The toppgene R/Bioconductor package provides a client interface to the ToppGene API for gene list enrichment analysis https://toppgene.cchmc.org/API.

Installation for development

require_ <- function(pkg) {
  if (! require(pkg, character.only = TRUE)) {
    install.packages(pkg, quiet = TRUE)
    require(pkg, character.only = TRUE)
  }
}
Sys.setenv(MAKEFLAGS = "-j")
invisible(sapply(c("BiocManager", "devtools"), require_))
options(repos = BiocManager::repositories())
remotes::install_deps(dependencies = TRUE)
BiocManager::valid()
devtools::load_all()

Unit tests

devtools::test()

Unit test coverage

require_("covr")
cvg <- covr::package_coverage()
cvg
covr::report(cvg)

Packages checks

devtools::check()
require_("BiocCheck")
BiocCheck::BiocCheck()
require_("lintr")
lintr::lint_package()

Documentation

devtools::build_rmd("vignettes/toppgene.Rmd", envir = new.env())