# OmniPath web service client and more

## Documentation for package ‘OmnipathR’ version 3.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I K L M N O P Q R S T U V W Z misc

OmnipathR-package | The OmnipathR package

## -- A --

all_interactions | Molecular interactions from OmniPath
all_uniprots | A table with all UniProt records
all_uniprot_acs | All UniProt ACs for one organism
ancestors | All ancestors in the ontology tree
annotated_network | Network interactions with annotations
annotations | Protein and gene annotations from OmniPath
annotation_categories | Annotation categories and resources
annotation_resources | Retrieves a list of available resources in the annotations database of OmniPath

## -- B --

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

## -- C --

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)
collectri | Molecular interactions from OmniPath
common_name | Common (English) names of organisms
complexes | Protein complexes from OmniPath
complex_genes | Get all the molecular complexes for a given gene(s)
complex_resources | Retrieve a list of complex resources available in Omnipath
config_path | Current config file path of OmnipathR
consensuspathdb_download | Retrieves the ConsensusPathDB network
consensuspathdb_raw_table | Downloads interaction data from ConsensusPathDB
cookie | Acquire a cookie if necessary
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

## -- D --

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
dorothea | Molecular interactions from OmniPath

## -- E --

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_attrs | Extra attribute names in an interaction data frame
extra_attrs_to_cols | New columns from extra attributes
extra_attr_values | Possible values of an extra attribute

## -- F --

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

## -- G --

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 | 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 | Causal effect enzyme-PTM 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
graph_interaction | Interaction data frame from igraph graph object
guide2pharma_download | Downloads interactions from the Guide to Pharmacology database

## -- H --

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

## -- I --

id_translation_resources | List available ID translation resources
id_types | ID types and synonyms in identifier translation
import_all_interactions | Molecular interactions from OmniPath
import_dorothea_interactions | Molecular interactions from OmniPath
import_intercell_network | Intercellular communication network
import_kinaseextra_interactions | Molecular interactions from OmniPath
import_ligrecextra_interactions | Molecular interactions from OmniPath
import_lncrna_mrna_interactions | Molecular interactions from OmniPath
import_mirnatarget_interactions | Molecular interactions from OmniPath
import_omnipath_annotations | Protein and gene annotations from OmniPath
import_omnipath_complexes | Protein complexes from OmniPath
import_omnipath_enzsub | Enzyme-substrate (PTM) relationships from OmniPath
import_omnipath_interactions | Molecular interactions from OmniPath
import_omnipath_intercell | Cell-cell communication roles from OmniPath
import_pathwayextra_interactions | Molecular interactions from OmniPath
import_post_translational_interactions | Molecular interactions from OmniPath
import_small_molecule_protein_interactions | Molecular interactions from OmniPath
import_tf_mirna_interactions | Molecular interactions from OmniPath
import_tf_target_interactions | Molecular interactions from OmniPath
import_transcriptional_interactions | Molecular interactions from OmniPath
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?

## -- 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_annotations | Protein pathway annotations
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
kinaseextra | Molecular interactions from OmniPath

## -- L --

latin_name | Latin (scientific) names of organisms
ligrecextra | Molecular interactions from OmniPath
lncrna_mrna | Molecular interactions from OmniPath
load_config | Load the package configuration from a config file
load_db | Load a built in database
logfile | Path to the current OmnipathR log file

## -- M --

mirna_target | Molecular interactions from OmniPath

## -- N --

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

## -- O --

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 | Molecular interactions from OmniPath
omnipath-interactions | Molecular interactions from OmniPath
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_config_path | Current config file path of OmnipathR
omnipath_for_cosmos | OmniPath PPI for the COSMOS PKN
omnipath_interactions | Molecular interactions from OmniPath
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_reset_config | Restore the built-in default values of all config parameters of a package
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

## -- P --

pathwaycommons_download | Interactions from PathwayCommons
pathwayextra | Molecular interactions from OmniPath
pivot_annotations | Converts annotation tables to a wide format
post_translational | Molecular interactions from OmniPath
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

## -- Q --

query_info | OmniPath query parameters

## -- R --

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
read_log | Browse the current OmnipathR log file
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
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
resource_info | OmniPath resource information

## -- S --

save_config | Save the current package configuration
set_loglevel | Sets the log level for the package logger
show_network | Visualize node neighborhood with SigmaJS
signed_ptms | Causal effect enzyme-PTM interactions
simplify_intercell_network | Simplify an intercell network
small_molecule | Molecular interactions from OmniPath
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

## -- T --

tfcensus_download | Downloads the list of transcription factors from TF census
tf_mirna | Molecular interactions from OmniPath
tf_target | Molecular interactions from OmniPath
transcriptional | Molecular interactions from OmniPath
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

## -- U --

uniprot_full_id_mapping_table | Creates an ID translation table from UniProt data
uniprot_genesymbol_cleanup | TrEMBL to SwissProt by gene names
uniprot_idmapping_id_types | ID types available in the UniProt ID Mapping service
uniprot_id_mapping_table | ID translation data from UniProt ID Mapping
uniprot_id_type | UniProt identifier type label
unique_intercell_network | Unique intercellular interactions
unnest_evidences | Separate evidences by direction and effect sign
uploadlists_id_type | UniProt Uploadlists identifier type label

## -- V --

vinayagam_download | Protein-protein interactions from Vinayagam 2011

## -- W --

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

## -- Z --

zenodo_download | Retrieves data from Zenodo

## -- misc --

.omnipathr_options_defaults | Default values for the package options