lumi

DOI: 10.18129/B9.bioc.lumi    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see lumi.

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: 3.11

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 <lhuang7 at uchicago.edu>

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

Installation

To install this package, start R (version "4.0") and enter:

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

BiocManager::install("lumi")

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

Documentation

PDF   Reference Manual
Text   NEWS

Details

biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel
Version 2.40.0
In Bioconductor since BioC 2.0 (R-2.5) (13.5 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
LinkingTo
Suggests beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
SystemRequirements
Enhances
URL
Depends On Me arrayMvout, eQTL, ffpeExampleData, iCheck, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData, wateRmelon
Imports Me anamiR, ffpe, methyAnalysis, 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_2.40.0.tar.gz
Windows Binary lumi_2.40.0.zip
macOS 10.13 (High Sierra) lumi_2.40.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/lumi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/lumi
Package Short Url https://bioconductor.org/packages/lumi/
Package Downloads Report Download Stats

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