "page": "nichenet_gr_network_trrust", "title": "NicheNet gene regulatory network from TRRUST", "topics": [ "nichenet_gr_network_trrust" ] }, { "page": "nichenet_ligand_activities", "title": "Calls the NicheNet ligand activity analysis", "topics": [ "nichenet_ligand_activities" ] }, { "page": "nichenet_ligand_target_links", "title": "Compiles a table with weighted ligand-target links", "topics": [ "nichenet_ligand_target_links" ] }, { "page": "nichenet_ligand_target_matrix", "title": "Creates a NicheNet ligand-target matrix", "topics": [ "nichenet_ligand_target_matrix" ] }, { "page": "nichenet_lr_network", "title": "Builds a NicheNet ligand-receptor network", "topics": [ "nichenet_lr_network" ] }, { "page": "nichenet_lr_network_guide2pharma", "title": "Ligand-receptor network from Guide to Pharmacology", "topics": [ "nichenet_lr_network_guide2pharma" ] }, { "page": "nichenet_lr_network_omnipath", "title": "Builds ligand-receptor network for NicheNet using OmniPath", "topics": [ "nichenet_lr_network_omnipath" ] }, { "page": "nichenet_lr_network_ramilowski", "title": "Ligand-receptor network from Ramilowski 2015", "topics": [ "nichenet_lr_network_ramilowski" ] }, { "page": "nichenet_main", "title": "Executes the full NicheNet pipeline", "topics": [ "nichenet_main" ] }, { "page": "nichenet_networks", "title": "Builds NicheNet network prior knowledge", "topics": [ "nichenet_networks" ] }, { "page": "nichenet_optimization", "title": "Optimizes NicheNet model parameters", "topics": [ "nichenet_optimization" ] }, { "page": "nichenet_remove_orphan_ligands", "title": "Removes experiments with orphan ligands", "topics": [ "nichenet_remove_orphan_ligands" ] }, { "page": "nichenet_results_dir", "title": "Path to the current NicheNet results directory", "topics": [ "nichenet_results_dir" ] }, { "page": "nichenet_signaling_network", "title": "Builds a NicheNet signaling network", "topics": [ "nichenet_signaling_network" ] }, { "page": "nichenet_signaling_network_cpdb", "title": "Builds signaling network for NicheNet using ConsensusPathDB", "topics": [ "nichenet_signaling_network_cpdb" ] }, { "page": "nichenet_signaling_network_evex", "title": "NicheNet signaling network from EVEX", "topics": [ "nichenet_signaling_network_evex" ] }, { "page": "nichenet_signaling_network_harmonizome", "title": "NicheNet signaling network from Harmonizome", "topics": [ "nichenet_signaling_network_harmonizome" ] }, { "page": "nichenet_signaling_network_inbiomap", "title": "NicheNet signaling network from InWeb InBioMap", "topics": [ "nichenet_signaling_network_inbiomap" ] }, { "page": "nichenet_signaling_network_omnipath", "title": "Builds signaling network for NicheNet using OmniPath", "topics": [ "nichenet_signaling_network_omnipath" ] }, { "page": "nichenet_signaling_network_pathwaycommons", "title": "NicheNet signaling network from PathwayCommons", "topics": [ "nichenet_signaling_network_pathwaycommons" ] }, { "page": "nichenet_signaling_network_vinayagam", "title": "NicheNet signaling network from Vinayagam", "topics": [ "nichenet_signaling_network_vinayagam" ] }, { "page": "nichenet_test", "title": "Run the NicheNet pipeline with a little dummy network", "topics": [ "nichenet_test" ] }, { "page": "nichenet_workarounds", "title": "Workarounds using NicheNet without attaching the package", "topics": [ "nichenet_workarounds" ] }, { "page": "obo_parser", "title": "Generic OBO parser", "topics": [ "obo_parser" ] }, { "page": "oma_code", "title": "Orthologous Matrix (OMA) codes of organisms", "topics": [ "oma_code" ] }, { "page": "oma_organisms", "title": "Organism identifiers from the Orthologous