Hello Flora,
The QualScore code can be found on our open online repository at:
https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/qualscore/
That being said, we have not updated it in some time, and have heard
reports that it might not be compatible with recent versions of Java. It
is on
Hello Pete,
I think the answer to your first question is it depends on the specifics of
your analysis.
You can pass iProphet files through iProphet again, since it will just use
the PeptideProphet probabilities which are not modified (only reported) by
iProphet. If the iProphet is from a single
