NormalyzerDE
This is the released version of NormalyzerDE; for the devel version, see NormalyzerDE.
Evaluation of normalization methods and calculation of differential expression analysis statistics
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, Metabolomics, MultipleComparison, Normalization, Proteomics, Software, Visualization |
| Version | 1.30.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (8 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://computationalproteomics.github.io/NormalyzerDE/ 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
Follow Installation instructions to use this package in your R session.
| Source Package | NormalyzerDE_1.30.0.tar.gz |
| Windows Binary (x86_64) | NormalyzerDE_1.30.0.zip |
| macOS Binary (big-sur-x86_64) | NormalyzerDE_1.30.0.tgz |
| macOS Binary (sonoma-arm64) | NormalyzerDE_1.30.0.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 |