STADyUM is probabilistic modeling software for analyzing simulated and experimental nascent RNA sequencing data to study transcriptional dynamics.
Nascent RNA sequencing methods—such as PRO-seq, GRO-seq, and 4sU-DRB-seq—are powerful tools for investigating transcription mechanisms, but their data can be challenging to interpret, and existing analysis tools are limited.
STADyUM provides:
Efficient simulation of sequencing read counts.
Robust estimation of key rate parameters, including RNAP density along gene bodies and pause regions, as well as pause site statistics.
A mechanistic model that accounts for steric hindrance between RNA polymerases, which can impact apparent transcription rates.
Comprehensive support for differential analysis of transcription-associated rates (such as initiation, pause-release, and elongation) across conditions, cell types, individuals, and species.
This framework offers a unified, statistically rigorous approach for dissecting transcription dynamics from nascent RNA data.
This is an R package.
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
install.packages("BiocManager")
BiocManager::install("STADyUM")
install.packages("devtools")
devtools::install_github("rhassett-cshl/STADyUM")
The vignette illustrating how to use the package can be accessed on Bioconductor or from R via:
vignette("STADyUM")
or
browseVignettes("STADyUM")
If you use this package, please cite: Zeng X, Barshad G, Hassett R, Rice EJ, Danko CG, Siepel A, Zhao Y. A comparative analysis of promoter-proximal pausing reveals kinetic and distributional dimensions of variation. bioRxiv (2026). Preprint: https://www.biorxiv.org/content/10.64898/2026.06.01.729264v1