wikipathways/rWikiPathways

Name: rWikiPathways

Owner: WikiPathways

Description: R package for WikiPathways API

Created: 2018-03-27 15:48:10.0

Updated: 2018-05-02 20:19:18.0

Pushed: 2018-05-01 15:49:52.0

Homepage: null

Size: 501

Language: R

GitHub Committers

User	Most Recent Commit	# Commits

Other Committers

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README

R Client Package for WikiPathways

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:

• BridgeDbR
• PathVisioRPC
• RCy3

Examples

• Overview vignette

How to install

Official bioconductor releases (recommended)

ce("https://bioconductor.org/biocLite.R")
Lite("rWikiPathways")

Unstable development code from this repo (at your own risk)

all.packages("devtools")
ary(devtools)
all_github('wikipathways/rWikiPathways', build_vignettes=TRUE)
ary(rWikiPathways)

Troubleshooting

1. If you see this error on a Mac: `make: gfortran-4.8: No such file or directory, then try reinstalling R via [homebrew](https://brew.sh/): ``brew update && brew reinstall r```
2. warning: this make take ~30 minutes

How to contribute

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

Development

all.packages("devtools")
all.packages("roxygen2") 
ary(devtools,roxygen2)
ools::install_github("AlexanderPico/docthis")
ary(docthis)
ools::document()
ools::check()
Check::BiocCheck('./')

Testing

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().

Bioconductor

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.

commit -m "informative commit message"
push origin master
push upstream master

http://bioconductor.org/developers/how-to/git/push-to-github-bioc/

Following each bioconductor release, a RELEASE_#_# branch is created here:

checkout -b RELEASE_3_7 upstream/RELEASE_3_7

Only bug fixes and documentation updates can be pushed to the official bioconductor release branch.

https://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

Vignettes

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.