methylumi
This is the development version of methylumi; for the stable release version, see methylumi.
Handle Illumina methylation data
Bioconductor version: Development (3.24)
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Maintainer: Sean Davis <seandavi at gmail.com>
citation("methylumi")):
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("methylumi")
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("methylumi")| methylumi.html | HTML | R Script |
| methylumi450k.html | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 2.59.3 |
| In Bioconductor since | BioC 2.5 (R-2.10) (17 years) |
| License | GPL-2 |
| Depends | Biobase, methods, R (>= 4.0), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19(>= 2.2.0), minfi |
| Imports | BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, grDevices, stats, utils, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures, BiocParallel |
| System Requirements | |
| URL | https://seandavi.github.io/methylumi/ https://github.com/seandavi/methylumi |
| Bug Reports | https://github.com/seandavi/methylumi/issues |
See More
| Suggests | lumi, limma, SQN, MASS, rtracklayer, Biostrings, quarto, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18(>= 2.2.0), Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | bigmelon, RnBeads, skewr, wateRmelon |
| Imports Me | ffpe, lumi, missMethyl |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | methylumi_2.59.3.tar.gz |
| Windows Binary (x86_64) | methylumi_2.59.0.zip |
| macOS Binary (big-sur-x86_64) | methylumi_2.59.3.tgz |
| macOS Binary (sonoma-arm64) | methylumi_2.59.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/methylumi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/methylumi |
| Bioc Package Browser | https://code.bioconductor.org/browse/methylumi/ |
| Package Short Url | https://bioconductor.org/packages/methylumi/ |
| Package Downloads Report | Download Stats |