.omnipathr_options_defaults
                        Default values for the package options
OmnipathR               The OmnipathR package
all_uniprot_acs         All UniProt ACs for one organism
all_uniprots            A table with all UniProt records
ambiguity               Inspect the ambiguity of a mapping
ancestors               All ancestors in the ontology tree
annotated_network       Network interactions with annotations
annotation_categories   Annotation categories and resources
annotation_resources    Retrieves a list of available resources in the
                        annotations database of OmniPath
annotations             Protein and gene annotations from OmniPath
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
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)
common_name             Common (English) names of organisms
complex_genes           Get all the molecular complexes for a given
                        gene(s)
complex_resources       Retrieve a list of complex resources available
                        in Omnipath
complexes               Protein complexes from OmniPath
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
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
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_attr_values       Possible values of an extra attribute
extra_attrs             Extra attribute names in an interaction data
                        frame
extra_attrs_to_cols     New columns from extra attributes
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
get_db                  Access a built in database
get_ontology_db         Access an ontology database
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
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
id_translation_resources
                        List available ID translation resources
id_types                ID types and synonyms in identifier translation
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?
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_organism_codes     All 3 letter organism code from KEGG
kegg_organisms          List of organisms in KEGG
kegg_pathway_annotations
                        Protein pathway annotations
kegg_pathway_download   Download one KEGG pathway
kegg_pathway_list       List of KEGG pathways
kegg_pathways_download
                        Download the KEGG Pathways database
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
latin_name              Latin (scientific) names of organisms
load_db                 Load a built in database
metalinksdb_sqlite      Open MetalinksDB as an SQLite3 connection
metalinksdb_table       A table from MetalinksDB
metalinksdb_tables      List tables in MetalinksDB
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
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-interactions   Molecular interactions from OmniPath
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_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_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
pathwaycommons_download
                        Interactions from PathwayCommons
pivot_annotations       Converts annotation tables to a wide format
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
query_info              OmniPath query parameters
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
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
resource_info           OmniPath resource information
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
show_network            Visualize node neighborhood with SigmaJS
signed_ptms             Causal effect enzyme-PTM interactions
simplify_intercell_network
                        Simplify an intercell network
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
tfcensus_download       Downloads the list of transcription factors
                        from TF census
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
uniprot_full_id_mapping_table
                        Creates an ID translation table from UniProt
                        data
uniprot_genesymbol_cleanup
                        TrEMBL to SwissProt by gene names
uniprot_id_mapping_table
                        ID translation data from UniProt ID Mapping
uniprot_id_type         UniProt identifier type label
uniprot_idmapping_id_types
                        ID types available in the UniProt ID Mapping
                        service
uniprot_organisms       UniProt taxonomy data
unique_intercell_network
                        Unique intercellular interactions
unnest_evidences        Separate evidences by direction and effect sign
uploadlists_id_type     UniProt Uploadlists identifier type label
vinayagam_download      Protein-protein interactions from Vinayagam
                        2011
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
zenodo_download         Retrieves data from Zenodo
