OmnipathR

DOI: 10.18129/B9.bioc.OmnipathR    

OmniPath web service client and more

Bioconductor version: Release (3.14)

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>

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

Installation

To install this package, start R (version "4.1") 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 networks around drug-targets using OmnipathR
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 3.2.0
In Bioconductor since BioC 3.10 (R-3.6) (2 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, stats, stringr, tibble, tidyr, tidyselect, tools, utils, xml2, yaml
LinkingTo
Suggests BiocStyle, 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
Links To Me
Build Report  

Package Archives

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

Source Package OmnipathR_3.2.0.tar.gz
Windows Binary OmnipathR_3.2.0.zip
macOS 10.13 (High Sierra) OmnipathR_3.2.0.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
Old Source Packages for BioC 3.14 Source Archive

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