wateRmelon

Tools to analyze & visualize Illumina Infinium methylation arrays.

Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.

"Methylation-Aware Genotype Association in R" (MAGAR) computes methQTL from DNA methylation and genotyping data from matched samples. MAGAR uses a linear modeling stragety to call CpGs/SNPs that are methQTLs. MAGAR accounts for the local correlation structure of CpGs.

Tools for quanlity control, analysis and visulization of Illumina DNA methylation array data.

The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.