To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("minfi")
In most cases, you don't need to download the package archive at all.
minfi
Analyze Illumina's 450k methylation arrays
Bioconductor version: 2.14
Tools for analyzing and visualizing Illumina's 450k array data
Author: Kasper Daniel Hansen [cre, aut], Martin Ayree [aut], Rafael A. Irizarry [aut], Andrew E. Jaffe [ctb], Jovana Maksimovic [ctb], E. Andres Houseman [ctb], Jean-Phillipe Fortin [ctb]
Maintainer: Kasper Daniel Hansen <khansen at jhsph.edu>
Citation (from within R,
enter citation("minfi")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("minfi")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("minfi")
| R Script | Minfi Guide | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DNAMethylation, DataImport, Microarray, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.10.2 |
| In Bioconductor since | BioC 2.9 (R-2.14) |
| License | Artistic-2.0 |
| Depends | methods, BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), lattice, GenomicRanges, Biostrings, utils, bumphunter(>= 1.1.9) |
| Imports | IRanges, beanplot, RColorBrewer, nor1mix, siggenes, limma, preprocessCore, illuminaio, matrixStats, mclust, genefilter, nlme, reshape |
| Suggests | IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19, minfiData(>= 0.4.1), quadprog, FlowSorted.Blood.450k(>= 1.0.1), RUnit, digest |
| System Requirements | |
| URL | |
| Depends On Me | ChAMP, CopyNumber450k, CopyNumber450kData, DMRcate, FlowSorted.Blood.450k, FlowSorted.DLPFC.450k, IlluminaHumanMethylation27kmanifest, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, methylumi, minfiData |
| Imports Me | methylumi |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | minfi_1.10.2.tar.gz |
| Windows Binary | minfi_1.10.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | minfi_1.10.2.tgz |
| Mac OS X 10.9 (Mavericks) | minfi_1.10.2.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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