phosphonormalizer
Compensates for the bias introduced by median normalization in
Bioconductor version: Release (3.19)
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 "4.4") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Normalization, Proteomics, Software, StatisticalMethod, WorkflowStep |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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_1.28.0.tar.gz |
| Windows Binary (x86_64) | phosphonormalizer_1.28.0.zip (64-bit only) |
| macOS Binary (x86_64) | phosphonormalizer_1.28.0.tgz |
| macOS Binary (arm64) | phosphonormalizer_1.28.0.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 |