Package: STADyUM 1.3.1

Rebecca Hassett

STADyUM: Statistical Transcriptome Analysis under a Dynamic Unified Model

STADyUM is a package with functionality for analyzing nascent RNA read counts to infer transcription rates. This includes utilities for processing experimental nascent RNA read counts as well as for simulating PRO-seq data. Rates such as initiation, pause release and landing pad occupancy are estimated from either synthetic or experimental data. There are also options for varying pause sites and including steric hindrance of initiation in the model.

Authors:Yixin Zhao [aut], Lingjie Liu [aut], Rebecca Hassett [aut, cre], Xin Zeng [aut, aut]

STADyUM_1.3.1.tar.gz
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STADyUM_1.3.1.tgz(r-4.6-x86_64)STADyUM_1.3.1.tgz(r-4.6-arm64)STADyUM_1.3.1.tgz(r-4.5-x86_64)STADyUM_1.3.1.tgz(r-4.5-arm64)
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STADyUM_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
STADyUM/json (API)
NEWS

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

Bug tracker:https://github.com/rhassett-cshl/stadyum/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:STADyUM-1.3.0(bioc 3.24)STADyUM-1.2.0(bioc 3.23)

statisticalmethodtranscriptomicstranscriptionsequencingpreprocessingcpp

4.26 score 1 stars 4 scripts 287 downloads 48 exports 86 dependencies

Last updated from:3d71693f5c. Checks:8 WARNING, 5 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING290
linux-devel-arm64WARNING452
linux-devel-x86_64WARNING627
source / vignettesERROR383
linux-release-arm64WARNING438
linux-release-x86_64WARNING546
macos-release-arm64ERROR410
macos-release-x86_64WARNING787
macos-oldrel-arm64WARNING311
macos-oldrel-x86_64WARNING594
windows-develERROR320
windows-releaseERROR369
windows-oldrelERROR407
wasm-releaseOK159

Exports:betaTblBetaViolinPlotchiTblChiViolinPlotcombinedCellsDatacountsestimateTranscriptionRatesfinalPositionMatrixgeneBodyRegionsgetAvailableTimePointsgetCombinedCellsDataAtTimegetPositionMatrixAtTimegetSdGroupCutofflikelihoodRatioTestlrtTblmergeBetaChiLRTStatsomegaScaleparameterspauseRegionspauseSitesplotBetaQuantileHeatmapplotBetaScatterplotBetaVsChiplotChiDistribplotCombinedCellsplotDeltaBetaSigmaplotExpectedVsActualPauseSiteCountsplotFksdDensityplotLfcMaplotMeanPauseDistribplotPauseSiteContourMapplotPauseSiteContourMapTwoConditionsplotPauseSitesplotPolymerasePCAplotPositionHeatmapplotScatterDensitypositionMatricesratesreadCountssampleReadCountsshowsimpolsimulatePolymerasesiteProbabilitiesspikeInFilestericHindrancetranscriptionRates1transcriptionRates2

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurldata.tableDelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2ggpointdensitygluegtablehmshttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigplyrangespracmaprettyunitsprogresspurrrR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Readme and manuals

Help Manual

Help pageTopics
Generic function for estimating transcription ratesestimateTranscriptionRates
Constructor for ExperimentTranscriptionRates objectcounts counts,ExperimentTranscriptionRates-method estimateTranscriptionRates,character-method ExperimentTranscriptionRates-class geneBodyRegions geneBodyRegions,ExperimentTranscriptionRates-method omegaScale omegaScale,ExperimentTranscriptionRates-method pauseRegions pauseRegions,ExperimentTranscriptionRates-method rates,ExperimentTranscriptionRates-method stericHindrance,ExperimentTranscriptionRates-method
Get SD Group CutoffgetSdGroupCutoff
Accessor for estimated ratesrates
Show method for ExperimentTranscriptionRates objectsshow,ExperimentTranscriptionRates-method
Constructor for SimulatePolymerase objectcombinedCellsData combinedCellsData,SimulatePolymerase-method finalPositionMatrix finalPositionMatrix,SimulatePolymerase-method getAvailableTimePoints getAvailableTimePoints,SimulatePolymerase-method getCombinedCellsDataAtTime getCombinedCellsDataAtTime,SimulatePolymerase-method getPositionMatrixAtTime getPositionMatrixAtTime,SimulatePolymerase-method parameters parameters,SimulatePolymerase-method pauseSites pauseSites,SimulatePolymerase-method plotCombinedCells plotCombinedCells,SimulatePolymerase-method plotPauseSites plotPauseSites,SimulatePolymerase-method plotPolymerasePCA plotPolymerasePCA,SimulatePolymerase-method plotPositionHeatmap plotPositionHeatmap,SimulatePolymerase-method positionMatrices positionMatrices,SimulatePolymerase-method readCounts readCounts,SimulatePolymerase-method sampleReadCounts sampleReadCounts,SimulatePolymerase-method show,SimulatePolymerase-method simulatePolymerase SimulatePolymerase-class siteProbabilities siteProbabilities,SimulatePolymerase-method
Constructor for SimulationTranscriptionRates objectestimateTranscriptionRates,SimulatePolymerase-method rates,SimulationTranscriptionRates-method show,SimulationTranscriptionRates-method simpol simpol,SimulationTranscriptionRates-method SimulationTranscriptionRates-class stericHindrance,SimulationTranscriptionRates-method
Accessor for steric hindrance flagstericHindrance
Base class for TranscriptionRates objectsplotBetaVsChi plotBetaVsChi,TranscriptionRates-method plotChiDistrib plotChiDistrib,TranscriptionRates-method plotExpectedVsActualPauseSiteCounts plotExpectedVsActualPauseSiteCounts,TranscriptionRates-method plotMeanPauseDistrib plotMeanPauseDistrib,TranscriptionRates-method plotPauseSiteContourMap plotPauseSiteContourMap,TranscriptionRates-method plotScatterDensity plotScatterDensity,TranscriptionRates-method TranscriptionRates-class
Constructor for TranscriptionRatesLRT objectbetaTbl betaTbl,TranscriptionRatesLRT-method BetaViolinPlot BetaViolinPlot,TranscriptionRatesLRT-method chiTbl chiTbl,TranscriptionRatesLRT-method ChiViolinPlot ChiViolinPlot,TranscriptionRatesLRT-method likelihoodRatioTest lrtTbl lrtTbl,TranscriptionRatesLRT-method mergeBetaChiLRTStats mergeBetaChiLRTStats,TranscriptionRatesLRT-method plotBetaQuantileHeatmap plotBetaQuantileHeatmap,TranscriptionRatesLRT-method plotBetaScatter plotBetaScatter,TranscriptionRatesLRT-method plotDeltaBetaSigma plotDeltaBetaSigma,TranscriptionRatesLRT-method plotFksdDensity plotFksdDensity,TranscriptionRatesLRT-method plotLfcMa plotLfcMa,TranscriptionRatesLRT-method plotPauseSiteContourMapTwoConditions plotPauseSiteContourMapTwoConditions,TranscriptionRatesLRT-method spikeInFile spikeInFile,TranscriptionRatesLRT-method transcriptionRates1 transcriptionRates1,TranscriptionRatesLRT-method transcriptionRates2 transcriptionRates2,TranscriptionRatesLRT-method TranscriptionRatesLRT-class