.omnipath_options_defaults
                        Default values for the package options
OmnipathR               The OmnipathR package
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
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
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
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
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
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
load_db                 Load a built in database
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
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
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
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
