HITS-CLIP: Difference between revisions

Revision as of 10:55, 3 August 2014

Revision as of 15:49, 2 December 2014

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== External links ==

* [http://cm.jefferson.edu/CLIPSim-MC/ CLIPSim-MC]: CLIPSim-MC is a tool that uses CLIP-seq data to find [[miRNA]]/MRE pairings using a Monte-Carlo-based approach<ref>{{citation |journal=Scientific Reports |author=Peter M. Clark, Phillipe Loher, Kevin Quann, Jonathan Brody, Eric R. Londin & Isidore Rigoutsos |title=Argonaute CLIP-Seq reveals miRNA targetome diversity across tissue types |volume=4 |issue=5947 |year=2014 |PMID=25103560 |doi=10.1038/srep05947}}</ref>.

* [http://starbase.sysu.edu.cn/ starBase database]: a database for exploring miRNA-mRNA, miRNA-[[lncRNA]], miRNA-[[sncRNA]], miRNA-[[circRNA]], miRNA-[[pseudogene]], protein-[[lncRNA]], '''[[protein-RNA]]''' interactions and [[ceRNA]] networks from '''HITS-CLIP''' ('''[[CLIP-Seq]]''', '''PAR-CLIP''', '''[[iCLIP]]''', '''CLASH''') data, and '''[http://www.targetscan.org TargetScan], PicTar, RNA22, miRanda and PITA''' microRNA target sites.

* [http://www.clipz.unibas.ch/ clipz]: a pipeline to analyze short RNA reads from HITS-CLIP experiments.

* [http://qbrc.swmed.edu/software/ dCLIP]: dCLIP is a Perl program for discovering differential binding regions in two comparative CLIP-Seq (HITS-CLIP, PAR-CLIP or iCLIP) experiments.

==References==