dCLIP: A computational approach for comparative CLIP-seq analyses

Research output: Contribution to journalArticlepeer-review

39 Scopus citations


Although comparison of RNA-protein interaction profiles across different conditions has become increasingly important to understanding the function of RNA-binding proteins (RBPs), few computational approaches have been developed for quantitative comparison of CLIP-seq datasets. Here, we present an easy-to-use command line tool, dCLIP, for quantitative CLIP-seq comparative analysis. The two-stage method implemented in dCLIP, including a modified MA normalization method and a hidden Markov model, is shown to be able to effectively identify differential binding regions of RBPs in four CLIP-seq datasets, generated by HITS-CLIP, iCLIP and PAR-CLIP protocols. dCLIP is freely available at http://qbrc.swmed.edu/software/.

Original languageEnglish (US)
Article numberR11
JournalGenome biology
Issue number1
StatePublished - 2014

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology


Dive into the research topics of 'dCLIP: A computational approach for comparative CLIP-seq analyses'. Together they form a unique fingerprint.

Cite this