SpliceWiz: interactive analysis and visualization of alternative splicing in R

• Published in: Briefings in bioinformatics Vol. 25; no. 1
• Main Authors: Wong, Alex C H, Wong, Justin J-L, Rasko, John E J, Schmitz, Ulf
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 22.11.2023
• Subjects: Algorithms; Alternative Splicing; Problem Solving Protocol; RNA Splicing; Sequence Analysis, RNA; Software; gene isoforms; data visualization; differential splicing; exon usage; intron retention; read coverage
• ISSN: 1467-5463; 1477-4054
• DOI: 10.1093/bib/bbad468

Alternative splicing (AS) is a crucial mechanism for regulating gene expression and isoform diversity in eukaryotes. However, the analysis and visualization of AS events from RNA sequencing data remains challenging. Most tools require a certain level of computer literacy and the available means of visualizing AS events, such as coverage and sashimi plots, have limitations and can be misleading. To address these issues, we present SpliceWiz, an R package with an interactive Shiny interface that allows easy and efficient AS analysis and visualization at scale. A novel normalization algorithm is implemented to aggregate splicing levels within sample groups, thereby allowing group differences in splicing levels to be accurately visualized. The tool also offers downstream gene ontology enrichment analysis, highlighting ASEs belonging to functional pathways of interest. SpliceWiz is optimized for speed and efficiency and introduces a new file format for coverage data storage that is more efficient than BigWig. Alignment files are processed orders of magnitude faster than other R-based AS analysis tools and on par with command-line tools. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization. SpliceWiz is a Bioconductor package and is also available on GitHub (https://github.com/alexchwong/SpliceWiz).