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

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

Introduction | Installation | Basic Usage | Simulate Polymerase | Estimate Transcription Rates from Simulated Data | Likelihood Ratio Tests for Simulated Data | Session Info