Difference between revisions of "DCLIP"
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|sw summary=dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments. | |sw summary=dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments. | ||
|bio domain=CLIP-Seq, HITS-CLIP, PAR-CLIP, iCLIP | |bio domain=CLIP-Seq, HITS-CLIP, PAR-CLIP, iCLIP | ||
| − | |bio method= | + | |bio method=Sequence alignment analysis, |
|bio tech=NGS | |bio tech=NGS | ||
| + | |created by=Tao Wang | ||
| + | |created at=UT Southwestern Medical Center | ||
| + | |maintained=Yes | ||
| + | |email address=tao.wang@utsouthwestern.edu | ||
| + | |input format=SAM, | ||
| + | |output format=BED, BEDGRAPH, .txt, | ||
| + | |language=Perl, C, | ||
| + | |library=PDL, PDL::Stats | ||
| + | |os=UNIX, Unix-like, | ||
}} | }} | ||
== Description == | == Description == | ||
<!-- Describe the application in the space below --> | <!-- Describe the application in the space below --> | ||
| − | + | 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/. | |
Latest revision as of 12:44, 3 November 2015
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Application data |
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| Created by | Tao Wang |
|---|---|
| Biological application domain(s) | CLIP-Seq, HITS-CLIP, PAR-CLIP, iCLIP |
| Principal bioinformatics method(s) | Sequence alignment analysis |
| Technology | NGS |
| Created at | UT Southwestern Medical Center |
| Maintained? | Yes |
| Input format(s) | SAM |
| Output format(s) | BED, BEDGRAPH, .txt |
| Programming language(s) | Perl, C |
| Software libraries | PDL, PDL::Stats |
| Operating system(s) | UNIX, Unix-like |
| Contact: | tao.wang@utsouthwestern.edu |
Summary: dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.
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Description
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/.
Links
References
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