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NormalyzerDE
This is thereleased version of NormalyzerDE; for the devel version, seeNormalyzerDE.
Evaluation of normalization methods and calculation of differential expression analysis statistics
Bioconductor version: Release (3.22)
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>
citation("NormalyzerDE")):Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("NormalyzerDE")For older versions of R, please refer to the appropriateBioconductor 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian,DifferentialExpression,Metabolomics,MultipleComparison,Normalization,Proteomics,Software,Visualization |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.1.0) |
| Imports | vsn,preprocessCore,limma,MASS,ape,car,ggplot2, methods, utils, stats,SummarizedExperiment,matrixStats,ggforce |
| System Requirements | |
| URL | https://github.com/ComputationalProteomics/NormalyzerDE |
See More
| Suggests | knitr,testthat,rmarkdown,roxygen2,hexbin,BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | PRONE |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | NormalyzerDE_1.28.0.tar.gz |
| Windows Binary (x86_64) | NormalyzerDE_1.28.0.zip |
| macOS Binary (x86_64) | NormalyzerDE_1.28.0.tgz |
| macOS Binary (arm64) | NormalyzerDE_1.28.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NormalyzerDE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NormalyzerDE |
| Bioc Package Browser | https://code.bioconductor.org/browse/NormalyzerDE/ |
| Package Short Url | https://bioconductor.org/packages/NormalyzerDE/ |
| Package Downloads Report | Download Stats |