multiRF-cluster/load_package.R at main · TransBioInfoLab/multiRF-cluster · GitHub

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## load_package.R
## Install and load packages used across the simulation, HNSC, and ADNI scripts.

cran_pkgs <- c(
  "dplyr",
  "tidyr",
  "ggplot2",
  "ggrepel",
  "patchwork",
  "cowplot",
  "survival",
  "survminer",
  "glmnet",
  "openxlsx",
  "mclust",
  "magick",
  "ggvenn",
  "remotes",
  "readr",
  "readxl",
  "SNFtool",
  "RGCCA",
  "IntNMF",
  "OmicsPLS",
  "InterSIM",
  "msigdbr"
)

bioc_pkgs <- c(
  "SummarizedExperiment",
  "TCGAbiolinks",
  "cBioPortalData",
  "MOFA2",
  "iClusterPlus",
  "r.jive",
  "minfi",
  "sesame",
  "missMethyl",
  "GSVA",
  "clusterProfiler",
  "org.Hs.eg.db",
  "reactome.db",
  "multiMiR",
  "miRBaseConverter",
  "IlluminaHumanMethylationEPICmanifest",
  "IlluminaHumanMethylationEPICanno.ilm10b4.hg19",
  "IlluminaHumanMethylation450kanno.ilmn12.hg19",
  "estimate"
)

install_if_missing <- function(pkgs, installer) {
  missing_pkgs <- pkgs[!vapply(pkgs, requireNamespace, logical(1), quietly = TRUE)]
  if (length(missing_pkgs)) {
    installer(missing_pkgs)
  }
}

install_if_missing(
  cran_pkgs,
  function(pkgs) install.packages(pkgs, repos = "https://cloud.r-project.org")
)

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager", repos = "https://cloud.r-project.org")
}

install_if_missing(
  bioc_pkgs,
  function(pkgs) BiocManager::install(pkgs, ask = FALSE, update = FALSE)
)

if (!requireNamespace("multiRF", quietly = TRUE)) {
  remotes::install_github("novawz/multiRF")
}

optional_github_pkgs <- list(
  xCell = "dviraran/xCell"
)

for (pkg in names(optional_github_pkgs)) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    message(
      sprintf(
        "Optional package '%s' is not installed. If you need the related analyses, install it with remotes::install_github('%s').",
        pkg,
        optional_github_pkgs[[pkg]]
      )
    )
  }
}

invisible(lapply(
  c("dplyr", "tidyr", "ggplot2", "survival"),
  require,
  character.only = TRUE
))