derfinderPlot

derfinderPlot visualizes differential expression regions (DERs) from RNA sequencing (RNA-seq) data to enable annotation-agnostic, base-resolution exploration and interpretation of derfinder-derived genome-wide analyses.

Key Features:

• Annotation-agnostic DER detection: Leverages derfinder's ability to identify contiguous regions of differential expression at single-base resolution without relying on existing gene annotations or transcript assemblies.
• Bump-hunting algorithm: Employs a computationally efficient bump-hunting approach for genome-scale detection of DERs across numerous samples.
• Flexible statistical modeling: Supports derfinder's statistical framework accommodating multi-group comparisons and time-course study designs.
• Base-resolution visualization: Provides visualizations that display expressed regions and single-base signals to reveal expression patterns outside known gene boundaries.
• Application to large public datasets: Has been applied to large-scale datasets including GTEx and BrainSpan to handle extensive sample sizes while maintaining high-resolution analysis.

Scientific Applications:

• Exploration of non-coding regions: Identifies expression outside annotated gene boundaries to aid discovery of regulatory elements and non-coding RNAs.
• Transcriptome-wide analysis: Enables both expressed region-level and single base-level analyses for comprehensive transcriptomic studies without full transcript reconstruction.
• Simulation and benchmarking: Demonstrates performance nearly comparable to traditional feature-level methods in simulations when complete annotation is available.

Methodology:

Uses derfinder's bump-hunting algorithm and statistical modeling framework to perform genome-wide DER analysis and provides visualization functions for base-resolution interpretation.