OmnipathR {OmnipathR} | R Documentation |
OmnipathR is an R package built to provide easy access to the data stored in the OmniPath web service:
And a number of other resources, such as BioPlex, ConsensusPathDB, EVEX, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011.
The OmniPath web service implements a very simple REST style API. This package make requests by the HTTP protocol to retreive the data. Hence, fast Internet access is required for a propser use of OmnipathR.
The package also provides some utility functions to filter, analyse and visualize the data. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation nichenetr (available in CRAN).
Alberto Valdeolivas <alvaldeolivas@gmail> and Denes Turei <turei.denes@gmail.com> and Attila Gabor <gaborattila87@gmail.com>
# Download post-translational modifications: enzsub <- import_omnipath_enzsub(resources = c("PhosphoSite", "SIGNOR")) # Download protein-protein interactions interactions <- import_omnipath_interactions(resources = c("SignaLink3")) # Convert to igraph objects: enzsub_g <- enzsub_graph(enzsub = enzsub) OPI_g <- interaction_graph(interactions = interactions ) # Print some interactions: print_interactions(head(ptms)) # interactions with references: print_interactions(tail(ptms),writeRefs=TRUE) # find interactions between kinase and substrate: print_interactions(dplyr::filter(ptms,enzyme_genesymbol=="MAP2K1", substrate_genesymbol=="MAPK3")) # find shortest paths on the directed network between proteins print_path_es(shortest_paths(OPI_g, from = "TYRO3", to = "STAT3", output = 'epath')$epath[[1]], OPI_g) # find all shortest paths between proteins print_path_vs( all_shortest_paths( enzsub_g, from = "SRC", to = "STAT1" )$res, enzsub_g )