OmnipathR
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see OmnipathR.
OmniPath web service client and more
Bioconductor version: 3.17
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("OmnipathR")
):
Installation
To install this package, start R (version "4.3") 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 |
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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics |
Version | 3.8.2 |
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, httr, igraph, jsonlite, later, logger, magrittr, progress, purrr, rappdirs, readr (>= 2.0.0), readxl, rlang, rmarkdown, rvest, stats, 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, 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_3.8.2.tar.gz |
Windows Binary | OmnipathR_3.8.2.zip |
macOS Binary (x86_64) | OmnipathR_3.8.2.tgz |
macOS Binary (arm64) | OmnipathR_3.8.2.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 3.17 | Source Archive |