Files in gmelloni/PrecisionTrialDesigner
A Tool to Analyze and Design NGS Based Custom Gene Panels
.Rbuildignore
.github/.gitignore
.github/workflows/check-bioc.yml
.github/workflows/check-standard.yaml
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/.gitkeep
R/annotateGeneLength.R
R/annotateVariationLength.R
R/cancerPanelClass.R
R/cancerPanelGetters.R
R/cancerPanelShow.R
R/checkDataAvailability.R
R/coocMutEx.R
R/copynumberHelper.R
R/coveragePlot.R
R/coverageStack.R
R/cpFreq.R
R/cpHelper.R
R/dataExtractor.R
R/expressionHelper.R
R/filterFusions.R
R/filterMutations.R
R/getAlterations.R
R/mutationHelper.R
R/panelDesigner.R
R/panelDesignerHelper.R
R/panelOptimizer.R
R/panelOptimizerClassAndMethods.R
R/panelOptimizerClassHelper.R
R/propPowerSampleSize.R
R/reposAppend.R
R/saturationPlot.R
R/showTumorType.R
R/subsetAlterations.R
R/survPowerSampleSize.R
R/survPowerSampleSize1Arm.R
R/tumWeightsFreqsHelper.R
R/utilitiesFunctions.R
README.md
data/.gitkeep
data/cpDesign.RData
data/cpObj.RData
data/cpObj2.RData
data/panelexample.RData
inst/.gitkeep
inst/CITATION
inst/extdata/CancerPanel_input_template.csv
inst/extdata/TCGAtranslocation.rds
inst/extdata/TCGAtranslocationSamples.rds
inst/extdata/cancerpanel_format.csv
inst/extdata/sharp_init_dataset.csv
man/.gitkeep
man/CancerPanel-class.Rd
man/PrecisionTrialDrawer-package.Rd
man/appendRepo.Rd
man/coocMutexPlot.Rd
man/coveragePlot.Rd
man/coverageStackPlot.Rd
man/cpArguments.Rd
man/cpData.Rd
man/cpDataSubset.Rd
man/cpDesign.Rd
man/cpFreq.Rd
man/cpObj.Rd
man/cpObj2.Rd
man/dataExtractor.Rd
man/filterFusions.Rd
man/filterMutations.Rd
man/getAlterations.Rd
man/newCancerPanel.Rd
man/panelDesigner.Rd
man/panelOptimizer.Rd
man/panelexample.Rd
man/propPowerSampleSize.Rd
man/saturationPlot.Rd
man/showCancerStudy.Rd
man/showTumorType.Rd
man/subsetAlterations.Rd
man/survPowerSampleSize.Rd
man/survPowerSampleSize1Arm.Rd
vignettes/.gitkeep
vignettes/PrecisionTrialDrawer.Rmd
