epiPortrait - Replicate-Aware Epigenomic Domain Profiling

Provides methods for replicate-aware quantitative phenotyping and comparison of epigenomic domains from normalized continuous signal tracks and per-sample native peak/domain calls (histone-mark ChIP-seq / CUT&Tag as the primary use case; also applicable to ATAC-seq-derived domains). It characterizes each shared genomic domain by integrated signal magnitude (Intensity), sample-specific native peak breadth geometry, and continuous within-domain signal architecture (SignalDispersion). Replicate-level evidence is retained and aggregated with specified support rules, enabling condition-specific classification of Intensity-Super, Breadth-Super, Dual-Super, Typical, or Uncertain domain states without using the consensus-domain width as the breadth caller. The package further supports condition transitions, continuous domain-width remodeling, signal quality control, genome-aware domain annotation with a three-level export (per-domain summary, per-domain-gene pair, and raw relationship detail), optional BEDPE contact evidence, expression-aware candidate-gene prioritization, differential domain analysis on continuous BigWig signal using limma, and result visualization.