OmnipathR

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

OmniPath web service client and more

Bioconductor version: Development (3.23)

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 "4.6") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("OmnipathR")

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

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics
Version	3.17.7
In Bioconductor since	BioC 3.10 (R-3.6) (6 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

Suggests	BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, R.matlab, sigmajs, smoof, testthat
Linking To
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Depends On Me
Imports Me
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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/OmnipathR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/OmnipathR
Package Short Url	https://bioconductor.org/packages/OmnipathR/
Package Downloads Report	Download Stats