NormalyzerDE

This package is for version 3.9 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: 3.9

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 immun.lth.se>

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

Installation

To install this package, start R (version "3.6") 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

Details

biocViews Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization
Version 1.2.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 years)
License Artistic-2.0
Depends R (>= 3.5)
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
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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_1.2.0.tar.gz
Windows Binary NormalyzerDE_1.2.0.zip
Mac OS X 10.11 (El Capitan) NormalyzerDE_1.2.0.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 3.9 Source Archive