Package: pKSEA
Type: Package
Title: Prediction-Based Kinase-Substrate Enrichment Analysis
Version: 0.0.1
Authors@R: person("Peter", "Liao", email = "pll21@case.edu", role = c("aut", "cre"))
Description: 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>.
Depends: R (>= 3.3.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Maintainer: Peter Liao <pll21@case.edu>
Repository: https://pll21.r-universe.dev
Date/Publication: 2017-12-21 19:30:15 UTC
RemoteUrl: https://github.com/pll21/pksea
RemoteRef: HEAD
RemoteSha: 7f871fb6e79a81fcd536194f17987e2faed49df1
NeedsCompilation: no
Packaged: 2026-10-01 10:09:25 UTC; root
Author: Peter Liao [aut, cre]