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Background correction software tools | DNA methylation microarray data analysis

The Illumina HumanMethylation450 BeadChip is increasingly utilized in epigenome-wide association studies, however, this array-based measurement of DNA methylation is subject to measurement variation. Appropriate data preprocessing to remove…
RnBeads
Desktop

RnBeads

An R package for comprehensive analysis of DNA methylation data obtained with…

An R package for comprehensive analysis of DNA methylation data obtained with any experimental protocol that provides single-CpG resolution, including Infinium 450K microarray and bisulfite…

lumi
Desktop

lumi

Provides class infrastructure and associated methods to construct an Illumina…

Provides class infrastructure and associated methods to construct an Illumina analysis workflow pipeline starting with raw data through functional analysis. Besides supporting the existing algorithms…

minfi
Desktop

minfi

A suite of computational tools that incorporate state-of-the-art statistical…

A suite of computational tools that incorporate state-of-the-art statistical techniques for the analysis of DNAm data. minfi provides methods for preprocessing, quality assessment and detection of…

Methylumi
Desktop

Methylumi

A package that provides classes for holding and manipulating Illumina…

A package that provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices…

wateRmelon
Desktop

wateRmelon

A user-friendly software package compatible with the existing methylumi, minfi…

A user-friendly software package compatible with the existing methylumi, minfi and IMA packages, that allows others to utilize the same normalization methods and data quality tests on 450K data.

LumiWCluster
Desktop

LumiWCluster

Allows to remove the source of biases in Illumina Methylation BeadArray.…

Allows to remove the source of biases in Illumina Methylation BeadArray. LumiWCluster is a weighted model-based clustering based on many positive control samples and enables to measure observation…

ENmix
Desktop

ENmix

Provides a background correction method which uses a mixture of exponential and…

Provides a background correction method which uses a mixture of exponential and truncated normal distributions to flexibly model signal intensity and uses a truncated normal distribution to model…

GenomeStudio
Desktop

GenomeStudio

Visualize and analyze data generated on Illumina array platforms. GenomeStudio…

Visualize and analyze data generated on Illumina array platforms. GenomeStudio supports the primary analysis of microarray data. Performance-optimized tools and a user-friendly graphical interface…

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