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rWikiPathways
Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.
6
mentions
2
contributors
Description
R Client library for the WikiPathways API (https://webservice.wikipathways.org/) (license: MIT).
WikiPathays is described in the following papers:
- 2016 NAR paper by Kutmon et al.
- 2018 NAR paper by Slenter et al.
- 2021 NAR paper by Martens et al.
- 2024 NAR paper by Agrawal et al.
If you like this package, or want to make it easier to work with Xrefs, then
you may also like these R packages:
Getting Started
How to install
Official bioconductor releases (recommended)
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rWikiPathways")
Note: Be sure to use the latest Bioconductor and recommended R version
Unstable development code from this repo (at your own risk)
install.packages("devtools")
library(devtools)
install_github('wikipathways/rWikiPathways', build_vignettes=TRUE)
library(rWikiPathways)
Participating organisations
Mentions
- 1.Author(s): Bailey A. T. Weatherbee, Antonia Weberling, Carlos W. Gantner, Lisa K. Iwamoto-Stohl, Zoe Barnikel, Amy Barrie, Alison Campbell, Paula Cunningham, Cath Drezet, Panagiota Efstathiou, Simon Fishel, Sandra Gutiérrez Vindel, Megan Lockwood, Rebecca Oakley, Catherine Pretty, Nabiha Chowdhury, Lucy Richardson, Anastasia Mania, Lauren Weavers, Leila Christie, Kay Elder, Phillip Snell, Magdalena Zernicka-GoetzPublished in Nature Cell Biology by Springer Science and Business Media LLC in 2024, page: 353-36510.1038/s41556-024-01367-1
- 2.Author(s): Yong Huang, Rob Guzy, Shwu-Fan Ma, Catherine A Bonham, Jonathan Jou, Jefree J Schulte, John S Kim, Andrew J Barros, Milena S Espindola, Aliya N Husain, Cory M Hogaboam, Anne I Sperling, Imre NothPublished in BMJ Open Respiratory Research by BMJ in 2023, page: e00139110.1136/bmjresp-2022-001391
- 3.Author(s): Ningning Xu, Aldo Solari, Jelle J. GoemanPublished in Biometrics by Oxford University Press (OUP) in 2022, page: 1103-111310.1111/biom.13693
- 4.Author(s): Jessica Roelands, Manon van der Ploeg, Marieke E Ijsselsteijn, Hao Dang, Jurjen J Boonstra, James C H Hardwick, Lukas J A C Hawinkels, Hans Morreau, Noel F C C de MirandaPublished in Gut by BMJ in 2022, page: 1326-133910.1136/gutjnl-2022-327608
- 5.Author(s): Yan Geng, Lin Li, Jie Yan, Kevin Liu, Aizhen Yang, Lin Zhang, Yingzhi Shen, Han Gao, Xuefeng Wu, Imre Noth, Yong Huang, Junling Liu, Xuemei FanPublished in Nature Communications by Springer Science and Business Media LLC in 202210.1038/s41467-022-34870-w
Contributors
AP
Alexander Pico
EW