scAB detects multiresolution cell states with clinical significance by integrating single-cell genomics and bulk sequencing data

Forked from scAB, see SigBridgeR for the usage of scAB. Independently usage of scAB is also viable.

News:

• 2025-11-21:
  • Tweaks for performance when selecting optimal alpha
• 2025-11-18:
  • tweaks for performance
  • deleted tutorial data and preprocessing code
  • writed some documentation
  • added some functions

Installation

scAB package can be easily installed from Github using pak:

pak::pkg_install("Exceret/scAB")

Install with ARMA_64BIT_WORD enabled:

repo_url <- "https://github.com/Exceret/scAB.git"
pkg_path <- file.path(tempdir(), "scAB")

system2("git", c("clone", repo_url, pkg_path))

makevars_file <- if (.Platform$OS.type == "windows") {
  file.path(pkg_path, "src", "Makevars.win")
} else {
  file.path(pkg_path, "src", "Makevars")
}
if (file.exists(makevars_file)) {
  lines <- readLines(makevars_file)
  lines <- gsub(
    "^(PKG_CXXFLAGS.*)$",
    "\\1 -DARMA_64BIT_WORD",
    lines
  )
  writeLines(lines, makevars_file)
}

devtools::install(pkg_path, build_vignettes = FALSE)

see DESCRIPTION for more details