Other packages > Find by keyword >

pKSEA  

Prediction-Based Kinase-Substrate Enrichment Analysis
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]
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 11 Apr. 2025.
Previous versions and publish date:
No previous versions
Other packages that cited pKSEA R package
View pKSEA citation profile
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
Downloads during the last 30 days
03/1203/1303/1403/1503/1603/1803/2003/2103/2203/2303/2403/2503/2603/2703/2803/3003/3104/0104/0204/0304/0404/0504/0604/0704/0804/09Downloads for pKSEA024681012141618TrendBars

Today's Hot Picks in Authors and Packages

Rwtss  
Client for Web Time-Series Service
Allows remote access to satellite image time series provided by the web time series service (WTSS) ...
Download / Learn more Package Citations See dependency  
GenAlgo  
Classes and Methods to Use Genetic Algorithms for Feature Selection
Defines classes and methods that can be used to implement genetic algorithms for feature selection. ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
multIntTestFunc  
Provides Test Functions for Multivariate Integration
Provides implementations of functions that can be used to test multivariate integration routines. T ...
Download / Learn more Package Citations See dependency  
extrafrail  
Estimation and Additional Tools for Alternative Shared Frailty Models
Provide estimation and data generation tools for some new multivariate frailty models. This version ...
Download / Learn more Package Citations See dependency  

24,012

R Packages

207,311

Dependencies

64,867

Author Associations

24,013

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA