STADyUM

STADyUM analyzes nascent RNA read counts to infer transcription rates including initiation, pause release, and landing pad occupancy from synthetic or experimental PRO-seq data.

Key Features:

• Nascent RNA read count processing: Utilities process experimental nascent RNA read counts for downstream rate estimation.
• PRO-seq data simulation: The package simulates PRO-seq data for method validation and benchmarking.
• Transcription rate estimation: Initiation, pause release, and landing pad occupancy rates are estimated from synthetic or experimental data.
• Variable pause site modeling: Options allow varying pause sites in the transcription model.
• Steric hindrance incorporation: The model can include steric hindrance of initiation.

Scientific Applications:

• Transcription dynamics analysis: Quantification of initiation and pause release rates from nascent RNA sequencing data.
• PRO-seq experimental design: Simulation of PRO-seq data to validate and optimize experimental parameters.
• Promoter-proximal pausing studies: Investigation of landing pad occupancy and pause site variation in transcriptional regulation.

Methodology:

STADyUM employs a dynamic unified model for statistical transcriptome analysis of nascent RNA read counts.