Introduction | Tutorial | Installation | epTypes: explore enviPath database structure | epLogin: log into an enviPath personal account | epList: retrieve lists of objects from enviPath | epLink: map between different types of objects | epGet: fetch raw objects from enviPath | epModel: predict compound biotransformation pathways | epLogout: log out of an enviPath personal account | Reproducibility | Cite enviPathR | Session info
Package: enviPathR 1.0.0
Giulio Benedetti
enviPathR: Client for the 'enviPath' 'RESTful' API
The environmental pathway database ('enviPath') is a key resource for the functional annotation and pathway prediction of microbial communities, providing knowledge on biotransformation pathways along with the chemical reactions and produced compounds. This package enables the programmatic access to 'enviPath' by porting the database 'RESTful' API from R. This includes methods to both retrieve entries and predict pathways for custom compounds.
Authors:
enviPathR_1.0.0.tar.gz
enviPathR_1.0.0.zip(r-4.7-any)enviPathR_1.0.0.zip(r-4.6-any)
enviPathR_1.0.0.tar.gz(r-4.7-any)enviPathR_1.0.0.tar.gz(r-4.6-any)
enviPathR_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
enviPathR/json (API)
| # Install 'enviPathR' in R: |
| install.packages('enviPathR', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/envipath/envipathr/issues
Pkgdown/docs site:https://envipath.github.io
softwaredataimportcheminformaticsannotationpathwaysfunctionalprediction
Last updated from:8127bb47b2. Checks:6 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 135 | ||
| source / vignettes | OK | 262 | ||
| linux-release | OK | 150 | ||
| windows-devel | OK | 105 | ||
| windows-release | OK | 121 | ||
| wasm-release | OK | 139 |
Exports:epGetepLinkepListepLoginepLogoutepModelepTypes
Dependencies:askpassBHBiocParallelclicodetoolscpp11curlformatRfutile.loggerfutile.optionsgluehttr2lambda.rlifecyclemagrittropensslR6rlangsnowstringistringrsysvctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| enviPathR: the R client for the enviPath RESTful API | enviPathR-package enviPathR |
| Get enviPath objects | epGet |
| Link enviPath objects | epLink |
| List enviPath objects | epList |
| Log into enviPath account | epLogin epLogout |
| Predict compound biotransformation pathways | epModel |
| Find available enviPath resources | epTypes |