Shiba

A unified computational method for systematic identification of differential RNA splicing. Shiba/scShiba can quantify and identify differential splicing events (DSEs) from bulk RNA-seq data and single-cell RNA-seq data. Shiba and scShiba are also implemented as Snakemake workflows, SnakeShiba and SnakeScShiba, respectively.

See CHANGELOG.md for the latest updates.

Report a bug

If you continue to encounter issues, please don't hesitate to open an issue on GitHub. The community and developers are here to help!

Contents

• Installation
• Quick Start
  • With bulk RNA-seq data
  • With single-cell RNA-seq data
• Output
  • Shiba/SnakeShiba
  • scShiba/SnakeScShiba
• Usage
  • shiba.py
  • snakeshiba.smk
  • scshiba.py
  • snakescshiba.smk

Citation

Kubota N, Chen L, Zheng S. Shiba: a versatile computational method for systematic identification of differential RNA splicing across platforms. Nucleic Acids Research 53(4), 2025, gkaf098.