| .. |
|
DataProcessingReport
|
This updates the script to produce a more tearsheet-like output for sample set statistics. Formatting will be updated for aesthetic improvements. There are also several database options that currently pull out misleading information because of changes in sequencing methodology that will be updated to show correct information. Eventually, plot formatting will be updated as well and additional informative plots will be added.
|
2011-01-13 15:59:06 +00:00 |
|
VariantRecalibratorReport
|
Removed unused dependency (it was causing a problem by looking for an X11 connection that didn't necessarily exist).
|
2010-09-09 19:56:00 +00:00 |
|
VariantReport
|
Changed VCF subsetting procedure.
|
2010-11-28 00:46:29 +00:00 |
|
analyzeConcordance
|
Using bitmap() instead of png() since the former doesn't rely on X11.
|
2010-02-23 05:31:51 +00:00 |
|
phasing
|
Vectorize() pDirectlyPhaseHetPairAtDistanceUsingDepth; deal with minor precision issues
|
2010-12-21 17:18:26 +00:00 |
|
src/gsalib
|
Namespace changes to avoid conflicts with other packages.
|
2011-01-06 15:33:26 +00:00 |
|
ADPRpages.R
|
Ready for integration with queue script
|
2010-09-24 19:46:01 +00:00 |
|
Data.Processing.Report.r
|
updated version of the DPR. Now produces part of the tearsheet as well as good depth of coverage figures
|
2010-09-01 15:38:58 +00:00 |
|
GATKRunReport.R
|
Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers
|
2010-12-15 14:56:12 +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 |
|
analyzeRodProfile.R
|
Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString
|
2010-11-24 14:59:16 +00:00 |
|
assessCallingPerformance.R
|
1)
|
2010-11-30 21:08:25 +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 |
|
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_GATK_performance_log.R
|
Now uses PNGs and a very high downsampling value to more clearly display the information
|
2011-01-03 13:57:51 +00:00 |
|
plot_OptimizationCurve.R
|
now plots tranches separately from optimizer
|
2010-08-10 12:02:52 +00:00 |
|
plot_Tranches.R
|
Default R script now plots sensitivity/specificity curve
|
2010-12-13 16:55:11 +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 |
|
privateMutations.R
|
FASTQ directory is gone
|
2011-01-13 15:16:06 +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
|
Better cumhist function
|
2011-01-02 23:32:20 +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 |
6b5474a00a