MBAmethyl
This is the released version of MBAmethyl; for the devel version, see MBAmethyl.
Model-based analysis of DNA methylation data
Bioconductor version: Release (3.23)
This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.
Author: Tao Wang, Mengjie Chen
Maintainer: Tao Wang <tao.wang.tw376 at yale.edu>
citation("MBAmethyl")):
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("MBAmethyl")
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("MBAmethyl")| MBAmethyl Vignette | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, MethylationArray, Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (12 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.15) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MBAmethyl_1.46.0.tar.gz |
| Windows Binary (x86_64) | MBAmethyl_1.46.0.zip |
| macOS Binary (big-sur-x86_64) | MBAmethyl_1.46.0.tgz |
| macOS Binary (sonoma-arm64) | MBAmethyl_1.46.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MBAmethyl |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MBAmethyl |
| Bioc Package Browser | https://code.bioconductor.org/browse/MBAmethyl/ |
| Package Short Url | https://bioconductor.org/packages/MBAmethyl/ |
| Package Downloads Report | Download Stats |