### Install devtools R Package

Source: https://github.com/ayadlab/scfocal/blob/main/README.md

Installs the devtools package from CRAN or the development version from GitHub. This is a prerequisite for installing scFOCAL.

```r
# Install devtools from CRAN
install.packages("devtools")

# Or the development version from GitHub:
# install.packages("devtools")
devtools::install_github("r-lib/devtools")
```

--------------------------------

### Launch scFOCAL Shiny GUI

Source: https://github.com/ayadlab/scfocal/blob/main/README.md

Loads the scFOCAL library and launches the graphical user interface (GUI) for the scFOCAL application. This requires the scFOCAL package to be installed.

```r
library(scFOCAL) # load the scFOCAL library including necessary drug signature data
scFOCAL::runscFOCAL() # launch the scFOCAL shiny GUI
```

--------------------------------

### Install BiocManager and Core Packages

Source: https://github.com/ayadlab/scfocal/blob/main/README.md

Installs the BiocManager package if not already present, then installs or updates core Bioconductor packages. This is necessary for some scFOCAL dependencies.

```r
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.17")
```

```r
BiocManager::install()
```

--------------------------------

### Install scFOCAL R Package

Source: https://github.com/ayadlab/scfocal/blob/main/README.md

Installs the scFOCAL R package from its GitHub repository using devtools. Ensure all dependencies are met before running this command.

```r
devtools::install_github("AyadLab/scFOCAL")
```

--------------------------------

### Subsample Seurat Object

Source: https://github.com/ayadlab/scfocal/blob/main/README.md

This R code demonstrates how to subsample a Seurat object to a specified number of cells and save the downsampled object. Ensure the Seurat package is installed and loaded.

```r
library(Seurat)
set.seed(1)

obj_toSub <- readRDS(file = "seuratObj.RDS")
downsampled.obj <- obj_toSub[, sample(colnames(obj_toSub), size = 500, replace=F)]
saveRDS(downsampled.obj, file = "downsampled_seuratObj.RDS")
```

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