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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("methylumi")
In most cases, you don't need to download the package archive at all.
methylumi
Handle Illumina methylation data
Bioconductor version: 2.14
This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.
Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Maintainer: Sean Davis <sdavis2 at mail.nih.gov>
Citation (from within R,
enter citation("methylumi")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("methylumi")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("methylumi")
| R Script | An Introduction to the methylumi package | |
| R Script | Working with Illumina 450k Arrays using methylumi | |
| Reference Manual | ||
| Text | README |
Details
| biocViews | CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 2.10.0 |
| In Bioconductor since | BioC 2.5 (R-2.10) |
| License | GPL-2 |
| Depends | Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, minfi |
| Imports | Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, BiocGenerics, illuminaio |
| Suggests | lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db(>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, GenomicRanges, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, FDb.InfiniumMethylation.hg19, TCGAMethylation450k, TxDb.Hsapiens.UCSC.hg19.knownGene, IlluminaHumanMethylation450kanno.ilmn12.hg19, Homo.sapiens, knitr |
| System Requirements | |
| URL | |
| Depends On Me | wateRmelon |
| Imports Me | asmn, ffpe, lumi, methyAnalysis |
| Suggests Me | IlluminaHumanMethylation450k.db |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | methylumi_2.10.0.tar.gz |
| Windows Binary | methylumi_2.10.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | methylumi_2.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | methylumi_2.10.0.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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