rpoplin
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46f3d3e39b
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Added comments to AnalyzeCovariates and R scripts. R script prevents residuals from going off the edge of the plot. Added skeleton code to the recalibration walkers showing how we plan to handle SOLID reference inserting behavior.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2233 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 23:15:52 +00:00 |
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rpoplin
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9c597309d3
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Changed the sizes of the dots and bars on the plots generated by the R script which is called from AnalyzeCovariates.java
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2223 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 19:47:48 +00:00 |
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rpoplin
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67179e2412
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Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2215 348d0f76-0448-11de-a6fe-93d51630548a
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2009-12-02 16:47:35 +00:00 |
andrewk
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575da25fde
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R script for selecting a variety of baits (using %GC content and normalized coverage) for Nanostring assessment from those used in the Agilent whole exome hybrid selection design.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1683 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-22 18:10:14 +00:00 |
hanna
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8f9dd03e87
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Get rid of unnecessary files for generating recalibration data.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1626 348d0f76-0448-11de-a6fe-93d51630548a
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2009-09-15 15:53:06 +00:00 |
depristo
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f5b00c20d0
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Updated python files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1182 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 14:15:39 +00:00 |
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depristo
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5289230eb8
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Version 0.2.1 (released) of the TableRecalibrator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 22:50:55 +00:00 |
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depristo
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9e26550b0d
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Apprach v2. Added python analysis script, so java no longer must be used to analyses quality score data. About to refactor out lots of unneeded code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1063 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-20 16:00:23 +00:00 |
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andrewk
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080af519cb
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Added R script and uncommented a line in recal_qual.py
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@886 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-03 03:15:45 +00:00 |