lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Bioconductor version: 3.24 · Package version: 2.65.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lumi")Details
| Maintainer | Lei Huang <lhuang1998@gmail.com> |
| Author | Pan Du, Richard Bourgon, Gang Feng, Simon Lin |
| License | LGPL (>= 2) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
| Package Short Url | https://bioconductor.org/packages/lumi/ |
Citation
From within R, enter citation("lumi"):
Pan Du, Richard Bourgon, Gang Feng, Simon Lin. lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays. doi:10.18129/B9.bioc.lumi, R package version 2.65.0, https://bioconductor.org/packages/lumi.
Generated from the package metadata; it may differ from the package's own citation.
Download
Follow the installation instructions to use this package in your R session.
| Source package | lumi_2.65.0.tar.gz |
| Windows binary (x86_64) | lumi_2.65.0.zip |
| macOS binary (arm64) | lumi_2.65.0.tgz |
| macOS binary (x86_64) | lumi_2.65.0.tgz |
Dependencies
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
Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer
Reverse dependencies
Depends On Me (9): ffpeExampleData, iCheck, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, mvoutData, wateRmelon
Imports Me (2): arrayMvout, ffpe
Suggests Me (6): beadarray, blima, Harman, maGUI, methylumi, tigre