msgbsR

"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.

Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.

Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.

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