NormalyzerDE
This package is for version 3.9 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: 3.9
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("NormalyzerDE")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (5.5 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 |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 [email protected]:packages/NormalyzerDE |
| Bioc Package Browser | https://code.bioconductor.org/browse/NormalyzerDE/ |
| Package Short Url | https://bioconductor.org/packages/NormalyzerDE/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |