Files in CRUKMI-ComputationalBiology/twoddpcr
Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/KRAScounts.R
R/KRASdata.R
R/clusterCentres.R
R/clusterStats.R
R/ddpcrPlate.R
R/ddpcrWell.R
R/dropletPlot.R
R/exportTable.R
R/facetPlot.R
R/flatPlot.R
R/ggplot.R
R/global.R
R/gridClassify.R
R/heatPlot.R
R/isTwoDimDataFrame.R
R/kmeansClassify.R
R/knnClassify.R
R/mahRain.R
R/normalise.R
R/numDroplets.R
R/parseCounts.R
R/plateSummary.R
R/readCSVDataFrame.R
R/relabelClasses.R
R/removeDropletClasses.R
R/sdRain.R
R/shinyVisApp.R
R/shinyVisGlobal.R
R/shinyVisServer.R
R/shinyVisUI.R
R/summaries.R
R/themes.R
R/twoddpcr.R
R/wellNameSort.R
README.md
data/KRAScounts.rda
data/KRAScountsQS.rda
data/KRAScountsWellCol.rda
data/KRASdata.rda
inst/CITATION
inst/NEWS
inst/extdata/amplitudes/sample_B03_Amplitude.csv
inst/extdata/more-amplitudes/sample_A04_Amplitude.csv
inst/extdata/more-amplitudes/sample_A05_Amplitude.csv
inst/extdata/more-amplitudes/sample_B06_Amplitude.csv
inst/rmd/report-html.Rmd
inst/testdata/sample_A04_Amplitude.csv
inst/testdata/sample_A05_Amplitude.csv
inst/testdata/sample_B03_Amplitude.csv
inst/testdata/sample_B06_Amplitude.csv
man/KRAScounts.Rd
man/KRASdata.Rd
man/amplitudes.Rd
man/basicsSummary.Rd
man/castSummary.Rd
man/classCov.Rd
man/classMeans.Rd
man/classStats.Rd
man/clusterCentres.Rd
man/copiesSummary.Rd
man/ddpcr.Rd
man/ddpcrPlate-class.Rd
man/ddpcrWell-class.Rd
man/ddpcrWell-methods.Rd
man/dot-classifyDfOnChannel.Rd
man/dot-classifyOnChannel.Rd
man/dot-classwiseMahalanobisRain.Rd
man/dot-cov.Rd
man/dot-dependentCols.Rd
man/dot-essentialDependentCols.Rd
man/dot-extractWellNames.Rd
man/dot-getAllSummary.Rd
man/dot-getChannelCentres.Rd
man/dot-getClassificationData.Rd
man/dot-getMutCopies.Rd
man/dot-getWellNames.Rd
man/dot-getWtCopies.Rd
man/dot-isTwoDimDataFrame.Rd
man/dot-isWideForm.Rd
man/dot-mahDist.Rd
man/dot-matrixInverse.Rd
man/dot-numberOfWells.Rd
man/dot-renormaliseByChannel.Rd
man/dot-renormaliseWell.Rd
man/dot-roundIt.Rd
man/dot-slice.Rd
man/dot-totalCopies.Rd
man/drawBlank.Rd
man/dropletPlot.Rd
man/elementType-SimpleList-method.Rd
man/exportTable.Rd
man/extractPlateName.Rd
man/extractWellNames.Rd
man/facetPlot.Rd
man/flatPlot.Rd
man/fullCopiesSummary.Rd
man/fullCountsSummary.Rd
man/getCutOff.Rd
man/ggplot.well.Rd
man/gridClassify.Rd
man/heatPlot.Rd
man/kmeansClassify.Rd
man/knnClassify.Rd
man/mahalanobisRain.Rd
man/mutantCopiesSummary.Rd
man/numDroplets.Rd
man/numericInputRow.Rd
man/parseClusterCounts.Rd
man/plateClassification.Rd
man/plateClassificationMethod.Rd
man/plateSummary.Rd
man/positiveCounts.Rd
man/readCSVDataFrame.Rd
man/relabelClasses.Rd
man/removeDropletClasses.Rd
man/renormalisePlate.Rd
man/sdRain.Rd
man/setChannelNames.Rd
man/setDropletVolume.Rd
man/shinyVis.Rd
man/shinyVisApp.Rd
man/shinyVisServer.Rd
man/shinyVisUI.Rd
man/sortDataFrame.Rd
man/sortWells.Rd
man/textInputRow.Rd
man/thresholdClassify.Rd
man/twoddpcr-package.Rd
man/wellClassification.Rd
man/wellClassificationMethod.Rd
man/whiteTheme.Rd
man/wildTypeCopiesSummary.Rd
tests/testthat.R
tests/testthat/testClasses.R
tests/testthat/testClassification.R
tests/testthat/testClusterStats.R
tests/testthat/testDroplets.R
tests/testthat/testFacet.R
tests/testthat/testGrid.R
tests/testthat/testKmeans.R
tests/testthat/testKnn.R
tests/testthat/testMahRain.R
tests/testthat/testRemoveDropletClasses.R
tests/testthat/testSdRain.R
tests/testthat/testSummary.R
vignettes/twoddpcr.Rmd
