To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("lumi")
In most cases, you don't need to download the package archive at all.
lumi
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
Bioconductor version: 2.14
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: Pan Du <dupan.mail at gmail.com>
Citation (from within R,
enter citation("lumi")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("lumi")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("lumi")
| R Script | Analyze Illumina Infinium methylation microarray data | |
| R Script | Evaluation of VST algorithm in lumi package | |
| R Script | Resolve the inconsistency of Illumina identifiers through nuID | |
| R Script | Using lumi A package processing Illumina Microarray | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 2.16.0 |
| In Bioconductor since | BioC 2.0 (R-2.5) |
| License | LGPL (>= 2) |
| Depends | R (>= 2.10), Biobase(>= 2.5.5) |
| Imports | affy(>= 1.23.4), methylumi(>= 2.3.2), GenomicFeatures, GenomicRanges, annotate, Biobase(>= 2.5.5), 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 |
| System Requirements | |
| URL | |
| Depends On Me | arrayMvout, ffpeExampleData, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData, wateRmelon |
| Imports Me | ffpe, methyAnalysis, MineICA |
| Suggests Me | beadarray, methylumi, tigre, virtualArray |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | lumi_2.16.0.tar.gz |
| Windows Binary | lumi_2.16.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | lumi_2.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | lumi_2.16.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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