Changes in version 0.99.9 (2026-05-09)
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Reviewer Response (Bisaloo, Bioconductor)

* Added package-level man page and runnable examples for all exported functions.
* Replaced sapply() with vapply(); removed <<- operator; eliminated dead code.
* Unified 0-based BED/BEDPE import and 1-based internal coordinate handling.
* Fixed GO enrichment table rendering (list-of-dataframes merge).
* Fixed expression matrix gene-name loss with single-sample-column input.
* Fixed OrgDb object handling via getFromNamespace() instead of get().
* Added whitelist-overlap cross-validation warning in expression refinement.
* Added empty-input guards for ChIPseeker::annotatePeak() and prepare_track_data().
* Replaced deprecated ggplot2 size aesthetic with linewidth.
* Improved test coverage to 84.70% with 29 dedicated regression tests.
* Updated default colour palettes to colourblind-friendly schemes (Set2, Paired, PuOr, viridis).
* looplook_report() template: enhanced metric cards, Sankey via saveWidget+iframe, aligned tables.
* Vignette: expanded comparison table, reproducibility note, BiocManager install placeholder.
* DESCRIPTION: Title case, non-package-name Description start, removed recursive SystemRequirements, expanded Suggests.
* Precomputed results now accepted as in-memory list or file path; bedpe_file optional.

Changes in version 0.99.0 (2026-03-02)
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* Comprehensive refactoring for Bioconductor submission, including Expression-Aware modules and enhanced vignettes.