SpliceWiz

SpliceWiz analyzes and visualizes alternative splicing (AS) events from RNA sequencing (RNA-seq) data to quantify splicing differences and support downstream functional interpretation.

Key Features:

• Visualization of AS events: Generates coverage and sashimi-style plots to represent splicing patterns and exon–junction usage.
• Novel normalization algorithm: Aggregates splicing levels within sample groups to enable accurate visualization and comparison of group-level splicing differences.
• Efficient data processing: Processes alignment files with performance reported faster than other R-based AS analysis tools and comparable to command-line alternatives.
• Optimized coverage file format: Introduces a coverage storage format with efficiency improvements reported to surpass BigWig for handling large datasets.
• Gene ontology enrichment analysis: Performs GO enrichment on genes with identified alternative splicing events to highlight involved functional pathways.

Scientific Applications:

• Regulation of gene expression and isoform diversity: Supports studies of alternative splicing mechanisms and isoform diversity in eukaryotes using RNA-seq data.
• Identification of functionally relevant AS events: Facilitates prioritization of alternative splicing events for downstream functional interpretation and pathway analysis.
• Translational research into disease mechanisms: Enables characterization of splicing changes that may be associated with disease processes.

Methodology:

Implemented as an R package; employs a novel normalization algorithm that aggregates splicing levels within sample groups; computes coverage and sashimi-style splicing visualizations from alignment files; uses an optimized coverage file format reported to exceed BigWig in efficiency; includes gene ontology enrichment analysis on genes with alternative splicing events.