This package is for version 3.12 of Bioconductor;
for the stable, up-to-date release version, see
lumi.
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Bioconductor version: 3.12
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
“4.0”) 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
Reference Manual | ||
Text | NEWS |
Details
biocViews | DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
Version | 2.42.0 |
In Bioconductor since | BioC 2.0 (R-2.5) (14 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 | ffpe, methyAnalysis, MineICA |
Suggests Me | beadarray, blima, Harman, methylumi, tigre |
Links To Me | |
Build Report |
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