DiffSegR

DiffSegR performs annotation-free identification of differentially expressed regions from RNA-Seq data by analyzing per-base log2 fold change to localize transcriptomic changes and support studies of RNA maturation and degradation.

Key Features:

• R package: Implemented as an R package.
• Annotation-Free Analysis: Identifies differential expression without requiring existing gene annotations, enabling detection across unannotated regions.
• Changepoint Detection Algorithm: Employs a multiple changepoints detection algorithm to delineate boundaries of differentially expressed regions based on per-base log2 fold change.
• Per-base log2 fold change: Uses per-base log2 fold change values as the input signal for region detection.
• Efficiency and Speed: Optimized for rapid computation suitable for large-scale transcriptomic studies.
• Novel biological insight: Has been used to predict roles of specific ribonucleases in RNA maturation and degradation.

Scientific Applications:

• Gene regulation and RNA dynamics: Enables detailed mapping of expression changes to study gene regulation and associated RNA-binding or enzymatic activities.
• Annotation-independent transcriptome discovery: Detects differential expression in unannotated regions when annotations are incomplete or absent.
• Ribonuclease function and RNA maturation studies: Facilitates prediction and analysis of ribonucleases' roles in RNA maturation and degradation.

Methodology:

Computes per-base log2 fold changes between two biological conditions and applies a multiple changepoints detection algorithm to identify boundaries of differentially expressed regions while operating without prior annotations.