AffyRNADegradation
This is the development version of AffyRNADegradation; for the stable release version, see AffyRNADegradation.
Analyze and correct probe positional bias in microarray data due to RNA degradation
Bioconductor version: Development (3.24)
The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.
Author: Mario Fasold
Maintainer: Mario Fasold <fasold at izbi.uni-leipzig.de>
citation("AffyRNADegradation")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("AffyRNADegradation")
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("AffyRNADegradation")| AffyRNADegradation Example | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, Microarray, OneChannel, Preprocessing, QualityControl, Software |
| Version | 1.59.0 |
| In Bioconductor since | BioC 2.10 (R-2.15) (14.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.9.0), methods, affy |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | AmpAffyExample, hgu133acdf |
| 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 | AffyRNADegradation_1.59.0.tar.gz |
| Windows Binary (x86_64) | AffyRNADegradation_1.59.0.zip |
| macOS Binary (big-sur-x86_64) | AffyRNADegradation_1.59.0.tgz |
| macOS Binary (sonoma-arm64) | AffyRNADegradation_1.59.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/AffyRNADegradation |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/AffyRNADegradation |
| Bioc Package Browser | https://code.bioconductor.org/browse/AffyRNADegradation/ |
| Package Short Url | https://bioconductor.org/packages/AffyRNADegradation/ |
| Package Downloads Report | Download Stats |