Package: grandR 0.2.5

Florian Erhard

grandR: Comprehensive Analysis of Nucleotide Conversion Sequencing Data

Nucleotide conversion sequencing experiments have been developed to add a temporal dimension to RNA-seq and single-cell RNA-seq. Such experiments require specialized tools for primary processing such as GRAND-SLAM, (see 'Jürges et al' <doi:10.1093/bioinformatics/bty256>) and specialized tools for downstream analyses. 'grandR' provides a comprehensive toolbox for quality control, kinetic modeling, differential gene expression analysis and visualization of such data.

Authors:Florian Erhard [aut, cre], Teresa Rummel [ctb], Lygeri Sakellaridi [ctb], Kevin Berg [ctb]

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NEWS

Peer review:

Bug tracker:https://github.com/erhard-lab/grandr/issues

On CRAN:

163 exports 7 stars 1.47 score 40 dependencies 16 scripts 292 downloads

Last updated 7 months agofrom:5527612e00. Checks:ERROR: 1 WARNING: 8. Indexed: yes.

Exports:AddAnalysisAddGenePlotAddGlobalPlotAddSlotAnalysesAnalyzeGeneSetsApplyContrastsas.Seurat.grandRCalibrateEffectiveLabelingTimeKineticFitCalibrateEffectiveLabelingTimeMatchHalflivesClassifyGenesColdataColdata<-ColumnsComputeAbsoluteComputeColumnStatisticsComputeExpressionPercentageComputeNonConstantParamComputeNtrCIComputeNtrPosteriorLowerComputeNtrPosteriorQuantileComputeNtrPosteriorUpperComputePseudoNtrComputeSteadyStateHalfLivesComputeSummaryStatisticsConditionCondition<-Correct4sUDropoutHLFactorCorrect4sUDropoutHLSplineCreatePdfsCreatePdfsComparisonCreatePdfsParametersCreatePdfsProfilesDefaultSlotDefaultSlot<-Deferdensity2dDESeq2BICDesignDesignSemanticsDropAnalysisDropPlotsDropSlotestimate.dispersionEstimate4sUDropoutPercentageEstimate4sUDropoutPercentageForSampleEstimateRegulationEvaluateNonConstantParamf.newf.nonconstf.nonconst.linearf.old.equif.old.nonequiFilterGenesFindno4sUPairsFindReferencesFitKineticsFitKineticsGeneLeastSquaresFitKineticsGeneLogSpaceLinearFitKineticsGeneNtrFitKineticsGeneSnapshotFitKineticsPulseRFitKineticsSnapshotFormatCorrelationGeneInfoGeneInfo<-GenesGetAnalysisTableGetContrastsGetDataGetDiagnosticParametersGetMatrixGetPairContrastsGetSignificantGenesGetSummarizeMatrixGetTablegrandRis.grandRIsParallelIsSparsekinetics2vectorLFCLikelihoodRatioTestListGeneSetsMakeColdataMAPlotmerge.grandRMetadataNormalizeNormalizeBaselineNormalizeFPKMNormalizeRPMNormalizeTPMPairwisePairwiseDESeq2plapplyPlot4sUDropoutPlot4sUDropoutAllPlot4sUDropoutDeferAllPlot4sUDropoutRankPlot4sUDropoutRankAllPlot4sUDropoutRankDeferAllPlotAnalysesPlotConversionFreqPlotGenePlotGeneGroupsBarsPlotGeneGroupsPointsPlotGeneOldVsNewPlotGeneProgressiveTimecoursePlotGeneSnapshotTimecoursePlotGeneTotalVsNtrPlotGlobalPlotHeatmapPlotMismatchPositionForSamplePlotMismatchPositionForTypePlotModelCompareConvPlotModelCompareErrPlotModelCompareErrPriorPlotModelCompareLLPlotModelCompareNtrPlotModelConvPlotModelErrPlotModelLabelTimeCoursePlotModelNtrPlotModelShapePlotPCAPlotProfileLikelihoodPlotsPlotScatterPlotSimulationPlotTypeDistributionPoolColumnspsapplyReadCountsReadFeatureCountsReadGRANDReadGRAND3ReadNewTotalRenameColumnsRotatateAxisLabelsSaveNtrSlotScaleSemantics.concentrationSemantics.timeServeGrandRSetParallelSimulateKineticsSimulateReadsForSampleSimulateTimeCourseSimulateTimeCourseNonConstantSlotsstructure2vectorSwapColumnsTitleToIndexTransform.logFCTransform.noTransform.VSTTransform.ZTransformSnapshotUpdateSymbolsUseNtrSlotVulcanoPlot

Dependencies:bitopsclicolorspacecowplotfansifarverggplot2gluegtableisobandlabelinglatticelfclifecyclemagrittrMASSMatrixmgcvminpack.lmmunsellnlmenumDerivpatchworkpillarpkgconfigplyrR6RColorBrewerRcppRCurlreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr