OmniPath web service client


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Documentation for package ‘OmnipathR’ version 2.0.0

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.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