Files in CRUKMI-ComputationalBiology/twoddpcr

Classify 2-d Droplet Digital PCR (ddPCR) data and quantify the number of starting molecules

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 inst/rmd/report-html.Rmd 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