OmnipathR

DOI: 10.18129/B9.bioc.OmnipathR    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see OmnipathR.

OmniPath web service client and more

Bioconductor version: 3.15

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] , Denes Turei [cre, aut] , Attila Gabor [aut]

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

Installation

To install this package, start R (version "4.2") 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")

 

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
Text		LICENSE

Details

biocViews	Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics
Version	3.4.7
In Bioconductor since	BioC 3.10 (R-3.6) (3 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, stats, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml
LinkingTo
Suggests	BiocStyle, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, rmarkdown, smoof, supraHex, testthat
SystemRequirements
Enhances
URL	https://saezlab.github.io/OmnipathR/
BugReports	https://github.com/saezlab/OmnipathR/issues
Depends On Me
Imports Me	wppi
Suggests Me	decoupleR
Links To Me
Build Report

Package Archives

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

Source Package	OmnipathR_3.4.7.tar.gz
Windows Binary	OmnipathR_3.4.7.zip
macOS Binary (x86_64)	OmnipathR_3.4.7.tgz
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