Package: grandR 0.2.7

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. Fast Wilcoxon tests are supported via the 'presto' package (available at https://github.com/immunogenomics/presto).

Authors:Florian Erhard [aut, cre], Teresa Rummel [ctb], Julian Selke [ctb]

grandR_0.2.7.tar.gz
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grandR_0.2.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
grandR/json (API)

# 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:

6.37 score 17 stars 1 packages 23 scripts 375 downloads 166 exports 33 dependencies

Last updated from:b8d45e98a5. Checks:13 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
linux-devel-arm64	WARNING	248
linux-devel-x86_64	WARNING	267
source / vignettes	ERROR	340
linux-release-arm64	WARNING	227
linux-release-x86_64	WARNING	279
macos-release-arm64	WARNING	159
macos-release-x86_64	WARNING	323
macos-oldrel-arm64	WARNING	184
macos-oldrel-x86_64	WARNING	226
windows-devel-arm64	WARNING	431
windows-devel-x86_64	WARNING	217
windows-release-arm64	WARNING	409
windows-release-x86_64	WARNING	189
windows-oldrel-x86_64	WARNING	189
wasm-release	OK	215

Exports:AddAnalysis AddGenePlot AddGlobalPlot AddSlot Analyses AnalyzeGeneSets ApplyContrasts as.Seurat.grandR CalibrateEffectiveLabelingTimeKineticFit CalibrateEffectiveLabelingTimeMatchHalflives ClassifyGenes Coldata Coldata<-Columns ComputeColumnStatistics ComputeExpressionPercentage ComputeNonConstantParam ComputeNtrCI ComputeNtrPosteriorLower ComputeNtrPosteriorQuantile ComputeNtrPosteriorUpper ComputePseudoNtr ComputeSteadyStateHalfLives ComputeSummaryStatistics ComputeTotalExpression Condition Condition<-Correct4sUDropoutHLFactor Correct4sUDropoutHLSpline CreatePdfs CreatePdfsComparison CreatePdfsParameters CreatePdfsProfiles DefaultSlot DefaultSlot<-Defer density2d DESeq2BIC Design DesignSemantics DropAnalysis DropPlots DropSlot estimate.dispersion Estimate4sUDropoutPercentage Estimate4sUDropoutPercentageForSample EstimateRegulation EvaluateNonConstantParam f.new f.nonconst f.nonconst.linear f.old.equi f.old.nonequi FilterGenes Findno4sUPairs FindReferences FitKinetics FitKineticsGeneLeastSquares FitKineticsGeneLogSpaceLinear FitKineticsGeneNtr FitKineticsGeneSnapshot FitKineticsPulseR FitKineticsSnapshot FormatCorrelation GeneInfo GeneInfo<-Genes GetAnalysisTable GetContrasts GetData GetDiagnosticParameters GetMatrix GetPairContrasts GetSignificantGenes GetSummarizeMatrix GetTable grandR is.grandR IsParallel IsSparse kinetics2vector LFC LikelihoodRatioTest ListGeneSets MakeColdata MAPlot merge.grandR Metadata Normalize NormalizeBaseline NormalizeFPKM NormalizeRPM NormalizeTPM Pairwise PairwiseDESeq2 plapply Plot4sUDropout Plot4sUDropoutAll Plot4sUDropoutDeferAll Plot4sUDropoutRank Plot4sUDropoutRankAll Plot4sUDropoutRankDeferAll PlotAnalyses PlotConversionFreq PlotGene PlotGeneGroupsBars PlotGeneGroupsPoints PlotGeneOldVsNew PlotGeneProgressiveTimecourse PlotGeneSnapshotTimecourse PlotGeneTotalVsNtr PlotGlobal PlotHeatmap PlotMismatchPositionForSample PlotMismatchPositionForType PlotModelCompareConv PlotModelCompareErr PlotModelCompareErrPrior PlotModelCompareLL PlotModelCompareNtr PlotModelConv PlotModelErr PlotModelLabelTimeCourse PlotModelNtr PlotModelShape PlotPCA PlotProfileLikelihood Plots PlotScatter PlotSimulation PlotTypeDistribution PoolColumns psapply ReadCounts ReadFeatureCounts ReadGRAND ReadGRAND3 ReadNewTotal RenameColumns Renamer RotatateAxisLabels SaveNtrSlot Scale Semantics.concentration Semantics.time ServeGrandR SetParallel SimulateKinetics SimulateReadsForSample SimulateTimeCourse SimulateTimeCourseNonConstant Slots structure2vector Summarize SwapColumns Title ToIndex Transform.logFC Transform.no Transform.VST Transform.Z TransformSnapshot UpdateSymbols UseNtrSlot VulcanoPlot Wilcoxon

Dependencies:bitops cli cowplot cpp11 farver ggplot2 glue gtable isoband labeling lattice lfc lifecycle magrittr MASS Matrix minpack.lm numDeriv patchwork plyr R6 RColorBrewer Rcpp RCurl reshape2 rlang S7 scales stringi stringr vctrs viridisLite withr

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

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