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>
NeedsCompilation: no
Packaged: 2017-12-21 19:56:06 UTC; pll21
Author: Peter Liao [aut, cre]
Repository: CRAN
Date/Publication: 2017-12-22 18:46:08 UTC
Built: R 4.6.0; ; 2025-07-18 04:41:45 UTC; unix
