lumi
BeadArray Specific Methods for Illumina Microarrays
Bioconductor version: 2.5
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level.
Author: Pan Du, Gang Feng, Warren Kibbe, Simon Lin
Maintainer: Pan Du <dupan at northwestern.edu>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("lumi")
To cite this package in a publication, start R and enter:
citation("lumi")
Documentation
| Bioc2007_lumi_presentation.pdf | ||
| R Script | lumi | |
| R Script | lumi | |
| R Script | lumi | |
| Reference Manual |
Details
| biocViews | Microarray, OneChannel, Preprocessing |
| Depends | R (>= 2.4.0), annotate, affy(>= 1.23.4), Biobase(>= 2.5.5), mgcv (>= 1.4-0), methods, preprocessCore, RSQLite, MASS |
| Imports | |
| Suggests | beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer |
| System Requirements | |
| License | LGPL (>= 2) |
| URL | |
| Depends On Me | arrayMvout, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData |
| Imports Me | |
| Suggests Me | beadarray |
| Version | 1.12.4 |
| Since | Bioconductor 2.0 (R-2.5) |
Package Downloads
| Package Source | lumi_1.12.4.tar.gz |
| Windows Binary | lumi_1.12.4.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | lumi_1.12.4.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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