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Probe filtering software tools | DNA methylation microarray data analysis

Several reasons can explain the generation of artifactual data. For example, the scanner can encounter some difficulties to correctly read the signal for some probes owing to their low intensities or to some spatial artifacts on the array. This…
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…

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.

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…

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