SpliceWiz: interactive analysis and visualization of alternative splicing in R

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Alternative splicing (AS) generates diverse gene isoforms, crucial for eukaryotic gene expression regulation.
• Analyzing and visualizing AS events from RNA sequencing (RNA-Seq) data presents significant computational challenges.
• Existing visualization methods like sashimi plots have limitations and can be misleading, requiring specialized bioinformatics skills.

Purpose of the Study:

• To develop an accessible and efficient tool for analyzing and visualizing alternative splicing events from RNA-Seq data.
• To address the limitations of current AS analysis tools by providing an interactive and scalable solution.
• To enable reliable identification and functional characterization of alternative splicing events.

Main Methods:

• Development of SpliceWiz, an R package featuring an interactive Shiny interface for AS analysis.
• Implementation of a novel normalization algorithm for accurate visualization of splicing level differences between sample groups.
• Introduction of an efficient file format for coverage data storage, outperforming BigWig.
• Optimization for speed, achieving processing times comparable to command-line tools.

Main Results:

• SpliceWiz enables easy and efficient large-scale analysis and visualization of AS events.
• The novel normalization algorithm accurately visualizes group-wise splicing level differences.
• The tool integrates downstream gene ontology enrichment analysis for functional pathway identification.
• SpliceWiz significantly accelerates alignment file processing compared to other R-based tools.

Conclusions:

• SpliceWiz streamlines the process of alternative splicing analysis, enhancing accessibility for researchers.
• The package provides reliable identification of functionally relevant AS events.
• SpliceWiz is available as a Bioconductor package and on GitHub, promoting widespread adoption.