OmnipathR

DOI: 10.18129/B9.bioc.OmnipathR    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see OmnipathR.

OmniPath web service client

Bioconductor version: 3.12

A client for the OmniPath web service (https://www.omnipathdb.org). It also includes functions to transform and pretty print some of the downloaded data.

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 "4.0") and enter:

if (!requireNamespace("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 protein networks around drug-targets using OmnipathR
HTML	R Script	OmnipathR: utility functions to work with OmniPath in R
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, Network, Pathways, Software, SystemsBiology, ThirdPartyClient
Version	2.0.0
In Bioconductor since	BioC 3.10 (R-3.6) (1.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.0), igraph, graphics, methods, utils, jsonlite
Imports	dplyr, stats, rlang, tidyr
LinkingTo
Suggests	dnet, gprofiler2, BiocStyle, testthat, knitr, rmarkdown, ggplot2, ggraph
SystemRequirements
Enhances
URL	https://saezlab.github.io/OmnipathR/
BugReports	https://github.com/saezlab/OmnipathR/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	OmnipathR_2.0.0.tar.gz
Windows Binary	OmnipathR_2.0.0.zip
macOS 10.13 (High Sierra)	OmnipathR_2.0.0.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