bigmelon

"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.

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

Tools to analyze & visualize Illumina Infinium methylation arrays.

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.

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.