OmnipathR
This is the development version of OmnipathR; for the stable release version, see OmnipathR.
OmniPath web service client and more
Bioconductor version: Development (3.21)
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:
Maintainer: Denes Turei <turei.denes at gmail.com>
citation("OmnipathR")):
Installation
To install this package, start R (version "4.5") 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 |
| 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Annotation, DataImport, DataRepresentation, GeneRegulation, GeneSignaling, GraphAndNetwork, KEGG, Network, Pathways, SingleCell, Software, SystemsBiology, ThirdPartyClient, Transcriptomics |
| Version | 3.15.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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, RSQLite, R.utils, rvest, 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 |
See More
| Suggests | BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, Rgraphviz, R.matlab, sigmajs, smoof, supraHex, 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_3.15.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |