drugfindR: An R package to search iLINCS databases for small molecules

drugfindR allows convenient access to the iLINCS Gene Knockdown, Gene Overexpression and Chemical Perturbagen databases and allows you to generate and investigate signatures to identify relevant genes and drugs.

Installation

You can install the released version of drugfindR from r-universe with:

install.packages("drugfindR",
    repos = c(
        "https://cogdisreslab.r-universe.dev",
        "https://cran.r-project.org"
    )
)

And the development version from GitHub with:

if (!requireNamespace("devtools", quietly = TRUE)) {
    install.packages("devtools")
}
devtools::install_github("CogDisResLab/drugfindR")

Usage

This package has two different interfaces that can be used to generate the results:

1. The first way is to use the individual building block functions to generate results. This is useful if you want to use the results in your own analysis pipeline or want more control over the results.

2. The second way is to use one of the convenience functions (investigateSignatures or investigateTarget) to generate results. This approach uses the building block functions under the hood with sensible defaults and returns a final result that can be used for further analysis.