nnNorm
This is the development version of nnNorm; for the stable release version, see nnNorm.
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
Bioconductor version: Development (3.24)
This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.
Author: Adi Laurentiu Tarca <atarca at med.wayne.edu>
Maintainer: Adi Laurentiu Tarca <atarca at med.wayne.edu>
citation("nnNorm")):
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("nnNorm")
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("nnNorm")| nnNorm Tutorial | R Script | |
| Reference Manual |
Details
| biocViews | Microarray, Preprocessing, Software, TwoChannel |
| Version | 2.77.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | LGPL |
| Depends | R (>= 2.2.0), marray |
| Imports | graphics, grDevices, marray, methods, nnet, stats |
| System Requirements | |
| URL | http://bioinformaticsprb.med.wayne.edu/tarca/ |
See More
| Suggests | |
| 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 | nnNorm_2.77.0.tar.gz |
| Windows Binary (x86_64) | nnNorm_2.77.0.zip |
| macOS Binary (big-sur-x86_64) | nnNorm_2.77.0.tgz |
| macOS Binary (sonoma-arm64) | nnNorm_2.77.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/nnNorm |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/nnNorm |
| Bioc Package Browser | https://code.bioconductor.org/browse/nnNorm/ |
| Package Short Url | https://bioconductor.org/packages/nnNorm/ |
| Package Downloads Report | Download Stats |