PolyaPeak is an R package for ranking ChIP-seq peaks with shape information. polyaPeak uses a Bayesian hierarchical model to incorporate the peak shapes in the ranking. The shapes are described by a mixture of multivariate Polya distributions. Real data analyses show that polyaPeak outperforms several popular peak calling software including MACS, CisGenome and PICS.
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PLoS One. 2014 Mar 7;9(3):e89694. doi: 10.1371/journal.pone.0089694. eCollection 2014.
PolyaPeak: detecting transcription factor binding sites from ChIP-seq using peak shape information.
Wu H1, Ji H