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OmniPath web service client and more

Bioconductor version: Release (3.19)

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))


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


To view documentation for the version of this package installed in your system, start R and enter:

Building networks around drug-targets using OmnipathR HTML R Script
Database manager HTML R Script
Extra attributes HTML R Script
OmniPath Bioconductor workshop HTML R Script
OmnipathR: an R client for the OmniPath web service HTML R Script
Pathway construction HTML R Script
Using NicheNet with OmnipathR HTML R Script
Reference Manual PDF


biocViews Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics
Version 3.11.10
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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Depends On Me
Imports Me gINTomics, wppi
Suggests Me decoupleR, dorothea
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Follow Installation instructions to use this package in your R session.

Source Package OmnipathR_3.11.10.tar.gz
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macOS Binary (x86_64) OmnipathR_3.11.10.tgz
macOS Binary (arm64) OmnipathR_3.11.10.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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