NormalyzerDE
This is the development version of NormalyzerDE; for the stable release version, see NormalyzerDE.
Evaluation of normalization methods and calculation of differential expression analysis statistics
Bioconductor version: Development (3.24)
NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.
Author: Jakob Willforss
Maintainer: Jakob Willforss <jakob.willforss at hotmail.com>
citation("NormalyzerDE")):Jakob Willforss. NormalyzerDE: Evaluation of normalization methods and calculation of differential expression analysis statistics. doi:10.18129/B9.bioc.NormalyzerDE, R package version 1.31.0, https://bioconductor.org/packages/NormalyzerDE.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("NormalyzerDE")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("NormalyzerDE")| Differential expression and countering technical biases using NormalyzerDE | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization |
| Version | 1.31.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| Imports | vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, utils, stats, SummarizedExperiment, matrixStats, ggforce |
| System Requirements | |
| URL | https://computationalproteomics.github.io/NormalyzerDE/ https://github.com/ComputationalProteomics/NormalyzerDE |
See More
| Suggests | knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | PRONE |
| Suggests Me | normScore |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | NormalyzerDE_1.31.0.tar.gz |
| Windows Binary (x86_64) | NormalyzerDE_1.31.0.zip |
| macOS Binary (big-sur-x86_64) | NormalyzerDE_1.31.0.tgz |
| macOS Binary (sonoma-arm64) | NormalyzerDE_1.31.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NormalyzerDE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NormalyzerDE |
| Package Short Url | https://bioconductor.org/packages/NormalyzerDE/ |
| Package Downloads Report | Download Stats |