NormalyzerDE

DOI: 10.18129/B9.bioc.NormalyzerDE    

Evaluation of normalization methods and calculation of differential expression analysis statistics

Bioconductor version: Release (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 (!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 1.2.0
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, 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_1.2.0.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
Package Short Url http://bioconductor.org/packages/NormalyzerDE/
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