pulseR

pulseR estimates RNA synthesis and decay rates from RNA-seq count data generated in metabolic labeling pulse-chase experiments.

Key Features:

• Negative-Binomial Model: Models RNA-seq count data using the negative-binomial distribution to account for overdispersion.
• Spike-In Handling: Integrates labeled and unlabeled spike-in controls for normalization and validation of count-based estimates.
• Labeling Bias Correction: Corrects for labeling biases including the number of uridine residues incorporated during metabolic labeling.
• Support for Metabolic Labeling Designs: Supports analysis of pulse-chase and other metabolic labeling experimental designs to derive kinetic parameters.
• Estimation of Synthesis and Degradation Rates: Computes RNA synthesis and degradation (decay) rates from labeled and total RNA counts.

Scientific Applications:

• RNA Dynamics: Quantifying RNA synthesis and decay to study RNA dynamics and transcriptional regulation.
• Comparative Condition Analysis: Assessing how treatments or conditions affect RNA stability and production.
• Normalization and Validation: Validating and normalizing metabolic labeling experiments using labeled and unlabeled spike-ins.

Methodology:

Models RNA-seq count data with a negative-binomial distribution, integrates labeled and unlabeled spike-in controls, and corrects for labeling biases such as uridine incorporation to estimate synthesis and decay rates from pulse-chase experiments.