Differntial peak analysis for MethylCap-seq
I have 8 aligned(sam) for MethylCap-seq data: 2 condition and their inputs, two 2 replicate each. Could someone direct me to a standard R documentation to process such data? I am interested in obtaining the differential region between two conditions. I have gone though R package like methylaction and qsea but I am not sure how to incorporate the information related to inputs and replicates.
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