diffUTR

diffUTR streamlines and improves differential exon usage analyses and extends existing differential exon usage frameworks to differential 3' UTR usage analysis using alternative poly-adenylation site databases.

Key Features:

• Uniform Interface: Provides a uniform interface for limma/edgeR/DEXSeq-powered differential bin/exon usage analysis.
• Plotting Functions: Includes plotting functions for visualizing differential bin/exon usage results.
• Improved diffSplice: Incorporates an improved version of the limma::diffSplice method.
• Differential UTR Usage: Extends differential exon usage frameworks to differential UTR usage analysis using poly-A site databases.

Scientific Applications:

• Differential Exon Usage: Facilitates differential exon usage analysis from standard transcriptomic data.
• Differential 3' UTR Usage: Enables detection of alternative poly-adenylation and 3' UTR length changes from standard transcriptomic data.
• Exploration of Results: Supports exploration and visualization of differential exon and UTR usage results.

Methodology:

diffUTR leverages limma, edgeR, and DEXSeq for differential bin/exon usage analysis, builds upon and improves the limma::diffSplice method, and integrates alternative poly-adenylation site databases for differential 3' UTR usage analysis.