regionReport

regionReport generates reports from derfinder outputs to summarize and visualize differentially expressed regions (DERs) identified in RNA-seq data at single base-pair resolution.

Key Features:

• Annotation-Agnostic Analysis: Identifies DERs without relying on existing gene annotations or transcript assemblies, enabling detection of novel expression outside annotated features.
• Bump-Hunting Approach: Implements a bump-hunting algorithm to detect contiguous genomic regions with differential expression signals.
• Flexible Statistical Modeling: Supports various experimental designs, including multi-group comparisons and time-course studies.
• Base-Resolution Visualization: Provides base-pair resolution visualizations of expressed regions to inspect local expression patterns.
• Integration with Public Datasets: Has been applied to Genotype-Tissue Expression (GTEx) and BrainSpan RNA-seq datasets to analyze hundreds of samples at base resolution.
• Robustness in Incomplete Annotation: Simulation results indicate base-resolution approaches remain effective when annotations are incomplete, offering an alternative to feature-level methods.

Scientific Applications:

• Exploration of unannotated regions: Enables differential expression analyses that examine genomic regions beyond annotated gene structures.
• Discovery of regulatory elements: Facilitates identification of novel regulatory elements by detecting DERs outside known gene boundaries.
• Characterization of complex expression: Supports investigation of complex spatial or temporal expression patterns, including those revealed in time-course or multi-group studies.
• Study of non-coding regions: Aids analysis of non-coding regions to investigate their potential functional roles in RNA-seq differential expression.

Methodology:

Builds on derfinder's annotation-agnostic methodology by applying a bump-hunting algorithm and a flexible statistical modeling framework to detect contiguous DERs and produce base-resolution visualizations.