Prediction-Based Kinase-Substrate Enrichment Analysis R package pKSEA version 0.0.1 A tool for inferring kinase activity changes from phosphoproteomics data. 'pKSEA' uses kinase-substrate prediction scores to weight observed changes in phosphopeptide abundance to calculate a phosphopeptide-level contribution score, then sums up these contribution scores by kinase to obtain a phosphoproteome-level kinase activity change score (KAC score). 'pKSEA' then assesses the significance of changes in predicted substrate abundances for each kinase using permutation testing. This results in a permutation score (pKSEA significance score) reflecting the likelihood of a similarly high or low KAC from random chance, which can then be interpreted in an analogous manner to an empirically calculated p-value. 'pKSEA' contains default databases of kinase-substrate predictions from 'NetworKIN' (NetworKINPred_db) <http://networkin.info> Horn, et. al (2014) <doi:10.1038/nmeth.2968> and of known kinase-substrate links from 'PhosphoSitePlus' (KSEAdb) <https://www.phosphosite.org/> Hornbeck PV, et. al (2015) <doi:10.1093/nar/gku1267>. Software Depends: R (>= 3.3.0) Peter Liao <pll21@case.edu> Comprehensive R Archive Network (CRAN) Peter Liao [aut, cre] MIT + file LICENSE (https://CRAN.R-project.org/package=pKSEA/LICENSE) 2017-12-22 application/tgz https://CRAN.R-project.org/package=pKSEA doi:10.32614/CRAN.package.pKSEA