NormalyzerDE

This package is for version 3.12 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: 3.12

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 "4.0") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization

Version 1.8.0

In Bioconductor since BioC 3.8 (R-3.5) (5.5 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

System Requirements

URL https://github.com/ComputationalProteomics/NormalyzerDE

Suggests knitr, testthat, rmarkdown, roxygen2, hexbin, BiocStyle

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me

Links To Me

Build Report Build Report