scrattch_dependencies <- list(
hicat = list(bioconductor = c("impute",
"limma",
"preprocessCore",
"WGCNA"),
github = c("JinmiaoChenLab/Rphenograph")),
io = list(bioconductor = c("rhdf5"),
github = c()),
vis = list(bioconductor = c(),
github = c())
)
#' Install dependencies for scrattch packages from Bioconductor
#'
install_bioc_deps <- function() {
if(length(scrattch_dependencies$hicat$bioconductor) > 0) {
BiocManager::install(scrattch_dependencies$hicat$bioconductor)
}
if(length(scrattch_dependencies$io$bioconductor) > 0) {
BiocManager::install(scrattch_dependencies$io$bioconductor)
}
if(length(scrattch_dependencies$vis$bioconductor) > 0) {
BiocManager::install(scrattch_dependencies$vis$bioconductor)
}
}
#' Install dependencies for scrattch packages from Github
#'
install_github_deps <- function() {
if(length(scrattch_dependencies$hicat$github) > 0) {
devtools::install_github(scrattch_dependencies$hicat$github)
}
if(length(scrattch_dependencies$io$github) > 0) {
devtools::install_github(scrattch_dependencies$io$github)
}
if(length(scrattch_dependencies$vis$github) > 0) {
devtools::install_github(scrattch_dependencies$vis$github)
}
}
#' Install all dependencies from Github and BioConductor
#'
install_scrattch_deps <- function() {
install_github_deps()
install_bioc_deps()
}
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