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pKSEA
View on CRAN: Click
here
Download and install pKSEA package within the R console
Install from CRAN:
install.packages("pKSEA")
Install from Github:
library("remotes")
install_github("cran/pKSEA")
Install by package version:
library("remotes")
install_version("pKSEA", "0.0.1")
Attach the package and use:
library("pKSEA")
Maintained by
Peter Liao
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2017-12-22
Latest Update: 2017-12-22
Description:
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)
and of known kinase-substrate links from 'PhosphoSitePlus'
(KSEAdb)
Hornbeck PV, et. al (2015) .
How to cite:
Peter Liao (2017). pKSEA: Prediction-Based Kinase-Substrate Enrichment Analysis. R package version 0.0.1, https://cran.r-project.org/web/packages/pKSEA. Accessed 22 Dec. 2024.
Previous versions and publish date:
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Other R packages that pKSEA depends,
imports, suggests or enhances
Complete documentation for pKSEA
Functions, R codes and Examples using
the pKSEA R package
Some associated functions: KSEAdb . KSEAfilter . NetworKINPred_db . batchrun . calc_contribution . compare . get_matched_data . getscores . getsubs . mk_runlabel . perc.permutation . perc.rank . permtest . results_write . run_on_matched .
Some associated R codes: datadoc.R . internal_functions.R . user_level_functions.R . Full pKSEA package functions and examples
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