Most of the services provided with the Phenoscape Knowledgebase web API return data in JSON format, plain text (usually tab-delimited), and NeXML. This package facilitates interfacing with the Phenoscape Knowledgebase for searching ontology terms, retrieving term info, and querying data matrices.
The development version of RPhenoscape is available on Github. It has not yet been released to CRAN. To install RPhenoscape from Github, use the
install_github() function in the
remotes package (which can be installed from CRAN using
build_opts parameter ensures that the vignette(s) will be built and installed as well. (The default for
build_opts will skip building vignettes.) Building vignettes requires recent versions of the
rmarkdown packages to be installed.
Once installed, the package can be loaded (“attached”) as any other R package:
The functionality and operations of the RPhenoscape package can be viewed on the dedicated package website: http://rphenoscape.phenoscape.org/
Use cases described there include the following: