TargetScore

TargetScore is a data-driven network modeling algorithm for drug response analysis in cancer.

Quick Start

Install Git, R 3.5 or later, and Pandoc. Pandoc is included with RStudio; the Docker validation uses R 4.6.

1. Clone the repository and enter its root directory:

git clone https://github.com/korkutlab/targetscore.git
cd targetscore

2. From the repository root, start R and install the package dependencies and TargetScore:

install.packages(
  c("remotes", "rmarkdown"),
  repos = "https://cloud.r-project.org"
)
remotes::install_github(
  "cmap/morpheus.R",
  dependencies = TRUE,
  upgrade = "never"
)
remotes::install_deps(
  "targetscore",
  dependencies = TRUE,
  upgrade = "never"
)
remotes::install_local(
  "targetscore",
  dependencies = FALSE,
  upgrade = "never"
)

3. In the same R session, render the tutorial:

dir.create("output", showWarnings = FALSE)
output_dir <- normalizePath("output")

rmarkdown::render(
  "targetscore/vignettes/target_score_tutorial.Rmd",
  output_format = "html_document",
  output_dir = output_dir,
  params = list(output_dir = output_dir)
)

4. Open output/target_score_tutorial.html in a web browser. All other files created by the tutorial are also retained in output/.

Installation requires access to CRAN and the public cmap/morpheus.R GitHub repository. Some R dependencies may require platform-specific compilers or system libraries when a prebuilt binary is unavailable.

Docker Validation and Server

A normal build runs both the Shiny startup check and the complete vignette pipeline before creating the production image:

docker build --tag targetscore .
docker run --rm --publish 3838:3838 targetscore

Open http://127.0.0.1:3838/ to use the application. The optional PORT environment variable changes the container's listening port; publish the same port when overriding it.

Build only through the verification stage:

docker build --target verify --tag targetscore-verify .

Force Buildx to rerun that stage without invalidating the dependency-installation cache:

docker buildx build --target verify --no-cache-filter verify --load --tag targetscore-verify .

Building requires network access to CRAN and the public cmap/morpheus.R GitHub repository. Running the production image requires no credentials, mounted data, external services, or network access.