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OmnipathR

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

OmniPath web service client and more


Bioconductor version: Development (3.19)

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 "4.4") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("OmnipathR")
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 HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics
Version 3.11.2
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License MIT + file LICENSE
Depends R (>= 4.0)
Imports checkmate, crayon, curl, digest, dplyr (>= 1.1.0), httr, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr (>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, withr, xml2, yaml
System Requirements
URL https://r.omnipathdb.org/
Bug Reports https://github.com/saezlab/OmnipathR/issues
See More
Suggests BiocStyle, biomaRt, bookdown, dnet, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, sigmajs, smoof, supraHex, testthat
Linking To
Enhances
Depends On Me
Imports Me wppi
Suggests Me decoupleR, dorothea
Links To Me
Build Report Build Report

Package Archives

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

Source Package OmnipathR_3.11.2.tar.gz
Windows Binary OmnipathR_3.11.2.zip
macOS Binary (x86_64) OmnipathR_3.11.2.tgz
macOS Binary (arm64) OmnipathR_3.11.1.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