NEWS
craftgrn 0.1.7 (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.
- Rebuilt the Module 2 top-TF report as a condition-aware regulon browser with
full or selected target sets, optional supporting TFs, correlation controls,
condition activity and expression views, and standalone SVG export.
- 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.
- Added condition-specific Gene weighting, optional condition term-IDF and
final Peak/Gene token balancing, configurable WarpLDA alpha mass, and new VAE
initialization, validation, regularization, and paired-term controls.
- Standardized Module 3 input-design QC as the default topic-assignment report,
with Gene and all-Peak UMAPs when available, condition-composition review,
optional Module 2 TF-target evidence, and full-universe retention funnels.
- 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 (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.