Matrix", "topics": [ "oma_organisms" ] }, { "page": "oma_pairwise", "title": "Orthologous gene pairs between two organisms", "topics": [ "oma_pairwise" ] }, { "page": "oma_pairwise_genesymbols", "title": "Orthologous pairs of gene symbols between two organisms", "topics": [ "oma_pairwise_genesymbols" ] }, { "page": "oma_pairwise_translated", "title": "Orthologous pairs between two organisms for ID types not supported by OMA", "topics": [ "oma_pairwise_translated" ] }, { "page": "omnipath_cache_autoclean", "title": "Keeps only the latest versions of complete downloads", "topics": [ "omnipath_cache_autoclean" ] }, { "page": "omnipath_cache_clean", "title": "Removes the items from the cache directory which are unknown by the cache database", "topics": [ "omnipath_cache_clean" ] }, { "page": "omnipath_cache_clean_db", "title": "Removes the cache database entries without existing files", "topics": [ "omnipath_cache_clean_db" ] }, { "page": "omnipath_cache_download_ready", "title": "Sets the download status to ready for a cache item", "topics": [ "omnipath_cache_download_ready" ] }, { "page": "omnipath_cache_filter_versions", "title": "Filters the versions from one cache record", "topics": [ "omnipath_cache_filter_versions" ] }, { "page": "omnipath_cache_get", "title": "Retrieves one item from the cache directory", "topics": [ "omnipath_cache_get" ] }, { "page": "omnipath_cache_key", "title": "Generates a hash which identifies an element in the cache database", "topics": [ "omnipath_cache_key" ] }, { "page": "omnipath_cache_latest_or_new", "title": "The latest or a new version of a cache record", "topics": [ "omnipath_cache_latest_or_new" ] }, { "page": "omnipath_cache_latest_version", "title": "Finds the most recent version in a cache record", "topics": [ "omnipath_cache_latest_version" ] }, { "page": "omnipath_cache_load", "title": "Loads an R object from the cache", "topics": [ "omnipath_cache_load" ] }, { "page": "omnipath_cache_move_in", "title": "Moves an existing file into the cache", "topics": [ "omnipath_cache_move_in" ] }, { "page": "omnipath_cache_remove", "title": "Removes contents from the cache directory", "topics": [ "omnipath_cache_remove" ] }, { "page": "omnipath_cache_save", "title": "Saves an R object to the cache", "topics": [ "omnipath_cache_save" ] }, { "page": "omnipath_cache_search", "title": "Searches for cache items", "topics": [ "omnipath_cache_search" ] }, { "page": "omnipath_cache_set_ext", "title": "Sets the file extension for a cache record", "topics": [ "omnipath_cache_set_ext" ] }, { "page": "omnipath_cache_update_status", "title": "Updates the status of an existing cache record", "topics": [ "omnipath_cache_update_status" ] }, { "page": "omnipath_cache_wipe", "title": "Permanently removes all the cache contents", "topics": [ "omnipath_cache_wipe" ] }, { "page": "omnipath_config_path", "title": "Current config file path of OmnipathR", "topics": [ "config_path", "omnipath_config_path" ] }, { "page": "omnipath_for_cosmos", "title": "OmniPath PPI for the COSMOS PKN", "topics": [ "omnipath_for_cosmos" ] }, { "page": "omnipath_load_config", "title": "Load the package configuration from a config file", "topics": [ "load_config", "omnipath_load_config" ] }, { "page": "omnipath_log", "title": "Browse the current OmnipathR log file", "topics": [ "omnipath_log", "read_log" ] }, { "page": "omnipath_logfile", "title": "Path to the current OmnipathR log file", "topics": [ "logfile", "omnipath_logfile" ] }, { "page": "omnipath_msg", "title": "Dispatch a message to the OmnipathR logger", "topics": [ "omnipath_msg" ] }, { "page": "omnipath_query", "title": "Download