To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ENmix")
In most cases, you don't need to download the package archive at all.
ENmix
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Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip
Bioconductor version: Release (3.1)
Illumina HumanMethylation450 BeadChip has a complex array design, and the measurement is subject to experimental variations. The ENmix R package provides tools for low level data preprocessing to improve data quality. It incorporates a model based background correction method ENmix, and provides functions for inter-array quantile normalization, data quality checking, exploration of multimodally distributed CpGs and source of data variation. To support large scale data analysis, the package also provides multi-processor parallel computing wrappers for some commonly used data preprocessing methods, such as BMIQ probe design type bias correction and ComBat batch effect correction.
Author: Zongli Xu [cre, aut], Liang Niu [aut], Leping Li [ctb], Jack Taylor [ctb]
Maintainer: Zongli Xu <xuz at niehs.nih.gov>
Citation (from within R,
enter citation("ENmix")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("ENmix")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ENmix")
| R Script | ENmix User's Guide | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | BatchEffect, DNAMethylation, DataImport, MethylationArray, Microarray, Normalization, OneChannel, Preprocessing, QualityControl, Software, TwoChannel |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (< 6 months) |
| License | Artistic-2.0 |
| Depends | minfi, parallel, doParallel, Biobase(>= 2.17.8), foreach |
| Imports | MASS, preprocessCore, wateRmelon, sva, geneplotter |
| LinkingTo | |
| Suggests | minfiData(>= 0.4.1), RPMM, RUnit, BiocGenerics |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | ENmix_1.0.0.tar.gz |
| Windows Binary | ENmix_1.0.0.zip |
| Mac OS X 10.6 (Snow Leopard) | ENmix_1.0.0.tgz |
| Mac OS X 10.9 (Mavericks) | ENmix_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/ENmix/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/ENmix/ |
| Package Downloads Report | Download Stats |
Documentation »
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