lumi
This is the released version of lumi; for the devel version, see lumi.
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Bioconductor version: Release (3.23)
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("lumi")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("lumi")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 2.64.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) (19.5 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 |
| 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 |
| Suggests Me | beadarray, blima, Harman, methylumi, tigre, maGUI |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | lumi_2.64.0.tar.gz |
| Windows Binary (x86_64) | lumi_2.64.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | lumi_2.64.0.tgz |
| macOS Binary (sonoma-arm64) | lumi_2.64.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/lumi |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/lumi |
| Bioc Package Browser | https://code.bioconductor.org/browse/lumi/ |
| Package Short Url | https://bioconductor.org/packages/lumi/ |
| Package Downloads Report | Download Stats |