lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: Release (3.17)

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

Author: Pan Du, Richard Bourgon, Gang Feng, Simon Lin

Maintainer: Lei Huang <lhuang1998 at gmail.com>

Citation (from within R, enter citation("lumi")):

Installation

To install this package, start R (version "4.3") and enter:

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

BiocManager::install("lumi")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF
NEWS	Text

Details

biocViews	DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version	2.52.0
In Bioconductor since	BioC 2.0 (R-2.5) (16.5 years)
License	LGPL (>= 2)
Depends	R (>= 2.10), Biobase(>= 2.5.5)
Imports	affy(>= 1.23.4), methylumi(>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, lattice, mgcv (>= 1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI, AnnotationDbi, MASS, graphics, stats, stats4, methods
Linking To
Suggests	beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
System Requirements
Enhances
URL

Depends On Me	ffpeExampleData, iCheck, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData, wateRmelon
Imports Me	arrayMvout, ffpe, MineICA
Suggests Me	beadarray, blima, Harman, methylumi, tigre
Links To Me
Build Report

Package Archives

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

Source Package	lumi_2.52.0.tar.gz
Windows Binary	lumi_2.52.0.zip
macOS Binary (x86_64)	lumi_2.52.0.tgz
macOS Binary (arm64)	lumi_2.52.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/lumi
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/lumi
Bioc Package Browser	https://code.bioconductor.org/browse/lumi/
Package Short Url	https://bioconductor.org/packages/lumi/
Package Downloads Report	Download Stats