The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
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 |
| 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 |
Please use the canonical form https://CRAN.R-project.org/package=pKSEA to link to this page.
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.
Health stats visible at Monitor.