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Bioconductor - NormalyzerDE (development version)

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 (3.22)

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 "4.5") 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 1.27.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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://github.com/ComputationalProteomics/NormalyzerDE See More Package Archives

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

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