CRAN/E | pKSEA

pKSEA

Prediction-Based Kinase-Substrate Enrichment Analysis

Installation

About

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) Horn, et. al (2014) doi:10.1038/nmeth.2968 and of known kinase-substrate links from 'PhosphoSitePlus' (KSEAdb) Hornbeck PV, et. al (2015) doi:10.1093/nar/gku1267.

Key Metrics

Version 0.0.1
R ≥ 3.3.0
Published 2017-12-22 2480 days ago
Needs compilation? no
License MIT
License File
CRAN checks pKSEA results

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Maintainer

Maintainer

Peter Liao

Authors

Peter Liao

aut / cre

Material

README
Reference manual
Package source

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Depends

R ≥ 3.3.0