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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>.
| Version: | 0.0.1 |
| Depends: | R (≥ 3.3.0) |
| Published: | 2017-12-22 |
| DOI: | 10.32614/CRAN.package.pKSEA |
| Author: | Peter Liao [aut, cre] |
| Maintainer: | Peter Liao <pll21 at case.edu> |
| License: | MIT + file LICENSE |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | pKSEA results |
| Reference manual: | pKSEA.pdf |
| Package source: | pKSEA_0.0.1.tar.gz |
| Windows binaries: | r-devel: pKSEA_0.0.1.zip, r-release: pKSEA_0.0.1.zip, r-oldrel: pKSEA_0.0.1.zip |
| macOS binaries: | r-release (arm64): pKSEA_0.0.1.tgz, r-oldrel (arm64): pKSEA_0.0.1.tgz, r-release (x86_64): pKSEA_0.0.1.tgz, r-oldrel (x86_64): pKSEA_0.0.1.tgz |
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.