ChIPDiff provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2). An HMM is employed in ChIPDiff to infer the states of histone modification changes
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An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data.
Xu H, Wei CL, Lin F, Sung WK.
Bioinformatics. 2008 Oct 15;24(20):2344-9