Package: pKSEA 0.0.1

pKSEA: Prediction-Based Kinase-Substrate Enrichment Analysis

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>.

Authors:Peter Liao [aut, cre]

pKSEA_0.0.1.tar.gz
pKSEA_0.0.1.zip(r-4.5)pKSEA_0.0.1.zip(r-4.4)pKSEA_0.0.1.zip(r-4.3)
pKSEA_0.0.1.tgz(r-4.4-any)pKSEA_0.0.1.tgz(r-4.3-any)
pKSEA_0.0.1.tar.gz(r-4.5-noble)pKSEA_0.0.1.tar.gz(r-4.4-noble)
pKSEA_0.0.1.tgz(r-4.4-emscripten)pKSEA_0.0.1.tgz(r-4.3-emscripten)
pKSEA.pdf |pKSEA.html
pKSEA/json (API)

# Install 'pKSEA' in R:
install.packages('pKSEA', repos = c('https://pll21.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/pll21/pksea/issues

Datasets:

On CRAN:

2.70 score 8 scripts 108 downloads 13 exports 0 dependencies

Last updated 7 years agofrom:7f871fb6e7. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 18 2024
R-4.5-winOKOct 18 2024
R-4.5-linuxOKOct 18 2024
R-4.4-winOKOct 18 2024
R-4.4-macOKOct 18 2024
R-4.3-winOKOct 18 2024
R-4.3-macOKOct 18 2024

Exports:batchruncalc_contributioncompareget_matched_datagetscoresgetsubsKSEAfiltermk_runlabelperc.permutationperc.rankpermtestresults_writerun_on_matched

Dependencies: