https://rhassett-cshl.r-universe.devRecent package updates in rhassett-cshlR-universehttps://github.com/rhassett-cshl.pnghttps://rhassett-cshl.r-universe.devMon, 22 Jun 2026 22:48:34 GMThassett@cshl.edu (Rebecca Hassett)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.https://github.com/r-universe/bioc/actions/runs/39574883737Mon, 22 Jun 2026 22:48:34 GMTSTADyUM1.3.2successhttps://bioc.r-universe.devhttps://github.com/bioc/STADyUMSTADyUM_LRT_Tutorial.RmdSTADyUM_LRT_Tutorial.htmlComparative Analysis of Promoter-Proximal Pausing using Likelihood Ratio Tests2026-06-10 21:46:402026-06-22 22:48:34STADyUM_Rate_Estimation_Tutorial.RmdSTADyUM_Rate_Estimation_Tutorial.htmlEstimating Transcription Rates with STADyUM from PRO-seq Data2026-06-10 21:46:402026-06-22 22:48:34STADyUM_Simulator_Tutorial.RmdSTADyUM_Simulator_Tutorial.htmlSTADyUM: Simulating and Analyzing Transcription Dynamics2026-06-10 21:46:402026-06-22 22:48:34