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DataProcessingReport
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Takes a list of BAMs, looks up the read group information in the sequencing platform's SQUID database, and computes the tearsheet stats. Also takes the VariantEval output (R format) and outputs the variant stats and some plots for the tearsheet. This script requires the gsalib library to be in the R library path (add the line '.libPaths('/path/to/Sting/R/')' to your ~/.Rprofile).
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2010-10-27 19:06:22 +00:00 |
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VariantRecalibratorReport
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Removed unused dependency (it was causing a problem by looking for an X11 connection that didn't necessarily exist).
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2010-09-09 19:56:00 +00:00 |
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VariantReport
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Fix to handle situation where there are no filtered variants.
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2010-10-04 18:34:01 +00:00 |
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analyzeConcordance
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Using bitmap() instead of png() since the former doesn't rely on X11.
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2010-02-23 05:31:51 +00:00 |
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src/gsalib
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* Added an R package, "gsalib", providing a place to store common, useful, documented R methods. To use this module, you must follow three steps:
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2010-10-04 00:27:59 +00:00 |
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ADPRpages.R
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Ready for integration with queue script
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2010-09-24 19:46:01 +00:00 |
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Data.Processing.Report.r
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updated version of the DPR. Now produces part of the tearsheet as well as good depth of coverage figures
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2010-09-01 15:38:58 +00:00 |
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GATKRunReport.R
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Better reporting -- figured out how to drop unused levels in subset
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2010-10-06 14:31:51 +00:00 |
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PlotDepthOfCoverage.R
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Moved CoverageStatistics to core. This will be (soon) renamed DepthOfCoverage; so please use CoverageStatistics
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2010-03-29 13:32:00 +00:00 |
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generateBySamplePlot.R
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R script for graphing depth of coverage by sample name, and generating a loess curve for each sample's data.
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2009-12-10 21:58:01 +00:00 |
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plot_Annotations_BinnedTruthMetrics.R
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Can run R scripts on the command line
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2010-07-09 00:13:18 +00:00 |
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plot_ClusterReport.R
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Can run R scripts on the command line
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2010-07-09 00:13:18 +00:00 |
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plot_OptimizationCurve.R
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now plots tranches separately from optimizer
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2010-08-10 12:02:52 +00:00 |
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plot_Tranches.R
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Nicer plotting routine for tranches. Add a third arg to suppress the legend.
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2010-08-17 19:20:58 +00:00 |
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plot_residualError_OtherCovariate.R
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Can run R scripts on the command line
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2010-07-09 00:13:18 +00:00 |
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plot_residualError_QualityScoreCovariate.R
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Can run R scripts on the command line
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2010-07-09 00:13:18 +00:00 |
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plot_variantROCCurve.R
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Can run R scripts on the command line
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2010-07-09 00:13:18 +00:00 |
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plotting_library.R
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Can run R scripts on the command line
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2010-07-09 00:13:18 +00:00 |
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tearsheet.r
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This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data
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2010-06-18 21:36:29 +00:00 |
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titvFPEst.R
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Suppl. tools for working with and displaying GATK run reports
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2010-08-31 20:32:22 +00:00 |
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whole_exome_bait_selection.R
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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.
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2009-09-22 18:10:14 +00:00 |
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