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Short description:
Please summarise the application in a few sentences. Avoid links here. dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.
Software version:
Biological application domain(s) (Phylogenetics, Genomics, ...):
CLIP-Seq, HITS-CLIP, PAR-CLIP, iCLIP
Principal bioinformatics method(s) (Assembly, Mapping, ...):
Sequence alignment analysis,
Technology (Sanger, Illumina, 454, SOLiD, Ion Torrent, ...):
NGS
Interface (Command line, Web UI, Desktop GUI, SOAP WS, HTTP WS, API, QL):
Resource type (Command-line tool, Web application, Desktop application, Script, Suite, Workbench, Database portal, Workflow, Plug-in, Library, Web API, Web service, SPARQL endpoint):
UT Southwestern Medical Center
== Description == <!-- 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/. <!-- -->
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