lumi

DOI: 10.18129/B9.bioc.lumi    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see lumi.

BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Bioconductor version: 3.8

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: Pan Du <dupan.mail at gmail.com>, Lei Huang <lhuang at bsd.uchicago.edu>, Gang Feng <g-feng at northwestern.edu>

Installation

To install this package, start R (version "3.5") 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	2.34.0
In Bioconductor since	BioC 2.0 (R-2.5) (12 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_2.34.0.tar.gz
Windows Binary	lumi_2.34.0.zip
Mac OS X 10.11 (El Capitan)	lumi_2.34.0.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	http://bioconductor.org/packages/lumi/
Package Downloads Report	Download Stats