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Quality control software tools | DNA methylation microarray data analysis

To monitor the quality of Illumina 450k data, the array contains 10 different types of quality control probes to evaluate the performance of both samples and specific steps in the process. The most frequently used type of quality control probe is…
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…

CpGassoc
Desktop

CpGassoc

An R package that can efficiently perform the statistical analysis needed for…

An R package that can efficiently perform the statistical analysis needed for increasingly large methylation datasets. CpGassoc can perform standard analyses of large datasets very quickly with no…

MethLAB
Desktop

MethLAB

Performs analyses of array-based DNA methylation data. MethLAB is a graphical…

Performs analyses of array-based DNA methylation data. MethLAB is a graphical user interface (GUI) package. For each cytosine–phosphate–guanine (CpG) site, the software models methylation as a…

MethylAid
Desktop

MethylAid

Provides complete insight in the quality of each sample in a large-scale EWAS…

Provides complete insight in the quality of each sample in a large-scale EWAS and gives the user full control on the selection of bad-quality samples that should be excluded from downstream analyses.…

NIMBL
Desktop

NIMBL Numerical Identification of Methylation Biomarker Lists

MATLAB code to quality control and prioritize differentially methylated markers…

MATLAB code to quality control and prioritize differentially methylated markers from illumina infinium arrays.

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…

charm
Desktop

charm

Implements analysis tools for DNA methylation data generated using Nimblegen…

Implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage…

shinyMethyl
Desktop

shinyMethyl

A Bioconductor package for interactive quality control of DNA methylation data…

A Bioconductor package for interactive quality control of DNA methylation data from Illumina 450k arrays. The package summarizes 450k experiments into small exportable R objects from which an…

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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