README.Rmd

---
output: github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

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

Forked from [scAB](https://github.com/jinworks/scAB), see [SigBridgeR](https://github.com/WangLabCSU/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`:

```{r,eval=FALSE}     
pak::pkg_install("Exceret/scAB")
```

Install with `ARMA_64BIT_WORD` enabled:

```{r,eval=FALSE}     
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