phosphonormalizer

DOI: 10.18129/B9.bioc.phosphonormalizer    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see phosphonormalizer.

Compensates for the bias introduced by median normalization in phosphoproteomics

Bioconductor version: 3.8

It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.

Author: Sohrab Saraei, Tomi Suomi, Otto Kauko, Laura L. Elo

Maintainer: Sohrab Saraei <sohrab.saraei at utu.fi>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("phosphonormalizer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("phosphonormalizer")

 

HTML	R Script	Pairwise normalization of phosphoproteomics data
PDF	R Script	phosphonormalizer: Phosphoproteomics Normalization
PDF		Reference Manual
Text		NEWS

Details

biocViews	Normalization, Proteomics, Software, StatisticalMethod, WorkflowStep
Version	1.6.0
In Bioconductor since	BioC 3.5 (R-3.4) (2 years)
License	GPL (>= 2)
Depends	R (>= 3.4.0)
Imports	plyr, stats, graphics, matrixStats
LinkingTo
Suggests	knitr, rmarkdown, testthat
SystemRequirements
Enhances	MSnbase
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	phosphonormalizer_1.6.0.tar.gz
Windows Binary	phosphonormalizer_1.6.0.zip
Mac OS X 10.11 (El Capitan)	phosphonormalizer_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/phosphonormalizer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/phosphonormalizer
Package Short Url	http://bioconductor.org/packages/phosphonormalizer/
Package Downloads Report	Download Stats