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Batch effect correction software tools | DNA methylation microarray data analysis

Large studies can be particularly susceptible to the effects of unwanted technical variation due to the large number of samples requiring processing. For example, processing may have to occur over several days or be performed by multiple researchers…
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…

ChAMP
Desktop

ChAMP

Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated…

Allows Illumina HumanMethylation BeadChip analysis. ChAMP is an integrated analysis pipeline including functions for (i) filtering low quality probes, adjustment for Infinium I and Infinium II probe…

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…

RUVm
Desktop

RUVm

A versatile method that effectively accounts for unwanted variation in DM…

A versatile method that effectively accounts for unwanted variation in DM analyses of 450k data across a wide variety of studies. RUVm performs particularly well in situations where the sources of…

BEclear
Desktop

BEclear

Identifies portions of the data that deviate statistically significant from the…

Identifies portions of the data that deviate statistically significant from the remaining data and replaces these portions by typical values reconstructed from neighboring data entries based on…

ComBat
Desktop

ComBat

Adjusting batch effects in microarray expression data using Empirical Bayes…

Adjusting batch effects in microarray expression data using Empirical Bayes methods. The modified ComBat (M-Combat) is designed specifically in the context of meta-analysis and batch effect…

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