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Merge pull request #53 from vyepez88/patch-1
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Update README.md
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ischeller authored Mar 30, 2023
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Expand Up @@ -15,14 +15,15 @@ Please cite our method paper if you use it in a publication:
## What's new

FRASER 2.0, an improved version of FRASER that uses the Intron Jaccard Index as
its splice metric instead of FRASER's previous three metrics along with some other
parameter optimizations of pseudocount, filtering settings and default delta cutoff,
is now available and used by default (version 1.99.0 and above).
FRASER 2.0, an improved version of FRASER, is now available and used by default (version 1.99.0 and above).
FRASER 2.0 uses the Intron Jaccard Index as its splice metric instead of FRASER's
previous three metrics along with some other parameter optimizations of pseudocount,
filtering settings and default delta cutoff.

To change the splice metric, set `fitMetrics(fds)` to one or more of the metrics
specified in `FRASER::psiTypes`. For FRASER 2.0 and the Intron Jaccard Index, the
new default delta cutoff is 0.1 instead of the previous value of 0.3. When using
the 3 previous metrics, the delta cutoff should therefore be manually set to 0.3
the 3 previous metrics, the delta cutoff should be set manually to 0.3
during results extraction, e.g. `results(fds, deltaPsiCutoff=0.3,...)`.

The manuscript describing these changes in more detail will be available soon.
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