.omnipath_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
ancestors               All ancestors in the ontology tree
annotated_network       Network interactions with annotations
annotation_categories   Annotation categories and resources
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
common_name             Common (English) names of organisms
consensuspathdb_download
                        Retrieves the ConsensusPathDB network
consensuspathdb_raw_table
                        Downloads interaction data from ConsensusPathDB
curated_ligand_receptor_interactions
                        Curated ligand-receptor interactions
curated_ligrec_stats    Statistics about literature curated
                        ligand-receptor interactions
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
enzsub_graph            Enzyme-substrate graph
evex_download           Interactions from the EVEX database
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_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
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
                        Retrieve a list of 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         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
harmonizome_download    Downloads a Harmonizome network dataset
has_extra_attrs         Tells if an interaction data frame has an
                        extra_attrs column
homologene_download     Orthology table for a pair of organisms
homologene_raw          Orthology data from NCBI HomoloGene
homologene_uniprot_orthology
                        Orthology table with UniProt IDs
homology_translate      Homology translation
hpo_download            Downloads protein annotations from Human
                        Phenotype Ontology
htridb_download         Downloads TF-target interactions from HTRIdb
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_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_omnipath_annotations
                        Imports annotations 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_intercell
                        Imports OmniPath intercell annotations
import_pathwayextra_interactions
                        Imports interactions from the 'pathway extra'
                        dataset of Omnipath
import_post_translational_interactions
                        All post-translational interactions from
                        OmniPath
import_small_molecule_protein_interactions
                        Interactions from the small molecule-protein
                        dataset of OmniPath
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
is_swissprot            Check for SwissProt IDs
is_trembl               Check for TrEMBL IDs
is_uniprot              Looks like a UniProt ID?
kegg_info               Information about a KEGG Pathway
kegg_open               Open a KEGG Pathway diagram in the browser
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
latin_name              Latin (scientific) names of organisms
load_db                 Load a built in database
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
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
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
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
simplify_intercell_network
                        Simplify an intercell 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 and protein identifiers
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 Uploadlists
uniprot_id_type         UniProt identifier type label
unique_intercell_network
                        Unique intercellular interactions
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
