Package: grandR 0.2.6

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]

grandR_0.2.6.tar.gz
grandR_0.2.6.zip(r-4.5)grandR_0.2.6.zip(r-4.4)grandR_0.2.6.zip(r-4.3)
grandR_0.2.6.tgz(r-4.5-x86_64)grandR_0.2.6.tgz(r-4.5-arm64)grandR_0.2.6.tgz(r-4.4-x86_64)grandR_0.2.6.tgz(r-4.4-arm64)grandR_0.2.6.tgz(r-4.3-x86_64)grandR_0.2.6.tgz(r-4.3-arm64)
grandR_0.2.6.tar.gz(r-4.5-noble)grandR_0.2.6.tar.gz(r-4.4-noble)
grandR_0.2.6.tgz(r-4.4-emscripten)grandR_0.2.6.tgz(r-4.3-emscripten)
 |grandR.html✨
grandR/json (API)
NEWS

# Install 'grandR' in R:
install.packages('grandR', repos = c('https://erhard-lab.r-universe.dev', 'https://cloud.r-project.org'))

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

On CRAN:

7.03 score 10 stars 1 packages 18 scripts 437 downloads 165 exports 40 dependencies

Last updated 3 days agofrom:d85d9200a0. Checks:1 ERROR, 10 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesFAILFeb 12 2025
R-4.5-win-x86_64WARNINGFeb 12 2025
R-4.5-mac-x86_64WARNINGFeb 12 2025
R-4.5-mac-aarch64WARNINGFeb 12 2025
R-4.5-linux-x86_64WARNINGFeb 12 2025
R-4.4-win-x86_64WARNINGFeb 12 2025
R-4.4-mac-x86_64WARNINGFeb 12 2025
R-4.4-mac-aarch64WARNINGFeb 12 2025
R-4.3-win-x86_64WARNINGFeb 12 2025
R-4.3-mac-x86_64WARNINGFeb 12 2025
R-4.3-mac-aarch64WARNINGFeb 12 2025

Exports:AddAnalysisAddGenePlotAddGlobalPlotAddSlotAnalysesAnalyzeGeneSetsApplyContrastsas.Seurat.grandRCalibrateEffectiveLabelingTimeKineticFitCalibrateEffectiveLabelingTimeMatchHalflivesClassifyGenesColdataColdata<-ColumnsComputeAbsoluteComputeColumnStatisticsComputeExpressionPercentageComputeNonConstantParamComputeNtrCIComputeNtrPosteriorLowerComputeNtrPosteriorQuantileComputeNtrPosteriorUpperComputePseudoNtrComputeSteadyStateHalfLivesComputeSummaryStatisticsComputeTotalExpressionConditionCondition<-Correct4sUDropoutHLFactorCorrect4sUDropoutHLSplineCreatePdfsCreatePdfsComparisonCreatePdfsParametersCreatePdfsProfilesDefaultSlotDefaultSlot<-Deferdensity2dDESeq2BICDesignDesignSemanticsDropAnalysisDropPlotsDropSlotestimate.dispersionEstimate4sUDropoutPercentageEstimate4sUDropoutPercentageForSampleEstimateRegulationEvaluateNonConstantParamf.newf.nonconstf.nonconst.linearf.old.equif.old.nonequiFilterGenesFindno4sUPairsFindReferencesFitKineticsFitKineticsGeneLeastSquaresFitKineticsGeneLogSpaceLinearFitKineticsGeneNtrFitKineticsGeneSnapshotFitKineticsPulseRFitKineticsSnapshotFormatCorrelationGeneInfoGeneInfo<-GenesGetAnalysisTableGetContrastsGetDataGetDiagnosticParametersGetMatrixGetPairContrastsGetSignificantGenesGetSummarizeMatrixGetTablegrandRis.grandRIsParallelIsSparsekinetics2vectorLFCLikelihoodRatioTestListGeneSetsMakeColdataMAPlotmerge.grandRMetadataNormalizeNormalizeBaselineNormalizeFPKMNormalizeRPMNormalizeTPMPairwisePairwiseDESeq2plapplyPlot4sUDropoutPlot4sUDropoutAllPlot4sUDropoutDeferAllPlot4sUDropoutRankPlot4sUDropoutRankAllPlot4sUDropoutRankDeferAllPlotAnalysesPlotConversionFreqPlotGenePlotGeneGroupsBarsPlotGeneGroupsPointsPlotGeneOldVsNewPlotGeneProgressiveTimecoursePlotGeneSnapshotTimecoursePlotGeneTotalVsNtrPlotGlobalPlotHeatmapPlotMismatchPositionForSamplePlotMismatchPositionForTypePlotModelCompareConvPlotModelCompareErrPlotModelCompareErrPriorPlotModelCompareLLPlotModelCompareNtrPlotModelConvPlotModelErrPlotModelLabelTimeCoursePlotModelNtrPlotModelShapePlotPCAPlotProfileLikelihoodPlotsPlotScatterPlotSimulationPlotTypeDistributionPoolColumnspsapplyReadCountsReadFeatureCountsReadGRANDReadGRAND3ReadNewTotalRenameColumnsRotatateAxisLabelsSaveNtrSlotScaleSemantics.concentrationSemantics.timeServeGrandRSetParallelSimulateKineticsSimulateReadsForSampleSimulateTimeCourseSimulateTimeCourseNonConstantSlotsstructure2vectorSummarizeSwapColumnsTitleToIndexTransform.logFCTransform.noTransform.VSTTransform.ZTransformSnapshotUpdateSymbolsUseNtrSlotVulcanoPlot

Dependencies:bitopsclicolorspacecowplotfansifarverggplot2gluegtableisobandlabelinglatticelfclifecyclemagrittrMASSMatrixmgcvminpack.lmmunsellnlmenumDerivpatchworkpillarpkgconfigplyrR6RColorBrewerRcppRCurlreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

Getting started

Rendered fromgetting-started.Rmdusingknitr::rmarkdownon Feb 12 2025.

Last update: 2025-01-21
Started: 2022-09-15