NormalyzerDE

DOI: 10.18129/B9.bioc.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 (3.17)

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>

Installation

To install this package, start R (version "4.3") 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")

 

PDF	R Script	Differential expression and countering technical biases using NormalyzerDE
PDF		Reference Manual

Details

biocViews	Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization
Version	1.17.0
In Bioconductor since	BioC 3.8 (R-3.5) (4 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
LinkingTo
Suggests	knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/ComputationalProteomics/NormalyzerDE
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	NormalyzerDE_1.17.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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