Package: STADyUM 1.2.0

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]

STADyUM_1.2.0.tar.gz
STADyUM_1.2.0.zip(r-4.7)STADyUM_1.2.0.zip(r-4.6)STADyUM_1.2.0.zip(r-4.5)
STADyUM_1.2.0.tgz(r-4.6-x86_64)STADyUM_1.2.0.tgz(r-4.6-arm64)STADyUM_1.2.0.tgz(r-4.5-x86_64)STADyUM_1.2.0.tgz(r-4.5-arm64)
STADyUM_1.2.0.tar.gz(r-4.7-arm64)STADyUM_1.2.0.tar.gz(r-4.7-x86_64)STADyUM_1.2.0.tar.gz(r-4.6-arm64)STADyUM_1.2.0.tar.gz(r-4.6-x86_64)
STADyUM_1.2.0.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-release.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)

statisticalmethodtranscriptomicstranscriptionsequencingcpp

5.26 score 1 stars 2 scripts 292 downloads 40 exports 82 dependencies

Last updated from:d0e8aad2a8 (on RELEASE_3_23). Checks:9 NOTE, 2 OK, 3 ERROR. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE221
linux-devel-arm64NOTE446
linux-devel-x86_64NOTE601
source / vignettesOK346
linux-release-arm64NOTE454
linux-release-x86_64NOTE524
macos-release-arm64NOTE282
macos-release-x86_64NOTE628
macos-oldrel-arm64NOTE394
macos-oldrel-x86_64NOTE880
windows-develERROR370
windows-releaseERROR342
windows-oldrelERROR308
wasm-releaseOK165

Exports:betaTblBetaViolinPlotchiTblChiViolinPlotcombinedCellsDatacountsestimateTranscriptionRatesfinalPositionMatrixgeneBodyRegionsgetAvailableTimePointsgetCombinedCellsDataAtTimegetPositionMatrixAtTimelikelihoodRatioTestomegaScaleparameterspauseRegionspauseSitesplotBetaVsChiplotChiDistribplotCombinedCellsplotExpectedVsActualPauseSiteCountsplotLfcMaplotMeanPauseDistribplotPauseSiteContourMapplotPauseSiteContourMapTwoConditionsplotPauseSitesplotPolymerasePCAplotPositionHeatmappositionMatricesratesreadCountssampleReadCountsshowsimpolsimulatePolymerasesiteProbabilitiesspikeInFilestericHindrancetranscriptionRates1transcriptionRates2

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurldata.tableDelayedArraydplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

STADyUM: Simulating and Analyzing Transcription Dynamics

Rebecca Hassett

Rendered fromSTADyUM.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-10-11
Started: 2025-04-22

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
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 TranscriptionRates-class
Constructor for TranscriptionRatesLRT objectbetaTbl betaTbl,TranscriptionRatesLRT-method BetaViolinPlot BetaViolinPlot,TranscriptionRatesLRT-method chiTbl chiTbl,TranscriptionRatesLRT-method ChiViolinPlot ChiViolinPlot,TranscriptionRatesLRT-method likelihoodRatioTest plotLfcMa plotLfcMa,TranscriptionRatesLRT-method plotPauseSiteContourMapTwoConditions plotPauseSiteContourMapTwoConditions,TranscriptionRatesLRT-method spikeInFile spikeInFile,TranscriptionRatesLRT-method transcriptionRates1 transcriptionRates1,TranscriptionRatesLRT-method transcriptionRates2 transcriptionRates2,TranscriptionRatesLRT-method TranscriptionRatesLRT-class