RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.

Remarkably, the top 5000 peaks from RIPSeeker, MACS and PARalyzer on PUM2 PAR-CLIP data are enriched for the exact PUM2 published motif in ( 35 ) as the top prediction by DREME with highly significant E-values (1e-60, 3.7e-201 and 3.3e-161 for RIPSeeker, MACS and PARalyzer, respectively) ( Supplementary Figures S12–S14 ), whereas the top 5000 peaks from HPeak have much less significant E-values (1e-6) ( Supplementary Figure S15 ).

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