Files in grandR

Comprehensive Analysis of Nucleotide Conversion Sequencing Data

NEWS.md README.md R/readsimulator.R R/shiny.R R/load.R R/diffexp.R R/plot.R R/diagnostics.R R/seurat.R R/paramest.R R/modeling.R R/utils.R R/dropout.R R/processing.R R/grandR.R inst/doc/getting-started.R inst/doc/getting-started.Rmd vignettes/getting-started.Rmd man/ApplyContrasts.Rd man/data.apply.Rd man/CreatePseudobulkTable.Rd man/GetContrasts.Rd man/PlotHeatmap.Rd man/PlotScatter.Rd man/PlotModelCompareLL.Rd man/DESeq2BIC.Rd man/FilterGenes.Rd man/Coldata.Rd man/PlotGeneTotalVsNtr.Rd man/FitKineticsPulseR.Rd man/PlotAnalyses.Rd man/Normalize.Rd man/GetData.Rd man/SetParallel.Rd man/ComputeExpressionPercentage.Rd man/ReadNewTotal.Rd man/ReadGRAND.Rd man/PlotSimulation.Rd man/NormalizeBaseline.Rd man/PlotModelCompareErr.Rd man/as.Seurat.grandR.Rd man/PlotModelNtr.Rd man/PlotConversionFreq.Rd man/ReadFeatureCounts.Rd man/ToIndex.Rd man/PlotMismatchPositionForSample.Rd man/PlotModelCompareConv.Rd man/SimulateTimeCourse.Rd man/dropoutpercent.Rd man/PlotModelErr.Rd man/MakeColdata.Rd man/Semantics.time.Rd man/TransformSnapshot.Rd man/f.old.equi.Rd man/Scale.Rd man/Summarize.Rd man/ClassifyGenes.Rd man/PoolColumns.Rd man/density2d.Rd man/GetMatrix.Rd man/SimulateTimeCourseNonConstant.Rd man/PairwiseDESeq2.Rd man/GetDiagnosticParameters.Rd man/ComputeAbsolute.Rd man/SimulateReadsForSample.Rd man/PlotGeneGroupsBars.Rd man/PlotModelShape.Rd man/GetPairContrasts.Rd man/GetSummarizeMatrix.Rd man/DefaultSlot.Rd man/dropout.Rd man/PlotGeneOldVsNew.Rd man/LikelihoodRatioTest.Rd man/AnalyzeGeneSets.Rd man/SaveNtrSlot.Rd man/ComputePseudoNtr.Rd man/PlotGeneProgressiveTimecourse.Rd man/Design.Rd man/Defer.Rd man/FitKineticsGeneLogSpaceLinear.Rd man/GetAnalysisTable.Rd man/PlotModelLabelTimeCourse.Rd man/ReadGRAND3.Rd man/VulcanoPlot.Rd man/UpdateSymbols.Rd man/PlotModelCompareNtr.Rd man/PlotModelConv.Rd man/EstimateRegulation.Rd man/structure2vector.Rd man/Slots.Rd man/correctdropout.Rd man/FitKineticsGeneSnapshot.Rd man/ComputeNtrPosteriorQuantile.Rd man/ComputeSteadyStateHalfLives.Rd man/PlotModelCompareErrPrior.Rd man/CreateConvolutionTable.Rd man/FormatCorrelation.Rd man/estimate.dispersion.Rd man/ComputeNonConstantParam.Rd man/Semantics.concentration.Rd man/RotatateAxisLabels.Rd man/psapply.Rd man/GetTable.Rd man/PlotTypeDistribution.Rd man/PlotGeneGroupsPoints.Rd man/Findno4sUPairs.Rd man/PlotPCA.Rd man/ListGeneSets.Rd man/ComputeSummaryStatistics.Rd man/Genes.Rd man/Condition.Rd man/FitKineticsGeneLeastSquares.Rd man/ComputeTotalExpression.Rd man/CreatePdfs.Rd man/FitKinetics.Rd man/grandR.Rd man/f.nonconst.linear.Rd man/ServeGrandR.Rd man/GeneInfo.Rd man/MAPlot.Rd man/CalibrateEffectiveLabelingTimeMatchHalflives.Rd man/FitKineticsSnapshot.Rd man/f.nonconst.Rd man/FitKineticsGeneNtr.Rd man/ReadCounts.Rd man/ComputeColumnStatistics.Rd man/IsParallel.Rd man/DesignSemantics.Rd man/GetSignificantGenes.Rd man/Pairwise.Rd man/FindReferences.Rd man/check.analysis.Rd man/Transform.no.Rd man/Analyses.Rd man/get.mode.slot.Rd man/LFC.Rd man/CalibrateEffectiveLabelingTimeKineticFit.Rd man/UseNtrSlot.Rd man/SimulateKinetics.Rd man/Plots.Rd man/PlotMismatchPositionForType.Rd man/PlotGeneSnapshotTimecourse.Rd man/PlotProfileLikelihood.Rd