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.
If you like this package, or want to make it easier to work with Xrefs, then you may also like these R packages:
Official bioconductor releases (recommended)
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("rWikiPathways")
Unstable development code from this repo (at your own risk)
install.packages("devtools")
library(devtools)
install_github('wikipathways/rWikiPathways', build_vignettes=TRUE)
library(rWikiPathways)
- If you see this error on a Mac:
make: gfortran-4.8: No such file or directory, then try reinstalling R via homebrew:brew update && brew reinstall r- warning: this make take ~30 minutes
This is a public, open source project. Come on in! You can contribute at multiple levels:
- Report an issue or feature request
- Fork and make pull requests
- Contact current WikiPathways developers and inquire about joining the team
install.packages("devtools")
install.packages("roxygen2")
library(devtools,roxygen2)
devtools::install_github("AlexanderPico/docthis")
library(docthis)
setwd("/git/wikipathways/rWikiPathways") #customize to your setup
devtools::document()
devtools::check()
BiocCheck::BiocCheck('./')
Unit tests are a crucial tool in software development. Be sure to add tests for any new methods implemented. These will be run as part of the devtools::check().
While this is the primary development repository for the rWikiPathways project, we also make regular pushes to official bioconductor repository (devel & release) from which the official releases are generated. This is the correct repo for all coding and bug reporting interests. The tagged releases here correspond to the bioconductor releases via a manual syncing process. The master branch here corresponds to the latest code in development and not yet released.
git commit -m "informative commit message"
git push origin master
git push upstream master
http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
Following each bioconductor release, a RELEASE_#_# branch is created here:
git checkout -b RELEASE_3_7 upstream/RELEASE_3_7
Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to master, then:
git checkout RELEASE_3_7
git cherry-pick master #for latest commit
# or git cherry-pick <commit number> #for specific commit
# bump version in DESCRIPTION
git add DESCRIPTION
git commit -m 'version bump'
git push origin RELEASE_3_7
# double check changes, and then...
git push upstream RELEASE_3_7
git checkout master
https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/
When adding or updating vignettes, consider the following tips for consistency:
- Copy/paste the header from an existing rWikiPathways vignette, including the global knitr options
- Number the VignetteIndexEntry names w.r.t. other vignettes (this determines their presentation order)
- Avoid spaces in Rmd filenames; causes CHECK errors
- When ready, run Knit to html_vignette_ and review the generated html
- Note: you don't need to save the html version; it will be generated anew at Bioconductor.
- In the end, you should just have an Rmd version of each vignette in the repo.