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Old 09-11-2014, 04:47 PM   #4
Gordon Smyth
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Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91
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We have are most of the way through a major overall and improvement of edgeR's spliceVariants() function. We haven't made the new version public yet -- will do when it is stable.

In the meantime, you might try the diffSplice() function in the limma package, which is very fast and controls the false discovery rate conservatively.
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