To install epigenomeR, R version 4.0 or greater is required. For best compatibility and fewer dependency version conflicts, R 4.4 or higher is recommended.

epigenomeR: Install from Github

epigenomeR is installed from Github and depends on packages from both CRAN and Bioconductor. To install, run:

# Enter commands in R (or R studio, if installed)
if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}

options(repos = BiocManager::repositories())
remotes::install_github(
  "Qingjie-Yu/epigenomeR",
  dependencies = TRUE,
  build_vignettes = FALSE
)

To install with parallel compilation enabled, run:

options(Ncpus = parallel::detectCores())
Sys.setenv(MAKEFLAGS = paste0("-j", parallel::detectCores()))

options(repos = BiocManager::repositories())
remotes::install_github(
  "Qingjie-Yu/epigenomeR",
  dependencies = TRUE,
  build_vignettes = FALSE
)

To install the latest version of epigenomeR, run:

options(repos = BiocManager::repositories())
remotes::install_github(
  "Qingjie-Yu/epigenomeR",
  dependencies = TRUE,
  build_vignettes = FALSE,
  force = TRUE
)