Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 11 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
4 of 13 committers (30.8%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.3%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
R package for WikiPathways API
Basic Info
- Host: GitHub
- Owner: wikipathways
- License: mit
- Language: HTML
- Default Branch: devel
- Homepage: https://r.wikipathways.org/
- Size: 9.13 MB
Statistics
- Stars: 17
- Watchers: 14
- Forks: 6
- Open Issues: 6
- Releases: 0
Topics
Metadata Files
README.md
R Client Package for WikiPathways
- Bioconductor Release Build
- Bioconductor Dev Build
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)
Troubleshooting
- 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
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
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(vignettes = F)
BiocCheck::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().
Updating site
We use pkgdown to generate the main site for rWikiPathways based on this README, metadata, man pages and vignettes. If you make changes to any of these, please take a moment to regenerate the site:
library(pkgdown)
pkgdown::build_site()
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 devel branch here corresponds to the latest code in development and not yet released.
git commit -m "informative commit message"
git push origin devel
git push upstream devel
http://bioconductor.org/developers/how-to/git/push-to-github-bioc/
Following each bioconductor release, a RELEASE_#_# branch is created. The new branch is fetched and devel is updated:
git fetch upstream
git checkout -b RELEASE_3_15 upstream/RELEASE_3_15
git push origin RELEASE_3_15
git checkout devel
git pull upstream devel
git push origin devel
Only bug fixes and documentation updates can be pushed to the official bioconductor release branch. After committing and pushing fixes to devel, then:
``` git checkout RELEASE315 git cherry-pick devel #for lastest commit
or git cherry-pick 1abc234 #for specific commit
or git cherry-pick 1abc234^..5def678 #for an inclusive range
bump release version in DESCRIPTION
git commit -am 'version bump' git push origin RELEASE315
double check changes, and then...
git push upstream RELEASE315 git checkout devel
bump dev version in DESCRIPTION
git commit -am 'version bump' git push origin devel git push upstream devel ```
And then finally, bump version and commit DESCRIPTION to devel and push to origin and upstream.
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 htmlvignette 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.
Owner
- Name: WikiPathways
- Login: wikipathways
- Kind: organization
- Website: https://www.wikipathways.org
- Twitter: WikiPathways
- Repositories: 148
- Profile: https://github.com/wikipathways
Open source software development related to the WikiPathways project
GitHub Events
Total
- Issues event: 3
- Watch event: 3
- Issue comment event: 13
- Push event: 4
- Fork event: 1
- Create event: 2
Last Year
- Issues event: 3
- Watch event: 3
- Issue comment event: 13
- Push event: 4
- Fork event: 1
- Create event: 2
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Alexander Pico | a****o@g****u | 105 |
| Egon Willighagen | e****n@g****m | 53 |
| Alexander Pico | a****o@g****u | 19 |
| Nitesh Turaga | n****a@g****m | 14 |
| J Wokaty | j****y@s****u | 4 |
| J Wokaty | j****y | 4 |
| Martina Summer-Kutmon | m****n | 4 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| Hervé Pagès | h****b@g****m | 1 |
| Kristina Hanspers | k****s@L****t | 1 |
| LiNk-NY | m****9@g****m | 1 |
| khanspers | k****s@g****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 31
- Total pull requests: 8
- Average time to close issues: 4 months
- Average time to close pull requests: 30 days
- Total issue authors: 15
- Total pull request authors: 3
- Average comments per issue: 2.35
- Average comments per pull request: 1.25
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 3
- Pull request authors: 0
- Average comments per issue: 5.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- AlexanderPico (10)
- egonw (7)
- kozo2 (2)
- shivangi1787 (1)
- ayeTown (1)
- emantzo (1)
- mkutmon (1)
- OliveIsLazy (1)
- d-henness (1)
- duanxiaoqian (1)
- Krithika-Bhuvan (1)
- Jorges1000 (1)
- qqwxp (1)
- GuangchuangYu (1)
- ShakiraAgata (1)
Pull Request Authors
- egonw (6)
- AlexanderPico (1)
- jlaw9 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 70,149 total
- Total dependent packages: 5
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: rWikiPathways
rWikiPathways - R client library for the WikiPathways API
- Homepage: https://github.com/wikipathways/rwikipathways
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/rWikiPathways/inst/doc/rWikiPathways.pdf
- License: MIT + file LICENSE
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Latest release: 1.28.0
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- RCurl * imports
- XML * imports
- data.table * imports
- httr * imports
- rjson * imports
- tidyr * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests