NEWS

---

GeneTrackR 0.99.2

Author identity correction

• Corrected the package author and maintainer display name to Shuchao Ren across DESCRIPTION, package help, vignettes, README citation guidance, and Bioconductor submission metadata.
• Updated the recommended package citation to: Shuchao Ren (2026). GeneTrackR: Genomic Track Visualization and Haplotype Analysis. R package version 0.99.2.
• Retained the GitHub account name Renscq in repository URLs; it is an account identifier rather than the package author name.
• Preserved all production R code and analysis behavior from GeneTrackR 0.99.1.

GeneTrackR 0.99.1

Package metadata and citation normalization

• Synchronized the package version, title, author identity, release date, README citation guidance, and Bioconductor submission metadata for the 0.99.1 review candidate.
• Standardized the recommended package citation as: Shuchao Ren (2026). GeneTrackR: Genomic Track Visualization and Haplotype Analysis. R package version 0.99.1.
• Kept package citation generation based on DESCRIPTION metadata instead of adding a custom inst/CITATION, avoiding a BiocCheck warning for a package-only citation without an associated publication DOI.
• Preserved all production analysis code, statistical behavior, genomic I/O behavior, tests, vignettes, and generated help content from 0.99.0.

GeneTrackR 0.99.0

Bioconductor submission candidate

• Promoted GeneTrackR from the 0.8.x Bioconductor-readiness series to the required 0.99.0 pre-release version for formal new-package submission.
• Raised the R dependency floor to R 4.6.0 so the submission candidate matches the current Bioconductor 3.24 devel build environment.
• Froze the public analysis APIs and pure-R genomic I/O implementation from GeneTrackR 0.8.9; this release does not introduce new analysis algorithms or change statistical behavior.
• Added final submission preparation and preflight tooling for a package-only GitHub default branch, Bioconductor devel validation, and the 2026 BiocContributions review workflow.
• Retained NEWS, executable vignettes, runnable help examples, deterministic bundled demo data, GRanges interoperability, and the GPL-3 license declaration required by the submission candidate.

GeneTrackR 0.8.9

Final BiocCheck source cleanup

• Added explicit return-value documentation to the advanced-parameter and deterministic-demo help topics so BiocCheck no longer reports missing \value sections.
• Moved the GenePred() runnable example into its roxygen source block so devtools::document() preserves the example instead of overwriting a manually synchronized Rd example.
• Replaced a stop(paste0(...)) condition with sprintf() and reworded the strict merge-conflict error message to avoid BiocCheck condition-signaling false positives without changing control flow.
• Kept network-dependent repository warnings, submission versioning, Support Site registration, ORCID/funding metadata, long-function notices, and package-wide formatting notes outside this source hotfix.

GeneTrackR 0.8.8

Runnable writer example hotfix

• Fixed the write_feature_track() runnable example to use bundled GenePred gene-model data converted with as_feature(), matching the wrapper's default BED12 requirement for transcript and exon information.
• Added a regression test that exercises the same GenePred-to-Feature-to-BED12 path used by the help example.
• Kept write_feature_track() implementation and all annotation-writing behavior unchanged.

GeneTrackR 0.8.7

Documentation and regression hotfix

• Linked all as_feature() S3 methods to the shared roxygen topic so devtools::document() no longer creates a nameless as_feature.GenePred topic.
• Updated the GenePred coercion example to exercise as_feature() directly with bundled demo annotation data.
• Aligned the duplicated-identifier regression test with the 0.8.6 BiocCheck-compliant error path: conflict = "error" now expects a direct error without a preliminary warning.
• Kept merge semantics, annotation conversion behavior, and all analysis algorithms unchanged.

GeneTrackR 0.8.6

Bioconductor compliance cleanup

• Expanded runnable examples across exported help pages to satisfy the Bioconductor documentation coverage requirement.
• Added missing return-value documentation for compatibility writer functions.
• Updated the R dependency floor to 4.5.0 and added the suggested VariantAnnotation biocView.
• Replaced avoidable 1: sequences, <<- state mutation, and BiocCheck-flagged condition patterns without changing analysis outputs.
• Kept large-scale formatting, long-function refactoring, and legitimate warning suppression out of this focused compatibility release.

GeneTrackR 0.8.5

Restore Bioconductor release notes

• Restored NEWS.md as a maintained package-level release history because Bioconductor strongly recommends NEWS files and BiocCheck includes dedicated NEWS checks.
• Restored the pkgdown News navigation entry and the submission-tree workflow so release notes remain available in both development documentation and the package-only Bioconductor source tree.
• Updated the Bioconductor preflight and submission preparation tools to require and preserve NEWS.md.
• Kept GeneTrackR analysis code, public APIs, statistical behavior, and genomic I/O unchanged from 0.8.4.

GeneTrackR 0.8.4

R CMD check cleanup

• Resolved the remaining package-owned R CMD check warning by documenting all arguments exposed in exported function usage sections.
• Declared data.table and ggplot2 non-standard-evaluation symbols reported by R CMD check, eliminating undefined-global-variable diagnostics without changing runtime behavior.
• Wrapped long Rd examples so generated manual examples no longer exceed the 100-character width check.
• Standardized the package license declaration to GPL-3 and removed the redundant top-level LICENSE file.
• The Windows-only future file timestamps NOTE remains an environment time-verification issue rather than a GeneTrackR source problem.

GeneTrackR 0.8.3

Bioconductor submission hygiene

• Separate the development workspace from the package-only Bioconductor submission tree.
• Add a development-side submission-tree preparation tool and expand the Bioconductor preflight checks for default-branch hygiene.
• Label every R code chunk in all package vignettes for current BiocCheck compatibility.
• Document bundled inst/extdata files and their deterministic provenance in a package help topic.
• Update README installation guidance to lead with the Bioconductor installation path while retaining GitHub development instructions.
• Keep GeneTrackR analysis APIs and executable package behavior unchanged.

GeneTrackR 0.8.2

• Hardened package documentation for Bioconductor build/check workflows without changing analysis algorithms or public APIs.
• Added author/date metadata, explicit Introduction and Installation sections, package landing-page links, and executable session information to all 15 formal vignettes.
• Numbered all 15 VignetteIndexEntry values so browseVignettes() follows the intended GeneTrackR workflow order instead of filename alphabetic order.
• Added build-aware vignette rendering: normal R package builds use 144 dpi to reduce CPU, memory, and artifact size, while the pkgdown workflow sets GENETRACKR_PKGDOWN=true to retain 300-dpi website figures.
• Kept publication export examples capable of 300-500 dpi output while executing vignette figure exports at the build-aware documentation DPI.
• Replaced all \dontrun{} examples in GeneTrackR roxygen/man documentation with compact, deterministic, runnable examples based on bundled gtr_demo_* data and temporary output paths.
• Reduced expensive signal examples to the compact RNA-seq demo where frame-specific Ribo-seq behavior was not essential to the function being documented.
• Added tools/bioc_preflight.003.R to audit runnable examples, vignette structure, documentation DPI policy, individual file size, estimated source-tree size, and R-build exclusion of development-only directories.

GeneTrackR 0.8.1

• Expanded Bioconductor interoperability so as_granges() now accepts annotation, in-memory signal (BwgTrack), and in-memory variant (VariantTrack) objects while preserving the existing annotation-level interface.
• Added retrieve_vcf(..., as = "GRanges") so indexed or in-memory variant retrieval can feed directly into standard Bioconductor genomic interval workflows.
• Added S4Vectors, grDevices, and tools to explicit runtime imports where GeneTrackR calls their namespaces directly; retained Rsamtools in Suggests because tabix-backed querying remains an optional acceleration path.
• Added dependency-placement and cross-track GRanges regression coverage, including lazy-track conversion diagnostics.
• Documented the boundary between GeneTrackR's native pure-R bedGraph/WIG/BigWig I/O and Bioconductor's rtracklayer infrastructure while keeping the native backend and public signal APIs unchanged.
• Added tools/bioc_preflight.002.R with dependency duplication, namespace-declaration, and interoperability checks while retaining the 0.8.0 preflight script for development history.

GeneTrackR 0.8.0

• Started the Bioconductor-readiness phase while keeping the 0.7.8 pure-R signal implementation and public analysis APIs unchanged.
• Added Bioconductor-oriented DESCRIPTION metadata, including software biocViews, a broader package title, and a three-sentence functional description that reflects annotation, signal, variant, haplotype, phenotype, LD, and variant-effect workflows.
• Kept NeedsCompilation: no, removed stale generated DESCRIPTION fields and the obsolete roxygen configuration pin, and added openxlsx to Suggests for the optional workbook workflow used in an executable vignette.
• Added RiboParser-style README navigation links for pkgdown documentation, issues, citation, and license, and added explicit Citation and License sections.
• Converted all pkgdown article Rmd files into formal R package vignettes with VignetteIndexEntry, VignetteEngine, and UTF-8 metadata so they can participate in R CMD build and R CMD check.
• Added a Bioconductor-readiness regression test for metadata and GRanges interoperability and a versioned developer preflight script for repository, vignette, compiled-code, and submission-boundary checks.
• Kept the package at version 0.8.0 during preflight development; the formal Bioconductor submission candidate will use the required 0.99.0 version series.

GeneTrackR 0.7.8

• Finalized the 0.7.x pure-R signal migration documentation without changing public APIs or signal calculations.
• Removed obsolete Rcpp, bundled libBigWig, src/, and compiled-backend wording from installation guides, signal/export tutorials, pkgdown vignettes, generated README content, and public signal help pages.
• Restored README.qmd as the canonical include-based source used by tools/render_readme.R; the clean 0.7.7 deployment artifact had retained the rendered README but stripped its include directives.
• Updated package-level documentation to state that bedGraph, WIG, and BigWig reading, regional querying, and writing use the built-in pure-R signal I/O architecture.
• Synchronized the public signal Rd pages with their roxygen sources and renamed legacy writer-test labels to match the pure-R implementation.
• Retained schema-v2 BwgTrack, 1-based closed internal coordinates, lazy/memory semantics, tabix bedGraph behavior, BigWig chromosome-size requirements, and all 0.7.7 signal behavior unchanged.

GeneTrackR 0.7.7

• Added full signal-subsystem regression coverage for lazy-versus-memory BigWig retrieval, chromosome-edge intervals, strand semantics, normalization parity, and cross-format round trips.
• Fixed the pure-R package boundary regression test so data.table key attributes are not mistaken for signal-value differences, while keeping compiled-helper absence as a hard requirement.
• Improved the compiled-helper failure diagnostic to identify stale namespace bindings and remind developers to remove R/bw_cpp_backend.R and restart R before testing.
• Prevented summary_bwg() and bin_bwg() from mutating caller-owned data.tables through data.table reference semantics.
• Fixed merge_bwg(sample_conflict = "keep_first") so duplicate sample IDs retain records and sequence metadata only from the first source, including lazy objects without in-memory signal data.
• Retained the pure-R bedGraph, WIG, and BigWig I/O architecture, schema-v2 BwgTrack contract, and public signal APIs unchanged.

GeneTrackR 0.7.6

• Removed the compiled libBigWig/Rcpp compatibility backend after native-R BigWig reading, querying, and writing had been migrated and unified in 0.7.2-0.7.5.
• Removed R/bw_cpp_backend.R and the complete src/ tree, including libBigWig C sources, the Rcpp bridge, platform Makevars files, and compiled build artifacts.
• Removed Rcpp from Imports and LinkingTo, removed the generated Rcpp import and GeneTrackR useDynLib() registration, and changed package metadata to NeedsCompilation: no.
• Replaced the obsolete compiled-reader parity test with native low-level-versus-adapter parity and added package-level regression checks that compiled BigWig helpers are absent from the namespace.
• Updated the BigWig writer architecture test to follow the 0.7.5 dispatcher design (write_bwg() -> write_signal_file_memory() -> write_bigwig_native()) instead of requiring a direct writer call from write_bwg().
• Retained the existing public signal APIs, schema-v2 BwgTrack contract, 1-based closed coordinates, tabix bedGraph behavior, and native-R BigWig round-trip behavior.

GeneTrackR 0.7.5

• Added a unified native-R signal I/O layer for bedGraph, WIG, and BigWig formats while preserving the existing public read_bwg(), retrieve_bwg(), and write_bwg() APIs.
• Centralized in-memory format dispatch through read_signal_file_memory() and write_signal_file_memory(), and centralized lazy per-sample retrieval through query_signal_file_region().
• Replaced duplicate bedGraph parsing in full-file and tabix query paths with one canonical 0-based half-open to 1-based closed parser.
• Reworked WIG text reading around the stabilized bwTools parser pattern, including fixedStep, variableStep, bedGraph-style records, comments, and gzip/bgzip text connections.
• Centralized signal-region clipping and sequence-metadata construction so all supported formats follow the same canonical six-column signal schema and schema-v2 seqinfo contract.
• Retained compatibility wrappers for existing internal text I/O helper names while removing their duplicate implementations from read_bwg.R and write_bwg.R.
• Added regression coverage for unified dispatch, compressed text inputs, interval clipping, and bedGraph/WIG round trips without coordinate drift.
• Kept Rcpp and src/ temporarily for compiled-backend parity code only; their final removal remains isolated to the next migration stage.

GeneTrackR 0.7.4

• Fixed schema-v2 seqinfo chromosome subsetting in retrieve_bwg(..., as = "BwgTrack") and slice_bwg(..., as = "BwgTrack"); the previous helper allowed the data.table chrom column to mask the function argument and therefore retained unrelated chromosomes.
• Added the native-R BigWig writer adapted from the stabilized bwTools 0.8.10 implementation, including binary packing, chromosome B+ tree construction, R-tree indexing, compressed data blocks, total summaries, and zoom-level generation.
• Switched write_bwg(..., format = "bigwig") from the bundled libBigWig/Rcpp writer to the native R writer without changing the public write_bwg() argument contract.
• Kept chrom_sizes mandatory for GeneTrackR BigWig export in this release to avoid mixing backend migration with API changes.
• Added native writer regression coverage for round-trip signal values, multiple samples, overlap and chromosome-boundary validation, and multi-level chromosome indexes.
• Retained the compiled backend only for temporary parity tests and later cleanup; public BigWig reading and writing now both use native R implementations.

GeneTrackR 0.7.3

• Switched the public BigWig read path from the bundled libBigWig/Rcpp reader to the native R reader introduced in 0.7.2.
• Added internal query_bigwig_native() and read_bigwig_whole_native() adapters that return the standard GeneTrackR signal schema.
• Updated read_bwg() memory loading and sequence metadata collection, lazy retrieve_bwg() queries, and legacy seqinfo_bwg() fallback to use the native R backend.
• Updated BwgTrack$meta$backend to GeneTrackR-native-R for newly read signal objects.
• Retained the compiled reader temporarily only for regression comparison; BigWig writing remains on the compiled backend until the writer migration.
• Added regression coverage that verifies public BigWig read functions no longer reference the compiled reader while preserving interval values, clipping, and schema behavior.

GeneTrackR 0.7.2

• Added the first native-R BigWig reader layer adapted from the stabilized bwTools 0.8.10 implementation.
• Added internal binary decoding for BigWig headers, chromosome B+ trees, R-tree indexes, compressed data blocks, and 32-bit floating-point signal values.
• Added internal bigwig_metadata_native(), bigwig_seqinfo_native(), and bigwig_query_native() functions using 1-based closed coordinates without Rcpp or .Call().
• Added metadata caching keyed by normalized path, file size, and modification time while keeping the native reader local-file only.
• Added a deterministic BigWig fixture and regression tests for chromosome metadata, interval decoding, clipping, empty ranges, invalid files, and parity with the existing compiled backend.
• Kept read_bwg() and retrieve_bwg() on the existing libBigWig/Rcpp backend in this release so the new reader can be verified before the public backend switch in 0.7.3.

GeneTrackR 0.7.1

• Established the schema-v2 BwgTrack object foundation for the 0.7.x pure-R signal subsystem migration.
• Added a stable seqinfo slot alongside samples, data, meta, and validation; chromosome lengths can be known or NA when the source format does not encode sequence lengths.
• Standardized BwgTrack metadata to coordinate = "1-based closed" and schema_version = "2" while preserving the existing public constructor argument order.
• Added sequence metadata collection for bigWig inputs and in-memory bedGraph/WIG inputs, and preserved relevant seqinfo through BwgTrack retrieval, slicing, and merging.
• Updated seqinfo_bwg() to use stored schema-v2 sequence metadata first while retaining the existing libBigWig fallback for legacy objects.
• Added regression tests for schema construction, sequence metadata validation, text-track sequence metadata, subset propagation, and merge propagation.
• Kept the existing libBigWig/Rcpp backend unchanged in this release; native BigWig replacement begins in the following 0.7.x development stages.

GeneTrackR 0.6.17

• Optimized pkgdown article figure layouts by increasing the graphics canvas according to plot complexity while keeping rendered figures at full article width.
• Standardized vignette web graphics to 150 dpi with fig.retina = 1; publication-oriented export examples continue to use 500 dpi.
• Reduced documentation-only plotting text sizes to 9-10 pt for functions that expose text_size or font, without changing GeneTrackR plotting defaults or package APIs.
• Enlarged annotation-specific figure heights and retained all R implementations, staged docs/*.qmd sources, tests, and statistical behavior unchanged.

GeneTrackR 0.6.16

• Removed the Documentation QA GitHub Actions workflow.
• Retained the pkgdown workflow as the single documentation build and deployment workflow.
• Kept README rendering, pkgdown articles, package code, tests, and generated documentation unchanged.

GeneTrackR 0.6.15

• Fixed pkgdown homepage code rendering by generating README.md from README.qmd and staged docs/*.qmd sources as display-only GitHub-Flavored Markdown; Quarto/knitr \``{r}fences are converted to standard```r` fences instead of being exposed as plain text.
• Added tools/render_readme.R as the single deterministic README assembly entry point. The script expands Quarto include directives without executing the 202 documentation code chunks and supports --check for CI synchronization checks.
• Added README synchronization to Documentation QA and made the pkgdown workflow regenerate README.md before site construction, preventing stale homepage content.
• No R implementation, API, vignette, statistical method, or plotting behavior was changed.

GeneTrackR 0.6.14

• Removed the noisy GitHub Pages 404 annotation from the pkgdown workflow by probing repository Pages availability before invoking actions/configure-pages.
• actions/configure-pages now runs only when the Pages REST endpoint is available; repositories without Pages enabled receive a clean pkgdown preview artifact and Step Summary without an Error or Warning annotation.
• Kept pkgdown site construction as a hard CI check and retained automatic native Pages deployment once repository-level Pages is enabled.
• No R implementation, API, vignette, test, or pkgdown content was changed.

GeneTrackR 0.6.13

• Synchronized the package-level Rd file with the roxygen2 8.1.0 output generated from DESCRIPTION URL and BugReports metadata.
• Added the automatically generated Useful links \seealso{} section so the documentation QA roxygen drift check remains clean.
• No R implementation, API, vignette, test, pkgdown workflow, or analysis behavior was changed.

GeneTrackR 0.6.12

• Made the pkgdown GitHub Pages deployment tolerant of repositories where Pages has not yet been enabled: pkgdown site construction remains a hard check, while Pages configuration/deployment is skipped with a clear warning instead of failing the entire workflow.
• Added a fallback pkgdown-site-preview workflow artifact when GitHub Pages is unavailable, so the generated site can still be inspected from the Actions run.
• Retained the native GitHub Pages artifact/deploy path automatically when actions/configure-pages succeeds; no R implementation, API, vignette, or pkgdown content was changed.

GeneTrackR 0.6.11

• Re-synchronized roxygen2 8.1.0 generated metadata, NAMESPACE, and package-level Rd documentation after the 0.6.10 GitHub commit omitted part of the generated-file update.
• Retained the documentation QA roxygen drift guard and the explicit [email protected] CI pin.

GeneTrackR 0.6.10

• Synchronized roxygen-generated package metadata, NAMESPACE, and package-level Rd documentation with roxygen2 8.1.0, matching the generator used by the documentation QA workflow.
• Pinned roxygen2 8.1.0 in the documentation-QA dependency set so future CI runs do not fail solely because a newer roxygen2 release reformats generated documentation.
• Preserved all R implementations, tests, pkgdown articles, staged Quarto sources, and package APIs unchanged; this release is limited to generated-documentation synchronization and CI reproducibility.

GeneTrackR 0.6.9

• Added a dedicated GitHub Actions documentation-QA workflow that rebuilds the pkgdown site in a clean R process, verifies roxygen-generated documentation is synchronized, checks internal site links, inventories generated figure dimensions, and runs R CMD check --as-cran.
• Added a Bioconductor release preflight for main-branch and manually triggered runs using the official bioconductor/bioconductor_docker:RELEASE_3_23 image and BiocCheck; package-specific documentation/coding errors fail CI, while submission-only biocViews checks are deferred until the formal Bioconductor submission phase.
• Modernized pkgdown deployment to the native GitHub Pages artifact workflow while retaining pkgdown-site/ as the generated-site directory.
• Kept the 0.6.8 article, Reference, API, and analysis implementations unchanged; this release is limited to documentation QA and CI integration.

GeneTrackR 0.6.8

• Added a dedicated export and reproducibility article covering standard genomic track writers, PDF/PNG figure export, tabular result preservation, LD matrix export, optional openxlsx workbooks, complete RDS objects, manifests, and sessionInfo() provenance.
• Added a production-oriented complete workflow article connecting annotation, interval features, RNA-seq/Ribo-seq signals, variants, haplotypes, phenotype association, LD, phenotype-guided refinement, variant-effect prioritization, and reproducible export through one consistent candidate-locus analysis.
• Added a Workflow & reproducibility section to the pkgdown Articles index while retaining core-workflows as the shorter Getting Started workflow.
• Kept the staged docs/13-export.qmd and docs/14-workflow.qmd sources unchanged while migrating their current workflows into formal pkgdown vignettes.

GeneTrackR 0.6.7

• Added a dedicated linkage-disequilibrium article covering genotype-dosage LD calculation, LDTrack result inspection, r2 and dosage-based D-prime interpretation, triangular heatmaps, regional gene/variant context, population subsets, variant filtering, and downstream regional haplotype handoff.
• Added a dedicated phenotype-guided haplotype-refinement article covering original-versus-refined haplotype state, pairwise merge evidence, effect_threshold, multi-trait grouping, grouped and collapsed refined-variant plots, and refined phenotype visualization.
• Added a dedicated variant-effect article covering binary genotype coding, absolute versus signed effects, adjusted P values, linked tied-effect interpretation, direct single-variant phenotype validation, and multi-trait prioritization.
• Extended the pkgdown Haplotype & association article sequence to Haplotype -> Phenotype -> LD -> Haplotype refinement -> Variant effect while keeping the staged docs/10-ld.qmd, docs/11-haplotype-refinement.qmd, and docs/12-variant-effect.qmd sources unchanged.

GeneTrackR 0.6.6

• Added a dedicated haplotype article covering gene-, transcript-, and region-defined HapVariant construction, genotype representations, missing-genotype filtering, sample/variant filtering, object inspection, and plot_hap_variant() visualization.
• Added a dedicated phenotype-association article covering phenotype import and QC, explicit sample-ID alignment checks, haplotype-phenotype testing, multi-trait inference, single-variant phenotype testing, and preservation of returned statistical tables.
• Added a task-oriented Haplotype & association section to the pkgdown Articles index, positioned after variant/browser visualization and before the later LD/refinement/variant-effect modules.
• Kept the staged docs/08-haplotype.qmd and docs/09-phenotype.qmd sources unchanged while migrating their current workflows into pkgdown vignettes.

GeneTrackR 0.6.5

• Added a dedicated pkgdown variant-track article covering VariantTrack construction, memory versus indexed lazy VCF access, validation, summaries, genomic/gene/transcript retrieval, ID/type/pattern filtering, variant plotting, site-level VCF export, and downstream handoff.
• Added a dedicated integrated browser-track article covering plot_tracks() locator semantics, gene/transcript/region views, strand-aware RNA-seq and Ribo-seq display, transcript-level Ribo-seq frame rendering, feature and variant panels, panel layout, highlighting, styling, and large-dataset usage.
• Extended the pkgdown Visualization section from gene models and signal tracks to the complete gene-model -> signal -> variant -> integrated-browser documentation sequence.
• Kept all staged docs/*.qmd sources unchanged for subsequent haplotype, phenotype, LD, refinement, variant-effect, export, and end-to-end workflow migration.

GeneTrackR 0.6.4

• Added a dedicated pkgdown gene-model visualization article covering gene, transcript, and regional structural views, genomic versus spliced transcript coordinates, transcript collapse, strand-direction arrows, labels, highlights, and explicit feature colors.
• Rebuilt the signal-track article around the complete BwgTrack workflow: reading, lazy versus in-memory access, strand semantics, regional retrieval, normalization, merging, binning, writing, gene/transcript/region visualization, Ribo-seq frame views, and integrated plot_tracks() figures.
• Separated gene-model structure from continuous-signal documentation so later variant/browser-track articles can build on a stable visualization foundation without duplicating annotation or signal basics.
• Added the gene-model article to the pkgdown Visualization section while retaining all staged docs/*.qmd sources unchanged for subsequent migration steps.

GeneTrackR 0.6.3

• Added a dedicated pkgdown annotation article covering GenePred/GenePredExt, GTF, GFF3, and BED inputs through one unified GeneTrackR workflow.
• Reorganized annotation documentation around native coordinate handling, object contracts, validation and summaries, feature retrieval, cross-format conversion, merging, writing, and round-trip checks.
• Added annotation-focused visualization examples for genes, transcripts, genomic regions, interval feature tracks, and gene-length distributions.
• Added a Data & annotation section to the pkgdown Articles index while retaining the existing Getting Started and Visualization navigation.
• Kept all staged docs/*.qmd sources unchanged for later module-specific migration.

GeneTrackR 0.6.2

• Rebuilt the pkgdown Get Started path around a dedicated first-run article that covers installation, package loading, bundled demo inputs, and a minimal annotation-to-haplotype/phenotype workflow.
• Added a deterministic example-data article documenting the shared file inventory, coordinate conventions, core dimensions, sample alignment rule, GeneA haplotype/phenotype truth, LD gradient, and strand-specific RNA-seq/Ribo-seq design.
• Updated the pkgdown article order to Getting started -> Example data -> Core workflow, while retaining signal-track documentation under Visualization.
• Added prerequisite navigation to the existing core workflow without changing its executable analysis workflow.
• Kept all staged docs/*.qmd sources unchanged for later module-by-module migration.

GeneTrackR 0.6.1

• Redesigned the pkgdown information architecture around a dedicated Get Started entry, task-oriented Articles, and a functionally grouped Reference index.
• Organized all current Rd topics into explicit Reference sections for core objects, annotation I/O and conversion, gene-model visualization, signal tracks, variant tracks, haplotype analysis, phenotype association, linkage disequilibrium, variant effect/refinement, and advanced diagnostics.
• Positioned core-workflows as the top-level Get Started workflow and retained signal-tracks under the Visualization article section.
• Added article descriptions to the existing vignettes so the pkgdown article index explains the purpose of each workflow.
• Kept the staged docs/*.qmd tutorial sources unchanged; additional task-oriented articles will be migrated into the established information architecture in subsequent 0.6.x releases.

GeneTrackR 0.6.0

• Initialized the GeneTrackR package website with pkgdown, replacing the abandoned MkDocs migration plan with an R-native documentation architecture.
• Added _pkgdown.yml with the canonical GitHub Pages URL, Bootstrap 5, the existing workflow vignettes, and a temporary pkgdown-site/ output directory.
• Added a GitHub Actions workflow to build the package website on pushes, pull requests, releases, and manual dispatches, and to deploy non-PR builds to the gh-pages branch.
• Added package website and issue-tracker metadata to DESCRIPTION, together with the website-only pkgdown dependency declaration.
• Preserved the existing docs/*.qmd documentation sources during staged migration; they remain the source material used by README.qmd and are not overwritten by pkgdown in this release.

GeneTrackR 0.5.37

• Fixed haplotype allele fill color helpers so the stable A, T, C, G, and indel mapping retains its names after alpha adjustment.
• Fixed variant marker color helpers so the stable SNP, Ind, and ... mapping retains its names after alpha adjustment.
• Updated plotting-default regression tests to preserve the intentional Reds default for plot_ld_block() while other plotting palettes remain Paired.
• Changed full-memory bigWig loading to emit one memory warning per read_bwg() call instead of one warning per input file, and made round-trip tests explicitly expect this warning.

GeneTrackR 0.5.36

• Rebuilt docs/13-export.qmd as a structured export workflow for genomic tracks, PDF/PNG figures, analysis tables, optional Excel workbooks, and complete RDS objects.
• Rebuilt docs/14-workflow.qmd as the end-to-end GeneTrackR candidate-locus workflow using the current GeneA haplotype, phenotype, LD-gradient, refinement, and variant-effect examples.
• Removed docs/15-notes.qmd and incorporated its large-data and object-return guidance into the end-to-end workflow.
• Synchronized README.qmd and README.md with the revised documentation sequence.

GeneTrackR 0.5.35

• Fixed plot_variant_effect() multi-trait reshaping so mixed integer and double phenotype columns no longer trigger data.table::melt() coercion warnings.
• Standardized selected numeric traits to double before long-format conversion without changing their values or effect statistics.
• Added regression coverage requiring the documented multi-trait variant-effect workflow to run silently.
• Clarified mixed numeric trait handling in docs/12-variant-effect.qmd.
• Bumped the package version to 0.5.35.

GeneTrackR 0.5.34

• Rebuilt docs/12-variant-effect.qmd as a complete regional variant-effect prioritization workflow.
• Added explicit guidance for binary genotype coding, absolute versus signed effects, adjusted P values, and multi-trait interpretation.
• Documented the deterministic GeneA effect truth: the p13-linked variant set has an effect of approximately +6 on protein_content, varA05 has an intermediate effect, and varA02 is a zero-effect control.
• Clarified that tied phenotype effects among linked variants do not identify a unique causal variant and should be interpreted together with LD, annotation, direct variant-phenotype plots, and refinement.
• Added regression coverage for the redesigned variant-effect documentation workflow.
• Bumped the package version to 0.5.34.

GeneTrackR 0.5.33

• Replaced docs/10-ld.qmd with the user-updated LD workflow while restoring valid executable QMD syntax.
• Redesigned the GeneA genotype/phenotype truth so refinement follows genotype-nearest haplotype pairs.
• Changed varA03 from the cross-cluster p23 pattern to the cluster-consistent p13 pattern.
• Redesigned phenotype means so Hap1/Hap2 are locally similar, Hap3/Hap4 are locally similar, and cross-cluster differences are larger.
• Updated the protein_content refinement truth to Hap1 + Hap2 versus Hap3 + Hap4.
• Updated phenotype, refinement, variant-effect, workflow, vignette, generator, validator, help examples, and regression tests.
• Bumped the package version to 0.5.33.

GeneTrackR 0.5.32

• Expanded the primary LD demo from 6 to 12 natural SNPs while preserving the 11-variant GeneA haplotype truth.
• Redesigned the primary LD demo to contain a perfect high-LD core plus progressively decorrelated downstream variants, producing a clear r2 gradient with both high- and low-LD pairs.
• Changed the default plot_ld_block() heatmap palette from Paired to Reds.
• Updated LD documentation, demo truth metadata, generated VCF data, and regression tests.

GeneTrackR 0.5.31

• Rebuilt docs/10-ld.qmd as a complete LD calculation, inspection, visualization, and downstream handoff workflow.
• Added deterministic high-LD, low-LD, and two-variant demo examples with explicit expected pairwise behavior.
• Documented the LDTrack object contract, pairwise statistics, LD matrix, genotype retention, sample/variant filtering, and plot_ld_block() return semantics.
• Clarified that GeneTrackR calculates pairwise LD but does not automatically call biological block boundaries from a fixed threshold.
• Added guidance on dosage-based Dprime limitations for unphased VCF data and recommended r2 as the primary generic metric.
• Added documentation regression coverage for the designed LD truth sets.

GeneTrackR 0.5.30

• Rebuilt docs/11-haplotype-refinement.qmd as a phenotype-guided refinement workflow.
• Changed the primary demo refinement trait to protein_content, which deterministically refines four GeneA haplotypes into two phenotype groups.
• Added explicit inspection of pairwise tests, merge decisions, trait-specific groups, original-to-refined mappings, grouped/collapsed refined variant plots, and refined phenotype plots.
• Added guidance on effect_threshold, trait dependence, negative-control refinement, and multi-trait refinement.
• Added documentation regression coverage for the designed 4 -> 2, 4 -> 4, and 4 -> 1 refinement outcomes.

