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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 <> and Attila Gabor <>


if (FALSE) {
# 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:

# interactions with references:

# find interactions between kinase and substrate:

# 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
        from = "SRC",
        to = "STAT1"