# OmniPath web service client

## Documentation for package ‘OmnipathR’ version 2.0.0

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

## Help Pages

.omnipath_options_defaults | Default values for the package options
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_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 | Retrieves a list of categories from 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_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 | get signs for ptms interactions
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 | Imports an intercellular network combining annotations and interactions
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
interaction_graph | Build Omnipath interaction graph
OmnipathR | The OmnipathR package
pivot_annotations | Converts annotation tables to a wide format
printPath_es | print network paths given by edge sequence
printPath_vs | print networks paths given by node sequence
print_interactions | print interactions
print_path_es | print network paths given by edge sequence
print_path_vs | print networks paths given by node sequence
ptms_graph | Post-translational modifications (PTMs) graph