MILLIPEDE is a method that outperforms a leading recent method, centipede, marginally in human but dramatically in yeast (average auROC across 20 TFs increases from 74% to 94%). The sofware is based on logistic regression and thus benefits from supervision, but we show that partially and completely unsupervised variants perform nearly as well.
- R package
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Pac Symp Biocomput. 2013:80-91.
Using DNase digestion data to accurately identify transcription factor binding sites.
Luo K, Hartemink AJ.