Ernst et al.

Focusing on cell-type-specific patterns of promoters and enhancers, Ernst et al. define multicell activity profiles for chromatin state, gene expression, regulatory motif enrichment and regulator expression. They use correlations between these profiles to link enhancers to putative target genes, and predict the cell-type-specific activators and repressors that modulate them.

Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., ... & Bernstein, B. E. (2011). Mapping and analysis of chromatin state dynamics in nine human cell types. Nature, 473(7345), 43-49.

As there was no source code available for Ernst et al., we integrated the predicted loops from these published papers, and no upload options for the algorithm.

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Ernst et al. test case:
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