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Bioconductor - OmnipathR

OmnipathR

This is the released version of OmnipathR; for the devel version, see OmnipathR.

OmniPath web service client and more

Bioconductor version: Release (3.21)

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).

Author: Alberto Valdeolivas [aut] ORCID: 0000-0001-5482-9023 , Denes Turei [cre, aut] ORCID: 0000-0002-7249-9379 , Attila Gabor [aut] ORCID: 0000-0002-0776-1182 , Diego Mananes [aut] ORCID: 0000-0001-7247-6794 , Aurelien Dugourd [aut] ORCID: 0000-0002-0714-028X

Maintainer: Denes Turei <turei.denes at gmail.com>

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

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("OmnipathR")

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

Documentation

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

browseVignettes("OmnipathR")

Details biocViews Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics Version 3.16.0 In Bioconductor since BioC 3.10 (R-3.6) (5.5 years) License MIT + file LICENSE 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 System Requirements URL https://r.omnipathdb.org/ Bug Reports https://github.com/saezlab/OmnipathR/issues See More Suggests BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, R.matlab, sigmajs, smoof, testthat Linking To Enhances Depends On Me Imports Me gINTomics, wppi Suggests Me decoupleR, dorothea Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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