funtooNorm
This is the development version of funtooNorm; for the stable release version, see funtooNorm.
Normalization Procedure for Infinium HumanMethylation450 BeadChip Kit
Bioconductor version: Development (3.24)
Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.
Author: Celia Greenwood <celia.greenwood at mcgill.ca>,Stepan Grinek <stepan.grinek at ladydavis.ca>, Maxime Turgeon <maxime.turgeon at mail.mcgill.ca>, Kathleen Klein <kathleen.klein at mail.mcgill.ca>
Maintainer: Kathleen Klein <kathleen.klein at mail.mcgill.ca>
citation("funtooNorm")):
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("funtooNorm")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DNAMethylation, Normalization, Preprocessing, Software |
| Version | 1.37.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.4) |
| Imports | pls, matrixStats, minfi, methods, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, GenomeInfoDb, grDevices, graphics, stats |
| System Requirements | |
| URL |
See More
| Suggests | prettydoc, minfiData, knitr, rmarkdown |
| 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 | funtooNorm_1.37.0.tar.gz |
| Windows Binary (x86_64) | funtooNorm_1.37.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | funtooNorm_1.37.0.tgz |
| macOS Binary (sonoma-arm64) | funtooNorm_1.37.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/funtooNorm |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/funtooNorm |
| Bioc Package Browser | https://code.bioconductor.org/browse/funtooNorm/ |
| Package Short Url | https://bioconductor.org/packages/funtooNorm/ |
| Package Downloads Report | Download Stats |