Deducing splicing events from transcript sets with splicelogic

Long-read RNA sequencing provides a more comprehensive capture of full-length transcripts, leading to improved isoform identification and discovery of novel isoforms. However, comparing transcripts across conditions or sets, such as novel and annotated isoforms, results in intricate isoform alterations that are challenging to manipulate, summarize, and visualize.

This complexity is amplified by the vertical integration of certain tools, where downstream analysis relies on the specific output of a particular upstream tool. To tackle this issue, a new R/Bioconductor package called splicelogic has been developed. This package transforms transcript-set comparisons into comprehensible splicing events, such as exon skipping, alternative splice sites, intron retention, and alternative transcription start and end sites.

The creators of splicelogic ensured that the package integrates seamlessly with existing RNA-seq workflows and tools. Designed with modularity, readability, and extensibility in mind, splicelogic empowers users to tailor the core logic to their specific scientific inquiries or novel splicing definitions. By extracting interpretable splicing events from transcript modifications, splicelogic facilitates downstream analyses, including the annotation of RNA-binding protein recognition sites, along with summary statistics and visualization. The splicelogic package is freely accessible and distributed through Bioconductor.