DOI: 10.18129/B9.bioc.OmnipathR  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see OmnipathR.

OmniPath web service client and more

Bioconductor version: 3.16

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")):


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HTML R Script 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
PDF   Reference Manual
Text   NEWS


biocViews Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics
Version 3.5.25
In Bioconductor since BioC 3.10 (R-3.6) (3.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports checkmate, crayon, curl, digest, dplyr, httr, igraph, jsonlite, later, logger, magrittr, progress, purrr, rappdirs, readr (>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml
Suggests BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, smoof, supraHex, testthat
Depends On Me
Imports Me wppi
Suggests Me decoupleR
Links To Me
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Source Package OmnipathR_3.5.25.tar.gz
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macOS Binary (x86_64) OmnipathR_3.6.0.tgz
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