Jointly analyzing MeDIP-seq and MRE-seq data

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methyMnM was developed for jointly analyzing MeDIP-seq and MRE-seq data, which were derived from methylated DNA immunoprecipitation (MeDIP) experiments [Weber et al., 2005] followed by sequencing (MeDIP-seq) and methyl-sensitive restriction enzymes experiments for unmethylated CpGs (MRE-seq). We have implemented the methylMnM method via a set of R functions with the computational intensive parts written in C. The method consists three steps: