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This is the development version of OmnipathR; for the stable release version, see OmnipathR.

OmniPath web service client and more

Bioconductor version: Development (3.20)

A client for the OmniPath web service ( 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).

Author: Alberto Valdeolivas [aut] , Denes Turei [cre, aut] , Attila Gabor [aut]

Maintainer: Denes Turei <turei.denes at>

Citation (from within R, enter citation("OmnipathR")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics
Version 3.13.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports checkmate, crayon, curl, digest, dplyr (>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr (>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml
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Suggests BiocStyle, biomaRt, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat
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Follow Installation instructions to use this package in your R session.

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