pulseTD

pulseTD estimates RNA life cycle dynamics (RLCD) by integrating 4sU-seq and RNA-seq time-course data to infer transcriptional production, splicing maturation, and degradation rates.

Key Features:

• Integration of Data Types: Combines 4sU-seq, which captures newly synthesized RNA, with RNA-seq total RNA abundance to characterize different stages of the RNA life cycle.
• Dynamic Analysis: Identifies and quantifies continuous changes in transcriptional production, processing (splicing maturation), and degradation rates over time.
• Predictive Capabilities: Predicts future trends in mRNA transcription and expression changes from time-course data.
• Robustness and Accuracy: Demonstrates superior robustness and accuracy in identifying RLCD compared to existing methods.
• Flexibility: Provides functions to adapt analyses to various experimental conditions and datasets without assuming a predefined functional form of RLCD.

Scientific Applications:

• Transcriptional Dynamics Research: Study time-dependent changes in transcription rates to investigate gene regulation mechanisms.
• Gene Expression Studies: Analyze and predict long-term effects of genetic or environmental perturbations on mRNA expression trajectories.
• RNA Processing and Degradation Analysis: Characterize splicing maturation and degradation processes to investigate post-transcriptional regulation and RNA stability.

Methodology:

Implements the pulse model to capture transient changes in RNA dynamics and integrates time-course 4sU-seq and RNA-seq data to generate temporal profiles of RNA synthesis, processing, and degradation, identifying RLCD without requiring a predefined functional form.