data from the OmniPath web service", "topics": [ "omnipath_query" ] }, { "page": "omnipath_save_config", "title": "Save the current package configuration", "topics": [ "omnipath_save_config", "save_config" ] }, { "page": "omnipath_set_cachedir", "title": "Change the cache directory", "topics": [ "omnipath_set_cachedir" ] }, { "page": "omnipath_set_console_loglevel", "title": "Sets the log level for the console", "topics": [ "omnipath_set_console_loglevel" ] }, { "page": "omnipath_set_logfile_loglevel", "title": "Sets the log level for the logfile", "topics": [ "omnipath_set_logfile_loglevel" ] }, { "page": "omnipath_set_loglevel", "title": "Sets the log level for the package logger", "topics": [ "omnipath_set_loglevel", "set_loglevel" ] }, { "page": "omnipath_show_db", "title": "Built in database definitions", "topics": [ "omnipath_show_db" ] }, { "page": "omnipath_unlock_cache_db", "title": "Removes the lock file from the cache directory", "topics": [ "omnipath_unlock_cache_db" ] }, { "page": "omnipath-interactions", "title": "Molecular interactions from OmniPath", "topics": [ "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" ] }, { "page": "OmnipathR", "title": "The OmnipathR package", "topics": [ "OmnipathR-package", "OmnipathR" ] }, { "page": "only_from", "title": "Recreate interaction data frame based on certain datasets and resources", "topics": [ "only_from" ] }, { "page": "ontology_ensure_id", "title": "Only ontology IDs", "topics": [ "ontology_ensure_id" ] }, { "page": "ontology_ensure_name", "title": "Only ontology term names", "topics": [ "ontology_ensure_name" ] }, { "page": "ontology_name_id", "title": "Translate between ontology IDs and names", "topics": [ "ontology_name_id" ] }, { "page": "organism_for", "title": "Make sure the resource supports the organism and it has the ID", "topics": [ "organism_for" ] }, { "page": "orthology_translate_column", "title": "Translate a column of identifiers by orthologous gene pairs", "topics": [ "orthology_translate_column" ] }, { "page": "pathwaycommons_download", "title": "Interactions from PathwayCommons", "topics": [ "pathwaycommons_download" ] }, { "page": "pivot_annotations", "title": "Converts annotation tables to a wide format", "topics": [ "pivot_annotations" ] }, { "page": "preppi_download", "title": "Interactions from PrePPI", "topics": [ "preppi_download" ] }, { "page": "preppi_filter", "title": "Filter PrePPI interactions by scores", "topics": [ "preppi_filter" ] }, { "page": "print_bma_motif_es", "title": "Prints BMA motifs to the screen from a sequence of edges", "topics": [ "print_bma_motif_es" ] }, { "page": "print_bma_motif_vs", "title": "Prints BMA motifs to the screen from a sequence of nodes", "topics": [ "print_bma_motif_vs" ] }, { "page": "print_interactions", "title": "Print OmniPath interactions", "topics": [ "print_interactions" ] }, { "page": "print_path_es", "title": "Prints network paths in an edge sequence", "topics": [ "print_path_es" ] }, { "page": "print_path_vs", "title": "Print networks paths given by node sequence", "topics": [ "print_path_vs" ] }, { "page": "pubmed_open", "title": "Open one or more PubMed articles", "topics": [ "pubmed_open" ] }, { "page": "query_info", "title": "OmniPath query parameters", "topics": [ "query_info" ] }, { "page": "ramilowski_download", "title": "Downloads ligand-receptor interactions from Ramilowski et al. 2015", "topics": [ "ramilowski_download" ] }, { "page": "ramp_id_mapping_table", "title": "Pairwise ID translation table from RaMP database", "topics": [ 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