Package: OmnipathR
Type: Package
Title: OmniPath web service client and more
Version: 4.1.0
Authors@R: c(
    person(
        given = "Alberto",
        family = "Valdeolivas",
        role = c("aut"),
        email = "alvaldeolivas@gmail.com",
        comment = c(ORCID = "0000-0001-5482-9023")),
    person(
        given = "Denes",
        family = "Turei",
        role = c("cre", "aut"),
        email = "turei.denes@gmail.com",
        comment = c(ORCID = "0000-0002-7249-9379")),
    person(
        given = "Attila",
        family = "Gabor",
        role = "aut",
        comment = c(ORCID = "0000-0002-0776-1182")),
    person(
        given = "Diego",
        family = "Mananes",
        role = "aut",
        comment = c(ORCID = "0000-0001-7247-6794")),
    person(
        given = "Aurelien",
        family = "Dugourd",
        role = "aut",
        comment = c(ORCID = "0000-0002-0714-028X")))
Description: A client for the OmniPath web service
        (https://www.omnipathdb.org) and many other resources. It also
        includes functions to transform and pretty print some of the
        downloaded data, functions to access a number of other
        resources such as BioPlex, ConsensusPathDB, EVEX, Gene
        Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome,
        HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway,
        Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF
        census, TRRUST and Vinayagam et al. 2011. Furthermore,
        OmnipathR features a close integration with the NicheNet method
        for ligand activity prediction from transcriptomics data, and
        its R implementation `nichenetr` (available only on github).
License: MIT + file LICENSE
URL: https://r.omnipathdb.org/
BugReports: https://github.com/saezlab/OmnipathR/issues
biocViews: GraphAndNetwork, Network, Pathways, Software,
        ThirdPartyClient, DataImport, DataRepresentation,
        GeneSignaling, GeneRegulation, SystemsBiology, Transcriptomics,
        SingleCell, Annotation, KEGG
Encoding: UTF-8
VignetteBuilder: knitr
Depends: R(>= 4.0)
Imports: checkmate, crayon, curl, digest, dplyr(>= 1.1.0), fs, httr2,
        igraph, jsonlite, later, logger, lubridate, magrittr, progress,
        purrr, rappdirs, readr(>= 2.0.0), readxl, rlang, rmarkdown,
        RSQLite, R.utils, rvest, sessioninfo, stats, stringi, stringr,
        tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML,
        xml2, yaml, zip
Suggests: BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr,
        mlrMBO, parallelMap, ParamHelpers, R.matlab, SBMLR, sigmajs,
        smoof, testthat
RoxygenNote: 7.3.3
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev libx11-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-29 10:26:56 UTC
RemoteUrl: https://github.com/bioc/OmnipathR
RemoteRef: HEAD
RemoteSha: 3e1139172d3036ffd772ebb945bc5e338ac63fde
NeedsCompilation: no
Packaged: 2026-07-04 06:03:15 UTC; root
Author: Alberto Valdeolivas [aut] (ORCID:
    <https://orcid.org/0000-0001-5482-9023>),
  Denes Turei [cre, aut] (ORCID: <https://orcid.org/0000-0002-7249-9379>),
  Attila Gabor [aut] (ORCID: <https://orcid.org/0000-0002-0776-1182>),
  Diego Mananes [aut] (ORCID: <https://orcid.org/0000-0001-7247-6794>),
  Aurelien Dugourd [aut] (ORCID: <https://orcid.org/0000-0002-0714-028X>)
Maintainer: Denes Turei <turei.denes@gmail.com>