OmniPath web service client and more
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Documentation for package ‘OmnipathR’ version 3.0.4
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A B C D E F G H I K L N O P R S T U V W Z misc
-- A --
| all_uniprots | A table with all UniProt IDs |
| ancestors | All ancestors in the ontology tree |
| annotated_network | Network interactions with annotations |
| annotation_categories | Annotation categories and resources |
-- B --
| 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 --
| consensuspathdb_download | Retrieves the ConsensusPathDB network |
| consensuspathdb_raw_table | Downloads interaction data from ConsensusPathDB |
-- D --
| descendants | All descendants in the ontology tree |
-- E --
| enzsub_graph | Enzyme-substrate graph |
| evex_download | Interactions from the EVEX database |
-- F --
| filter_by_resource | Filters OmniPath data by resources |
| filter_intercell_network | Quality filter an intercell network |
| filter_sources | Filters OmniPath data by resources |
| find_all_paths | All paths between two groups of vertices |
-- G --
| get_annotation_databases | Retrieves a list of available resources in the annotations database of OmniPath |
| get_annotation_resources | Retrieves a list of available resources in the annotations database of OmniPath |
| get_complexes_databases | Retrieve a list of complex resources available in 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_databases | Retrieve a list of interaction resources available in Omnipath |
| get_interaction_resources | Retrieve a list of interaction resources available in Omnipath |
| get_intercell_categories | Categories in the intercell database of OmniPath |
| get_intercell_classes | Retrieves a list of the generic 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_ptms_databases | Retrieves a list of enzyme-substrate resources available in OmniPath |
| get_resources | Retrieve the available resources for a given query type |
| get_signed_ptms | Signs for enzyme-substrate 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 |
| guide2pharma_download | Downloads interactions from the Guide to Pharmacology database |
-- H --
| harmonizome_download | Downloads a Harmonizome network dataset |
| hpo_download | Downloads protein annotations from Human Phenotype Ontology |
| htridb_download | Downloads TF-target interactions from HTRIdb |
-- I --
| import_AllInteractions | Imports all interaction datasets available in OmniPath |
| import_all_interactions | Imports all interaction datasets available in OmniPath |
| import_dorothea_interactions | From the OmniPath webservice imports interactions from the DoRothEA dataset |
| import_intercell_network | Intercellular communication network |
| import_KinaseExtra_Interactions | Imports interactions from the 'kinase extra' dataset of OmniPath |
| import_kinaseextra_interactions | Imports interactions from the 'kinase extra' dataset of OmniPath |
| import_LigrecExtra_Interactions | Imports interactions from the 'ligrec extra' dataset of OmniPath |
| import_ligrecextra_interactions | Imports interactions from the 'ligrec extra' dataset of OmniPath |
| import_lncrna_mrna_interactions | Imports interactions from the lncRNA-mRNA dataset of OmniPath |
| import_miRNAtarget_Interactions | Imports interactions from the miRNA-target dataset of OmniPath |
| import_mirnatarget_interactions | Imports interactions from the miRNA-target dataset of OmniPath |
| import_OmniPath_annotations | Imports annotations from OmniPath |
| import_Omnipath_annotations | Imports annotations from OmniPath |
| import_omnipath_annotations | Imports annotations from OmniPath |
| import_OmniPath_complexes | Imports protein complexes from OmniPath |
| import_Omnipath_complexes | Imports protein complexes from OmniPath |
| import_omnipath_complexes | Imports protein complexes from OmniPath |
| import_omnipath_enzsub | Imports enzyme-substrate relationships from OmniPath |
| import_OmniPath_Interactions | Imports interactions from the 'omnipath' dataset of Omnipath |
| import_Omnipath_Interactions | Imports interactions from the 'omnipath' dataset of Omnipath |
| import_omnipath_interactions | Imports interactions from the 'omnipath' dataset of Omnipath |
| import_OmniPath_intercell | Imports OmniPath intercell annotations |
| import_Omnipath_intercell | Imports OmniPath intercell annotations |
| import_omnipath_intercell | Imports OmniPath intercell annotations |
| import_OmniPath_PTMS | Imports enzyme-substrate relationships from OmniPath |
| import_Omnipath_PTMS | Imports enzyme-substrate relationships from OmniPath |
| import_PathwayExtra_Interactions | Imports interactions from the 'pathway extra' dataset of Omnipath |
| import_pathwayextra_interactions | Imports interactions from the 'pathway extra' dataset of Omnipath |
| import_post_translational_interactions | Imports all post-translational interactions from OmniPath |
| import_TFregulons_Interactions | From the OmniPath webservice imports interactions from the DoRothEA dataset |
| import_tfregulons_interactions | From the OmniPath webservice imports interactions from the DoRothEA dataset |
| import_tf_mirna_interactions | Imports interactions from the TF-miRNA dataset of OmniPath |
| import_tf_target_interactions | Imports interactions from the TF-target dataset of OmniPath |
| import_transcriptional_interactions | Imports all TF-target interactions from OmniPath |
| inbiomap_download | Downloads and preprocesses network data from InWeb InBioMap |
| inbiomap_raw | Downloads network data from InWeb InBioMap |
| interaction_graph | Build Omnipath interaction graph |
| intercell_categories | Full list of intercell categories and resources |
| intercell_consensus_filter | Quality filter for intercell annotations |
| is_ontology_id | Looks like an ontology ID |
-- K --
| kegg_info | Information about a KEGG Pathway |
| kegg_open | Open a KEGG Pathway diagram in the browser |
| kegg_pathways_download | Download the KEGG Pathways database |
| 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 |
-- L --
| load_db | Load a built in database |
-- N --
| 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 |
| 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_get_config_path | Current config file path |
| 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_reset_config | Restores the built-in default values of all config parameters |
| 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 |
| ontology_ensure_id | Only ontology IDs |
| ontology_ensure_name | Only ontology term names |
| ontology_name_id | Translate between ontology IDs and names |
-- P --
| pathwaycommons_download | Interactions from PathwayCommons |
| pivot_annotations | Converts annotation tables to a wide format |
| printPath_es | Prints network paths in an edge sequence |
| printPath_vs | Print networks paths given by node sequence |
| 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 |
| ptms_graph | Enzyme-substrate graph |
-- R --
| ramilowski_download | Downloads ligand-receptor interactions from Ramilowski et al. 2015 |
| 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 |
| resources_colname | Name of the column with the resources |
-- S --
| simplify_intercell_network | Simplify an intercell network |
| swap_relations | Reverse the direction of ontology relations |
-- T --
| tfcensus_download | Downloads the list of transcription factors from TF census |
| translate_ids | Translate gene and protein identifiers |
| trrust_download | Downloads TF-target interactions from TRRUST |
-- U --
| uniprot_full_id_mapping_table | Creates an ID translation table from UniProt data |
| uniprot_id_mapping_table | Retrieves an identifier translation table from the UniProt uploadlists service |
| unique_intercell_network | Unique intercellular interactions |
-- V --
| vinayagam_download | Protein-protein interactions from Vinayagam 2011 |
-- W --
| walk_ontology_tree | All nodes of a subtree starting from the selected nodes |
-- Z --
| zenodo_download | Retrieves data from Zenodo |
-- misc --
| .omnipath_options_defaults | Default values for the package options |