NormalyzerDE

DOI: 10.18129/B9.bioc.NormalyzerDE    

This package is for version 3.8 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: 3.8

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>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("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")

 

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

Details

biocViews	Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.8 (R-3.5) (0.5 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
LinkingTo
Suggests	knitr, testthat, rmarkdown, roxygen2, hexbin
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_1.0.0.tar.gz
Windows Binary	NormalyzerDE_1.0.0.zip
Mac OS X 10.11 (El Capitan)	NormalyzerDE_1.0.0.tgz
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	http://bioconductor.org/packages/NormalyzerDE/
Package Downloads Report	Download Stats