NormalyzerDE

DOI: 10.18129/B9.bioc.NormalyzerDE    

Evaluation of normalization methods and calculation of differential expression analysis statistics

Bioconductor version: Release (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>

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

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("NormalyzerDE", version = "3.8")

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
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/
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