OmnipathR {OmnipathR} | R Documentation

## The OmnipathR package

### Description

OmnipathR is an R package built to provide easy access to the data stored in the OmniPath web service:

https://omnipathdb.org/

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).

### Author(s)

Alberto Valdeolivas <alvaldeolivas@gmail> and Denes Turei <turei.denes@gmail.com> and Attila Gabor <gaborattila87@gmail.com>

### Examples

    # 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
    )

[Package OmnipathR version 3.0.0 Index]