OmnipathR

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see OmnipathR.

Import Omnipath network


Bioconductor version: 3.11

Import data from https://www.omnipathdb.org webservice. It also includes functions to transform and print this data.

Author: Attila Gabor, Denes Turei, Alberto Valdeolivas

Maintainer: Alberto Valdeolivas Urbelz <alvaldeolivas at gmail.com>

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

Installation

To install this package, start R (version "4.0") 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")
Building protein networks around drug-targets using OmnipathR HTML R Script
OmnipathR: utility functions to work with Omnipath in R PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DataImport, DataRepresentation, GraphAndNetwork, Network, Pathways, Software, ThirdPartyClient
Version 1.2.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 3.6.0), igraph, graphics, methods, utils
Imports dplyr, rlang
System Requirements
URL https://github.com/saezlab/OmnipathR
See More
Suggests tidyr, dnet, gprofiler2, BiocStyle, testthat, knitr, rmarkdown, ggplot2, ggraph
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package OmnipathR_1.2.1.tar.gz
Windows Binary OmnipathR_1.2.1.zip
macOS 10.13 (High Sierra) OmnipathR_1.2.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/OmnipathR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/OmnipathR
Bioc Package Browser https://code.bioconductor.org/browse/OmnipathR/
Package Short Url https://bioconductor.org/packages/OmnipathR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.11 Source Archive