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Normalization software tools | DNA methylation microarray data analysis

Normalisation concerns the removal of sources of experimental artefacts, random noise and technical and systematic variation caused by microarray technology, which, if left unaddressed, has the potential to mask true biological differences (Sun et…
FastDMA
Desktop

FastDMA

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which…

A software analyzing Illumina Infinium HumanMethylation450 BeadChip data, which is featured as multiple core parallel computing.

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…

SWAN
Desktop

SWAN Subset-quantile Within Array Normalization

A within array normalization method that substantially reduces the technical…

A within array normalization method that substantially reduces the technical variability between the probe types whilst maintaining the important biological differences. The SWAN method makes the…

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…

missMethyl
Desktop

missMethyl

Performs normalisation, removal of unwanted variation in differential…

Performs normalisation, removal of unwanted variation in differential methylation analysis, differential variability testing and gene set analysis for the 450K array. The functions have been written…

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.

G T A T C G C T A
quantro
Desktop

quantro

Provides a data-driven solution to test the assumptions of global normalization…

Provides a data-driven solution to test the assumptions of global normalization methods. Group level information about each sample (such as tumor/normal status) must be provided because the test…

BMIQ
Desktop

BMIQ

Beta Mixture Quantile Method for normalisation of Illumina Infinium 450k data.

Beta Mixture Quantile Method for normalisation of Illumina Infinium 450k data.

funtooNorm
Desktop

funtooNorm

An R package for normalization of data from the Illumina Infinium Human…

An R package for normalization of data from the Illumina Infinium Human Methylation450 BeadChip (Illumina 450 K) built on the concepts in the recently published funNorm method, and introducing…

Meffil
Desktop

Meffil

Proceeds quality control, normalizes and performs epigenome-wide association…

Proceeds quality control, normalizes and performs epigenome-wide association studies (EWAS). Meffil permits to minimize computational memory requirements to 5% of that required by other R packages…

ADMIRE
Desktop
Web

ADMIRE Analysis of DNA methylation in genomic regions

Allows to analyze and visualize differential methylation in genomic regions.…

Allows to analyze and visualize differential methylation in genomic regions. ADMIRE is a semi-automatic pipeline that features five different normalization methods and performs two one-sided…

ARRmNormalizati…
Desktop

ARRmNormalization

Performs the Adaptive Robust Regression method (ARRm) for the normalization of…

Performs the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.

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