Files in gerstung-lab/BarrettsProgressionRisk
Prognositc adenocarcinoma risk prediction for Barrett's Esophagus
.Rbuildignore
DESCRIPTION
NAMESPACE
R/plot_utilities.R
R/process_swgs.R
R/risk_prediction.R
R/sysdata.rda
R/utility_functions.R
README.md
data/ExampleQDNAseqData.rda
example/endoscopy.xlsx
example/qdnaseq.output.binSize50.fittedReadCounts.txt
example/qdnaseq.output.binSize50.rawReadCounts.txt
inst/bin/generate_report.R
inst/extdata/example/endoscopy.xlsx
inst/extdata/example/qdnaseq.output.binSize50.fittedReadCounts.txt
inst/extdata/example/qdnaseq.output.binSize50.rawReadCounts.txt
inst/extdata/hg18_info.txt
inst/extdata/hg19_info.txt
inst/extdata/hg38_info.txt
inst/extdata/qDNAseq_blacklistedRegions.txt
inst/rmd/RiskReport.Rmd
inst/rmd/img/Human_body_silhouette-BLUE.png
inst/rmd/img/Human_body_silhouette-GREY.png
inst/rmd/img/Human_body_silhouette-RED.png
inst/rmd/img/Human_body_silhouette-YELLOW.png
inst/rmd/img/Human_body_silhouette.svg
man/absoluteRiskCI.Rd
man/adjustRisk.Rd
man/copyNumberMountainPlot.Rd
man/dot-plotSegmentedGenome.Rd
man/loadSampleInformation.Rd
man/patientEndoscopyPlot.Rd
man/patientRiskTilesPlot.Rd
man/plotCorrectedCoverage.Rd
man/plotSegmentData.Rd
man/predictRiskFromSegments.Rd
man/predictions.Rd
man/relativeRiskCI.Rd
man/riskColors.Rd
man/runQDNAseq.Rd
man/rx.Rd
man/rxRules.Rd
man/sampleNames.Rd
man/sampleResiduals.Rd
man/scoreCX.Rd
man/segmentRawData.Rd
man/segmentedValues.Rd
man/showModelPredictions.Rd
man/showPredictionCalibration.Rd
man/subtractArms.Rd
man/tileSegments.Rd
tests/testthat.R
tests/testthat/test_process_Data.R
