Changelog

Source: NEWS.md

craftgrn 0.1.7

CRAN release: 2026-06-19

• Added Module 1 condition-comparison, TF-TF co-binding, and interactive TFBS UMAP visualization utilities, plus a provenance-aware QC Run Summary.
• Redesigned the Module 1 QC report to match the report plan, with exact run metrics, full-width raincloud distributions, metadata-aware labeled PCA, threshold-colored correlations, and responsive Binding, Co-binding, and Motif explorers embedded in one HTML file. Motif rankings now retain the true top 20 and report canonical TF references with their actual rank or not-predicted status.
• Refined the Module 1 QC visual hierarchy with focused distribution, PCA, and count review modes, cleaner violin summaries, full-width PCA panels, larger correlation plots, compact guidance, and an automatically populated co-binding view.
• Made the Module 1 ATAC master input optional, retained raw-footprint provenance for regenerated QC reports, and added responsive 1080p and 4K report layouts with ATAC-aware diagnostics.
• Corrected Module 1 correlation QC to persist all-evaluated Pearson, Spearman, and best-R histograms with the actual run cutoffs, including negative correlations and an explicit legacy recomputation path.
• Redesigned the Module 2 QC report around the Module 1 review hierarchy with sticky navigation, accessible tabbed diagnostics, compact condition and correlation views, clearer candidate and final-link evidence, and a collapsed technical appendix that preserves all detailed checks.
• Updated Module 3 topic optimization to merge small, similar topics while preserving Gene/Peak assignments and improving TF-term versus document-theta correspondence. Merged-topic theta QC uses the maximum member-topic value.
• Updated DESCRIPTION references to include author-year text for the next CRAN update.
• Fixed a CRAN macOS test failure by comparing config-resolved relative paths against the canonical project directory path.

craftgrn 0.1.6

CRAN release: 2026-06-18

• Revised DESCRIPTION references to avoid CRAN incoming spell-check notes and replaced the arXiv URL reference with the requested arXiv DOI format.

craftgrn 0.1.5

• Addressed CRAN resubmission feedback by adding method references to DESCRIPTION, completing value documentation, replacing \dontrun{} examples, avoiding default writes to the working directory, and removing a fixed seed from package function code.

craftgrn 0.1.4

• Added production-oriented Module 3 APIs for regulatory topic modeling: run_topic_modeling(), module3_construct_docs(), module3_train_topic_models(), module3_extract_topics(), and build_module3_qc_report().
• Added reusable Module 3 topic-input caches and compact pass-only topic-link output as the default production behavior.
• Added visualize_topic_modeling_results() and visualize_differential_grns() for standard Module 3 result browsers.

craftgrn 0.1.3

• Fixed Windows incoming pretest failures by normalizing path comparisons in report tests and hardening temporary topic-model fixture directory creation.
• Revised CRAN-facing package metadata wording to reduce incoming spell-check notes for abbreviated scientific terms.

craftgrn 0.1.2

• Initial CRAN submission candidate.
• Added Module 1 TFBS prediction, Module 2 TF-target prediction, and Module 3 regulatory topic modeling workflows.
• Added package-native QC reports and pkgdown documentation.