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
By default, this will skip building the package vignettes. To build and install package vignettes as well, you must have recent versions of the
rmarkdown packages installed, and use additional parameters, depending on the version of the
remotes package you have installed, to request building vignettes.
If the version is 2.1.0 or higher, use the
build_vignettes parameter (which by default is FALSE):
remotes::install_github("phenoscape/rphenoscape", build_vignettes = TRUE)
If the version of
remotes is lower, use the
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: