methylumi

This is the released version of methylumi; for the devel version, see methylumi.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Handle Illumina methylation data

Bioconductor version: Release (3.23)

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 (from within R, enter citation("methylumi")):

Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla. methylumi: Handle Illumina methylation data. doi:10.18129/B9.bioc.methylumi, R package version 2.58.1, https://bioconductor.org/packages/methylumi.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version	2.58.1
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
Bug Reports	https://github.com/seandavi/methylumi/issues/new

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, r-universe

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	methylumi_2.58.1.tar.gz
Windows Binary (x86_64)	methylumi_2.58.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	methylumi_2.58.1.tgz
macOS Binary (sonoma-arm64)	methylumi_2.58.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/methylumi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/methylumi
Package Short Url	https://bioconductor.org/packages/methylumi/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive