SpliceTools

SpliceTools analyzes transcriptome-wide alternative splicing (AS) from RNA sequencing (RNA-seq) data to generate summary statistics, provide mechanistic insights, and assess functional consequences.

Key Features:

• Data Processing Modules: Includes modules that streamline analysis of large RNA-seq datasets to derive interpretable splicing results.
• Summary Statistics: Produces summary statistics of alternative splicing events across samples and experimental conditions.
• Mechanistic Insights: Distinguishes splicing disruptions from regulated transcript isoform changes and aids interpretation of splicing inhibition mechanisms.
• Functional Impact Assessment: Assesses functional consequences of AS events, including effects on cell cycle progression.

Scientific Applications:

• Pharmacologic Studies: Analyzes the transcriptome footprint of pharmacologic splicing inhibitors such as indisulam and helps identify predicted neo-epitopes arising from such interventions.
• Gene Knockdown and NMD Inhibition: Applied to RNA binding protein knockdowns (including a dataset of 186 knockdowns) and nonsense-mediated RNA decay (NMD) inhibition to study AS dynamics.

Methodology:

Analyzes RNA-seq datasets from experimental conditions including 186 RNA binding protein knockdowns, nonsense-mediated RNA decay inhibition, and pharmacologic splicing inhibition to characterize AS events across biological contexts.