SIRFindeR

SIRFindeR quantifies intron retention from second‑generation (short‑read) and third‑generation (long‑read) RNA sequencing using a Stable Intron Retention ratio to mitigate biases in measurement.

Key Features:

• Stable Intron Retention ratio: Introduces the Stable Intron Retention ratio as a metric to reduce common biases for more reliable intron retention measurement.
• Sequencing support: Processes second‑generation (short‑read) and third‑generation (long‑read) RNA sequencing data.
• Validation on datasets: Demonstrates improved accuracy and higher consistency between replicates through testing on simulated and real RNA‑seq datasets.
• Long‑read concordance: Shows strong agreement with intron retention levels computed from long‑read sequencing data.
• Implementation: Provided as an R package.
• Bias mitigation: Addresses biases and artifacts that impair accurate intron retention analysis.

Scientific Applications:

• Gene expression and splicing analysis: Quantifies intron retention to study gene expression regulation and alternative splicing mechanisms.
• Functional investigation: Supports exploration of the functional roles of intron retention within genes and post‑transcriptional regulation.
• Cross‑technology comparison: Enables comparison and validation of intron retention measurements across short‑read and long‑read RNA‑seq technologies.

Methodology:

Implements a computational algorithm that leverages the Stable Intron Retention ratio to measure intron retention levels and was validated on simulated and real RNA‑seq datasets.