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depristo 41fee2d75e Publication tranches report is now the default output 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3967 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-07 13:58:59 +00:00
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VariantRecalibratorReport Default max variants is now 5000 2010-08-07 13:58:32 +00:00
VariantReport A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object. 2010-07-19 12:38:26 +00:00
analyzeConcordance Using bitmap() instead of png() since the former doesn't rely on X11. 2010-02-23 05:31:51 +00:00
Data.Processing.Report.r This replaces tearsheet.r, neatens up graphics, and allows the script to be used in R's interactive environment 2010-06-24 01:02:58 +00:00
PlotDepthOfCoverage.R Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics 2010-03-29 13:32:00 +00:00
generateBySamplePlot.R R script for graphing depth of coverage by sample name, and generating a loess curve for each sample's data. 2009-12-10 21:58:01 +00:00
gsacommons.R A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object. 2010-07-19 12:38:26 +00:00
plot_Annotations_BinnedTruthMetrics.R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
plot_ClusterReport.R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
plot_OptimizationCurve.R Publication tranches report is now the default output 2010-08-07 13:58:59 +00:00
plot_residualError_OtherCovariate.R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
plot_residualError_QualityScoreCovariate.R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
plot_variantROCCurve.R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
plotting_library.R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
tearsheet.r This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data 2010-06-18 21:36:29 +00:00
titvFPEst.R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
whole_exome_bait_selection.R 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. 2009-09-22 18:10:14 +00:00