This repository holds some of my scripts and findings for comparing differential chip-seq methods (paper recently submitted).
- DIME -- Some matlab code that I ported over to R. Method took too long to run so I gave up
- MAnorm -- Rewrote most of this program so it runs faster, requires replicates, and uses edgeR
- edgeR-DiffBind-DBChIP -- I go over how to use these three methods and document some differences between them