To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://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: 3.2
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:
## try http:// if https:// URLs are not supported
source("https://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")
| Analyze Illumina Infinium methylation microarray data | ||
| Evaluation of VST algorithm in lumi package | ||
| Resolve the inconsistency of Illumina identifiers through nuID | ||
| Using lumi A package processing Illumina Microarray | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, Microarray, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 2.22.1 |
| In Bioconductor since | BioC 2.0 (R-2.5) (9 years) |
| 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 |
| LinkingTo | |
| Suggests | beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | arrayMvout, ffpeExampleData, iCheck, lumiBarnes, lumiHumanIDMapping, lumiMouseIDMapping, lumiRatIDMapping, MAQCsubset, MAQCsubsetILM, mvoutData, wateRmelon |
| Imports Me | ffpe, methyAnalysis, MineICA |
| Suggests Me | beadarray, blima, methylumi, tigre |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | lumi_2.22.1.tar.gz |
| Windows Binary | lumi_2.22.1.zip |
| Mac OS X 10.6 (Snow Leopard) | lumi_2.22.0.tgz |
| Mac OS X 10.9 (Mavericks) | lumi_2.22.1.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/lumi/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/lumi/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
