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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 (3.19)

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 (from within R, enter citation("NormalyzerDE")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
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 PDF
NEWS Text

Details

biocViews Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization
Version 1.21.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 4.1.0)
Imports vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, utils, stats, SummarizedExperiment, matrixStats, ggforce
System Requirements
URL https://github.com/ComputationalProteomics/NormalyzerDE
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Suggests knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
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Package Archives

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

Source Package NormalyzerDE_1.21.0.tar.gz
Windows Binary NormalyzerDE_1.21.0.zip
macOS Binary (x86_64) NormalyzerDE_1.21.0.tgz
macOS Binary (arm64) NormalyzerDE_1.21.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NormalyzerDE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NormalyzerDE
Bioc Package Browser https://code.bioconductor.org/browse/NormalyzerDE/
Package Short Url https://bioconductor.org/packages/NormalyzerDE/
Package Downloads Report Download Stats