This is the development version of lumi; for the stable release version, see lumi.
BeadArray Specific Methods for Illumina Methylation and Expression MicroarraysBioconductor version: Development (3.22)
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, entercitation("lumi")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("lumi")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation Details biocViews DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel Version 2.61.0 In Bioconductor since BioC 2.0 (R-2.5) (18 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 iCheck, wateRmelon, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, ffpeExampleData, lumiBarnes, MAQCsubset, mvoutData Imports Me arrayMvout, ffpe, MineICA Suggests Me beadarray, blima, Harman, methylumi, tigre, maGUI Links To Me Build Report Build Report Package ArchivesFollow Installation instructions to use this package in your R session.
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