benchmarKIN provides two complementary benchmarking approaches to evaluate kinase activity inference tools. This has already been applied to a number of computational algorithms and prior knowledge resources here.
To run the benchmarking approaches yourself please check out the documentation.
To install benchmarKIN please run:
# Install specific versions of dependencies (currently has to be done separate)
remotes::install_version("Matrix", version="1.6-5", repos="http://cran.us.r-project.org")
remotes::install_version("MASS", version="7.3-60", repos="http://cran.us.r-project.org")
# Install the package from GitHub
remotes::install_github("saezlab/benchmarKIN")
Mueller-Dott, Sophia, Eric J. Jaehnig, Khoi Pham Munchic, Wen Jiang, Tomer M. Yaron-Barir, Sara R. Savage, Martin Garrido-Rodriguez, et al. 2024. “Comprehensive Evaluation of Phosphoproteomic-Based Kinase Activity Inference.” bioRxiv. https://doi.org/10.1101/2024.06.27.601117.