dCLIP is written in Perl for discovering differential binding regions in two CLIP-Seq (HITS-CLIP or PAR-CLIP) experiments. It is appropiate in experiments where the common binding regions that are significantly enriched in both conditions tend to have similar binding strength and when researchers are more interested in the difference in binding strength rather than the binary event of whether binding site is common or not.
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Genome Biol. 2014 Jan 7;15(1):R11. doi: 10.1186/gb-2014-15-1-r11.
dCLIP: a computational approach for comparative CLIP-seq analyses.
Wang T, Xie Y, Xiao G.