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CLIIQ is a computational method for simultaneous identification and quantification of expressed isoforms from multiple samples in a population. Given the RNA-seq mapping results and gene annotation, CLIIQ reports the list of expressed isoforms in the sample(s) by solving the ILP (Integer Linear Program) problems.
Before the wiki page is back, please check http://www.sfu.ca/~yenyil/cliiq.html for instructions for installation and execution of CLIIQ.
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