OmnipathR

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see OmnipathR.

OmniPath web service client and more

Bioconductor version: 3.21

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] ORCID iD ORCID: 0000-0001-5482-9023 , Denes Turei [cre, aut] ORCID iD ORCID: 0000-0002-7249-9379 , Attila Gabor [aut] ORCID iD ORCID: 0000-0002-0776-1182 , Diego Mananes [aut] ORCID iD ORCID: 0000-0001-7247-6794 , Aurelien Dugourd [aut] ORCID iD ORCID: 0000-0002-0714-028X

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

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

Installation

To install this package, start R (version "4.5") 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 networks around drug-targets using OmnipathR HTML R Script

COSMOS PKN 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics

Version 3.16.2

In Bioconductor since BioC 3.10 (R-3.6) (6 years)

License MIT + file LICENSE

Depends R (>= 4.0)

Imports checkmate, crayon, curl, digest, dplyr (>= 1.1.0), fs, httr2, igraph, jsonlite, later, logger, lubridate, magrittr, progress, purrr, rappdirs, readr (>= 2.0.0), readxl, rlang, rmarkdown, RSQLite, R.utils, rvest, sessioninfo, stats, stringi, stringr, tibble, tidyr, tidyselect, tools, utils, vctrs, withr, XML, xml2, yaml, zip

System Requirements

URL https://r.omnipathdb.org/

Bug Reports https://github.com/saezlab/OmnipathR/issues

Suggests BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, R.matlab, sigmajs, smoof, testthat

Linking To

Enhances

Depends On Me

Imports Me gINTomics, 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_3.16.2.tar.gz

Windows Binary (x86_64) OmnipathR_3.16.0.zip

macOS Binary (x86_64) OmnipathR_3.16.2.tgz

macOS Binary (arm64) OmnipathR_3.16.2.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 3.21 Source Archive