GeneTrackR 0.5.29

• Reorganized docs/09-phenotype.qmd into a self-contained phenotype-association workflow covering phenotype QC, sample matching, haplotype association, multiple testing, single-variant association, result objects, and downstream reuse.
• Documented the designed demo phenotype roles for seed_weight, plant_height, protein_content, flowering_time, and flower_color.
• Clarified numeric versus categorical phenotype support and the relationship among raw p-values, adjusted p-values, and displayed significance brackets.
• Added documentation regression checks for sample-ID matching and the phenotype workflow.

GeneTrackR 0.5.28

• Reorganized docs/08-haplotype.qmd into a self-contained, stepwise haplotype workflow from VCF input through downstream analysis handoff.
• Documented the HapVariant object structure, genotype representations, missing-genotype filtering, flanking-region semantics, sample/variant filtering, and haplotype plotting controls.
• Established the GeneA gene body as the primary tutorial haplotype definition (11 variants, 36 samples, four balanced haplotypes) and separated the upstream missing-genotype example from the main analysis.

GeneTrackR 0.5.27

• Added variant_palette and variant_colors controls to plot_tracks() and forwarded them to integrated variant panels.
• Standardized all plotting palette defaults to Paired, including signal, frame, feature, variant, LD, haplotype-table, and phenotype fill palettes.
• Updated browser-track documentation and regression tests for variant color control and package-wide palette defaults.

GeneTrackR 0.5.26

• Improved browser-track feature legends by adding automatic compact feature grouping in plot_tracks() and plot_feature_track().
• Added transcript-centered automatic Ribo-seq frame rendering in plot_tracks() via ribo_signal_type = "auto".
• Updated docs/07-browser-tracks.qmd to explain feature legend grouping and transcript-centered Ribo-seq frame behavior.

GeneTrackR 0.5.25

• Reorganized docs/07-browser-tracks.qmd into a self-contained browser-track workflow covering input preparation, gene/transcript/region locators, signal selection, feature/variant integration, layout, heights, highlighting, and large-data usage.
• Clarified the exact-one-locator rule used by plot_tracks() and the distinction between browser-level genomic signal plotting and transcript-coordinate/frame-specific signal visualization.
• Updated browser examples to use the current public read_vcf() API and explicit strand/sample selection.
• Documented current panel ordering, named feature/variant list behavior, and the compact styling scope of integrated feature/variant tracks.

GeneTrackR 0.5.24

• Fix fixed-string pattern filtering so fixed = TRUE no longer passes the incompatible ignore.case argument to grepl().
• Preserve case-insensitive fixed-string matching by normalizing both the pattern and candidate fields before matching.
• Add regression tests for warning-free fixed matching and case-insensitive fixed-string VCF retrieval.

GeneTrackR 0.5.23

• Fix summary_vcf() so an in-memory VariantTrack can be summarized without supplying a genomic region.
• Fix retrieve_vcf() so region, gene, and transcript filters are optional for in-memory/full-file queries; ID, type, and pattern filters can now be used independently as documented.
• Add validation for incomplete direct regions and flank arguments used without a gene/transcript locator.
• Add regression tests for whole-object summaries and non-regional VCF retrieval.

GeneTrackR 0.5.22

• Reorganized docs/06-variant.qmd into a continuous VCF workflow covering reading, validation, summaries, region/gene/transcript retrieval, ID/type/pattern filtering, and plotting.
• Clarified VariantTrack versus data.table return semantics for retrieve_vcf().
• Added explicit guidance for indexed lazy VCF access and strand-aware gene/transcript retrieval.
• Documented the current site-level scope of write_vcf() to avoid implying genotype-preserving round-trip export.

GeneTrackR 0.5.21

• Changed discrete signal palette assignment so sample, group, and frame levels use RColorBrewer class colors in strict level order instead of interpolating between palette endpoints; this also fixes plot_signal_region() color ordering.
• Kept heatmap palettes continuous while separating continuous-gradient generation from discrete signal color assignment.
• Reworked demo Ribo-seq counts so frame 0, frame 1, and frame 2 have visibly heterogeneous heights and different occupied codons while preserving approximately 80%/10%/10% total counts.
• Increased frame-0 codon occupancy while reducing off-frame occupancy, producing a dense but visually varied RPF pattern; initiation and termination frame-0 counts remain approximately two-fold over the internal mean.
• Added regression checks for discrete palette order and within-frame Ribo-seq count variability.

GeneTrackR 0.5.20

• Fixed signal qualitative palettes so discrete levels use RColorBrewer colors strictly in palette order; frame0, frame1, and frame2 now map to the first three Set1 colors by default.
• Reworked demo Ribo-seq counts to moderate density with approximately 80%/10%/10% frame0/frame1/frame2 total-count proportions.
• Reduced demo Ribo-seq initiation and termination peaks to approximately two times the internal frame-0 mean.