NormalyzerDE

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see NormalyzerDE.

Evaluation of normalization methods and calculation of differential expression analysis statistics

Bioconductor version: 3.16

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 "4.2") and enter:


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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization

Version 1.16.0

In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)

License Artistic-2.0

Depends R (>= 3.6)

Imports vsn, preprocessCore, limma, MASS, ape, car, ggplot2, methods, Biobase, RcmdrMisc, raster, utils, stats, SummarizedExperiment, matrixStats, ggforce

System Requirements

URL https://github.com/ComputationalProteomics/NormalyzerDE

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_1.16.0.tar.gz

Windows Binary NormalyzerDE_1.16.0.zip

macOS Binary (x86_64) NormalyzerDE_1.16.0.tgz

macOS Binary (arm64) NormalyzerDE_1.16.0.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

Old Source Packages for BioC 3.16 Source Archive