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  "Title": "Prediction-Based Kinase-Substrate Enrichment Analysis",
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  "Description": "A tool for inferring kinase activity changes from\nphosphoproteomics data. 'pKSEA' uses kinase-substrate\nprediction scores to weight observed changes in phosphopeptide\nabundance to calculate a phosphopeptide-level contribution\nscore, then sums up these contribution scores by kinase to\nobtain a phosphoproteome-level kinase activity change score\n(KAC score). 'pKSEA' then assesses the significance of changes\nin predicted substrate abundances for each kinase using\npermutation testing. This results in a permutation score (pKSEA\nsignificance score) reflecting the likelihood of a similarly\nhigh or low KAC from random chance, which can then be\ninterpreted in an analogous manner to an empirically calculated\np-value. 'pKSEA' contains default databases of kinase-substrate\npredictions from 'NetworKIN' (NetworKINPred_db)\n<http://networkin.info> Horn, et. al (2014)\n<doi:10.1038/nmeth.2968> and of known kinase-substrate links\nfrom 'PhosphoSitePlus' (KSEAdb) <https://www.phosphosite.org/>\nHornbeck PV, et. al (2015) <doi:10.1093/nar/gku1267>.",
  "License": "MIT + file LICENSE",
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  "Maintainer": "Peter Liao <pll21@case.edu>",
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  "Date/Publication": "2017-12-21 19:30:15 UTC",
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      "title": "Running pKSEA::compare() on multiple files",
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