<!-- README.md is generated from README.Rmd. Please edit that file --> # STADyUM <!-- badges: start --> <!-- badges: end --> 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. ## Installation This is an [R](https://www.r-project.org) package. ### [Bioconductor](https://bioconductor.org) stable version ``` r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") install.packages("BiocManager") BiocManager::install("STADyUM") ``` ### [devtools](https://cran.r-project.org/package=devtools) development version ``` r install.packages("devtools") devtools::install_github("rhassett-cshl/STADyUM") ``` ## Vignette The vignette illustrating how to use the package can be accessed on Bioconductor or from R via: ``` r vignette("STADyUM") ``` or ``` r browseVignettes("STADyUM") ```