.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 |