DeepSEA is a deep learning-based algorithmic framework for predicting the chromatin effects of sequence alterations with single nucleotide sensitivity. DeepSEA can accurately predict the epigenetic state of a sequence, including transcription factors binding, DNase I sensitivities and histone marks in multiple cell types, and further utilize this capability to predict the chromatin effects of sequence variants and prioritize regulatory variants.
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Zhou J, Troyanskaya OG.
Predicting effects of noncoding variants with deep learning-based sequence model.
Nat Methods. 2015 Oct;12(10):931-4. doi: 10.1038/nmeth.3547. Epub 2015 Aug 24. PMID: 26301843; PMCID: PMC4768299.