derfinderHelper

The software tool "derfinderHelper" enhances the annotation-agnostic approach to RNA-seq analysis introduced by "derfinder." "derfinder" utilizes a differentially expressed region (DER) finder that identifies contiguous genomic regions with differential expression signals at single-base resolution. "derfinderHelper" improves this approach by implementing a computationally efficient bump-hunting strategy for identifying DERs, enabling genome-scale analyses in numerous samples. It introduces a flexible statistical modeling framework, accommodating multi-group and time-course analyses and new visualizations for expressed region analysis. Applied to public RNA-seq data from projects like GTEx and BrainSpan, "derfinderHelper" permits the analysis of hundreds of samples at base resolution, identifies expression beyond known gene boundaries, and visualizes expressed regions at single-base resolution.