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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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Fixed a bug where the script looked for the wrong column name. Also, all results are now returned in a single plot.
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2010-09-06 14:19:57 +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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ADPRpages.R
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This is an updated version of the automated data processing report. Each page in the report is a stand alone function, which are linked together with a function which pulls all appropriate data (assuming a standard naming convention) and generates the pdf. This script still need to respond appropriately when it doesn't find the data it needs, database access, and a way of getting some information from sequencing for the tearsheet.
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2010-09-23 18:08:16 +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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GATKReport.R
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A data structure that allows data to be collected over the course of a walker's computation, then have that data written to a PrintStream such that it's human-readable, AWK-able, and R-friendly (given that you load it using the GATKReport loader module).
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2010-08-29 05:39:24 +00:00 |
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GATKRunReport.R
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improvements to the report code
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2010-09-15 00:45:13 +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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gsacommons.R
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Fixed a bug where the script looked for the wrong column name. Also, all results are now returned in a single plot.
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2010-09-06 14:19:57 +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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