HMPL User Manual Shuying Sun ssun5211 yahoo com or s_s355 txstate edu Texas State University Peng Li pxl119 case edu Case Western Reserve University June 18 2015 Contents 1 General Overview and Installation 1 1 General Overview 1 2 Installation 2 Pipeline Walkthrough 2 1 Usage 2 2 Initial Input 2 3 Pre HMPL pl Hemimethylation preprocessing pipeline 2 4 Parse HMPL pl Hemimethylation data parsing pipeline 2 5 Testing HMPL using a small dataset and exampl
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