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lumi

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays


Bioconductor version: Release (3.18)

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 2.54.0
In Bioconductor since BioC 2.0 (R-2.5) (17 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
System Requirements
URL
See More
Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
Linking To
Enhances
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 Build Report

Package Archives

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

Source Package lumi_2.54.0.tar.gz
Windows Binary lumi_2.54.0.zip (64-bit only)
macOS Binary (x86_64) lumi_2.54.0.tgz
macOS Binary (arm64) lumi_2.54.0.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