OmnipathR
This is the development version of OmnipathR; for the stable release version, see OmnipathR.
OmniPath web service client and more
Bioconductor version: Development (3.24)
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]
, Diego Mananes [aut]
, Aurelien Dugourd [aut]
Maintainer: Denes Turei <turei.denes at gmail.com>
citation("OmnipathR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 Cache System | 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 | 4.1.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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 |
See More
| Suggests | BiocStyle, bookdown, ggplot2, ggraph, gprofiler2, knitr, mlrMBO, parallelMap, ParamHelpers, R.matlab, SBMLR, sigmajs, smoof, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | gINTomics, MetaProViz, 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_4.1.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | OmnipathR_4.1.0.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 |