Package: STADyUM 1.3.2

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_1.3.2.tar.gz
STADyUM_1.3.2.zip(r-4.7)STADyUM_1.3.2.zip(r-4.6)STADyUM_1.3.2.zip(r-4.5)
STADyUM_1.3.2.tgz(r-4.6-x86_64)STADyUM_1.3.2.tgz(r-4.6-arm64)STADyUM_1.3.2.tgz(r-4.5-x86_64)STADyUM_1.3.2.tgz(r-4.5-arm64)
STADyUM_1.3.2.tar.gz(r-4.7-arm64)STADyUM_1.3.2.tar.gz(r-4.7-x86_64)STADyUM_1.3.2.tar.gz(r-4.6-arm64)STADyUM_1.3.2.tar.gz(r-4.6-x86_64)
STADyUM_1.3.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
STADyUM/json (API)

# 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

5.71 score 1 stars 4 scripts 48 exports 99 dependencies

Last updated from:5006f5643e. Checks:9 NOTE, 2 OK, 3 ERROR. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE243
linux-devel-arm64NOTE440
linux-devel-x86_64NOTE522
source / vignettesOK618
linux-release-arm64NOTE426
linux-release-x86_64NOTE508
macos-release-arm64NOTE267
macos-release-x86_64NOTE830
macos-oldrel-arm64NOTE235
macos-oldrel-x86_64NOTE693
windows-develERROR363
windows-releaseERROR373
windows-oldrelERROR349
wasm-releaseOK194

Exports:betaTblBetaViolinPlotchiTblChiViolinPlotcombinedCellsDatacountsestimateTranscriptionRatesfinalPositionMatrixgeneBodyRegionsgetAvailableTimePointsgetCombinedCellsDataAtTimegetPositionMatrixAtTimegetSdGroupCutofflikelihoodRatioTestlrtTblmergeBetaChiLRTStatsomegaScaleparameterspauseRegionspauseSitesplotBetaQuantileHeatmapplotBetaScatterplotBetaVsChiplotChiDistribplotCombinedCellsplotDeltaBetaSigmaplotExpectedVsActualPauseSiteCountsplotFksdDensityplotLfcMaplotMeanPauseDistribplotPauseSiteContourMapplotPauseSiteContourMapTwoConditionsplotPauseSitesplotPolymerasePCAplotPositionHeatmapplotScatterDensitypositionMatricesratesreadCountssampleReadCountsshowsimpolsimulatePolymerasesiteProbabilitiesspikeInFilestericHindrancetranscriptionRates1transcriptionRates2

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobcachemcigarilloclicodetoolscpp11crayoncurldata.tableDBIdbplyrDelayedArraydplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicRangesggplot2ggpointdensitygluegtablehmshttrhttr2IRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigplyrangespracmaprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryaml

Comparative Analysis of Promoter-Proximal Pausing using Likelihood Ratio Tests
Introduction | Setup | Load Required Libraries and Data | Running STADyUM | Likelihood Ratio Test Calculations | Visualization | Pause-escape Rate Quantile Heatmap | Pause-escape Rate Scatter Plot | Pause-escape Rate and Pausing Dispersion Contour Plot | Pausing Dispersion Contour Plot | Summary | Session Information
Rendered fromSTADyUM_LRT_Tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-06-22
Started: 2026-06-10

Estimating Transcription Rates with STADyUM from PRO-seq Data
Introduction | Setup | Load Required Libraries | Data Loading and TSS Selection | Load TSS Annotations | Select Single TSS per Gene | Building Read-Count Regions | Load Transcript Annotations | Define Pause and Gene Body Regions | Running STADyUM | Estimate Transcription Rates | Visualization | CD4 Visualizations | Pause Release Rate vs. Transcription Activity | Pause Release Rate vs. Elongation Parameters | Summary | Session Information
Rendered fromSTADyUM_Rate_Estimation_Tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-06-22
Started: 2026-06-10

STADyUM: Simulating and Analyzing Transcription Dynamics
Introduction | Installation | Basic Usage | Simulate Polymerase | Estimate Transcription Rates from Simulated Data | Likelihood Ratio Tests for Simulated Data | Session Info
Rendered fromSTADyUM_Simulator_Tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-06-22
Started: 2026-06-10

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