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phosphonormalizer

Compensates for the bias introduced by median normalization in


Bioconductor version: Release (3.18)

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 [aut, cre], Tomi Suomi [ctb], Otto Kauko [ctb], Laura Elo [ths]

Maintainer: Sohrab Saraei <sohrab.saraei at blueprintgenetics.com>

Citation (from within R, enter citation("phosphonormalizer")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
Pairwise normalization of phosphoproteomics data HTML R Script
phosphonormalizer: Phosphoproteomics Normalization PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Normalization, Proteomics, Software, StatisticalMethod, WorkflowStep
Version 1.26.0
In Bioconductor since BioC 3.5 (R-3.4) (7 years)
License GPL (>= 2)
Depends R (>= 4.0)
Imports plyr, stats, graphics, matrixStats, methods
System Requirements
URL
See More
Suggests knitr, rmarkdown, testthat
Linking To
Enhances MSnbase
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package phosphonormalizer_1.26.0.tar.gz
Windows Binary phosphonormalizer_1.26.0.zip
macOS Binary (x86_64) phosphonormalizer_1.26.0.tgz
macOS Binary (arm64) phosphonormalizer_1.26.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/phosphonormalizer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phosphonormalizer
Bioc Package Browser https://code.bioconductor.org/browse/phosphonormalizer/
Package Short Url https://bioconductor.org/packages/phosphonormalizer/
Package Downloads Report Download Stats