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.
If you are interested in the benchmark data or any of the prior knowledge resources used check out our Zenodo repository.
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.