OmnipathR: The OmnipathR package

In saezlab/OmnipathR: OmniPath web service client and more

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 <[e-mail]> and Attila Gabor <[e-mail]>

See Also

Useful links:

• https://r.omnipathdb.org/

• Report bugs at https://github.com/saezlab/OmnipathR/issues

Examples

## Not run: 
# Download post-translational modifications:
enzsub <- enzyme_substrate(resources = c("PhosphoSite", "SIGNOR"))

# Download protein-protein interactions
interactions <- omnipath(resources = "SignaLink3")

# Convert to igraph objects:
enzsub_g <- enzsub_graph(enzsub = enzsub)
OPI_g <- interaction_graph(interactions = interactions)

# Print some interactions:
print_interactions(head(enzsub))

# interactions with references:
print_interactions(tail(enzsub), 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
)

## End(Not run)

saezlab/OmnipathR documentation built on Nov. 10, 2024, 11:02 p.m.