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:
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')) |
Bug tracker:https://github.com/pll21/pksea/issues
- KSEAdb - KSEAdb
- NetworKINPred_db - NetworKINPred_db
Last updated 7 years agofrom:7f871fb6e7. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 17 2024 |
R-4.5-win | OK | Nov 17 2024 |
R-4.5-linux | OK | Nov 17 2024 |
R-4.4-win | OK | Nov 17 2024 |
R-4.4-mac | OK | Nov 17 2024 |
R-4.3-win | OK | Nov 17 2024 |
R-4.3-mac | OK | Nov 17 2024 |
Exports:batchruncalc_contributioncompareget_matched_datagetscoresgetsubsKSEAfiltermk_runlabelperc.permutationperc.rankpermtestresults_writerun_on_matched
Dependencies:
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Running pKSEA::compare() on multiple files | batchrun |
Running analysis runs on known substrates, predicted substrates, and both. | compare |
Filtering data to matched predictions | get_matched_data |
KSEAdb | KSEAdb |
NetworKINPred_db | NetworKINPred_db |
Runs pKSEA analysis on a dataset result from get_matched_data. | run_on_matched |