Changes in version 0.99.5                        

  - Minor fix in .onAttach() to avoid errors when checking ggplot2
    version and ensure the startup warning works correctly.

                       Changes in version 0.99.4                        

General

  - Addressed feedback from the Bioconductor review process with updates
    to documentation and vignette style.

Documentation and vignette

  - Updated vignette style to Bioconductor’s BiocStyle with automatic
    table of contents.
  - Improved vignette content with small corrections.
  - Revised dataset documentation by adding explicit usage: data(object)
    entries.

Functions

  - Updated geneset_similarity() color handling: replaced the single
    color_values parameter with three new parameters — color,
    neutral_color, and cold_color, for more interpretable visualization.

                       Changes in version 0.99.3                        

Package size and structure

  - Reduced package size below the 5 MB limit by converting long
    vignettes into pkgdown articles and keeping only a shorter vignette
    in the package.
  - Moved inst/Paper to a dedicated paper branch for better repository
    organization.
  - Removed unnecessary LICENSE file (already declared in DESCRIPTION).

Documentation

  - Added a concise main vignette (markeR) with installation,
    introduction, and a basic workflow.
  - Converted three longer vignettes into pkgdown articles (linked at
    the end of the main vignette).
  - Added runnable examples for VariableAssociation.

NAMESPACE and dependencies

  - Replaced broad imports with importFrom() for most packages (except
    ggplot2, retained as full import).
  - Removed unused patchwork import.
  - Added missing imports from stats and grDevices to resolve R CMD
    check notes.

Code quality

  - Replaced all sapply() calls with vapply().
  - Replaced 1:... usage with seq_len() or seq_along().
  - Standardized assignment to <- instead of =.
  - Fixed some redundant stop()/warning() conditions to provide clearer
    input validation.
  - Addressed “no visible binding” notes by using .data$ or
    utils::globalVariables().

                       Changes in version 0.99.2                        

  - Minor fixes in documentation

                       Changes in version 0.99.1                        

  - Fix documentation (invalid characters, deep nesting, missing value
    in data)
  - Remove citation, given that a DOI is not yet available
  - Removed unwanted files from the repository

                       Changes in version 0.99.0                        

  - First submission to Bioconductor

                        Changes in version 0.9.5                        

  - Added VisualiseIndividualGenes() wrapper to unify individual gene
    visualisation functions (ExpressionHeatmap, ROCandAUCplot, etc.)
    under a single, user-friendly interface.
  - Ensured all data arguments are data frames for consistency across
    functions.
  - Minor bug fix: corrected p-value rounding in PlotScores

                        Changes in version 0.9.4                        

  - Minor bug fix: corrected p-value rounding in PlotScores

                        Changes in version 0.9.3                        

  - Updated documentation and internal code to meet Bioconductor
    submission guidelines.
  - Fixed minor bugs across multiple functions.
  - Added unit tests using testthat for all exported functions.
  - Reduced size of demo data to improve package loading time and final
    size.

                        Changes in version 0.9.2                        

  - Fixed broken links in README and vignettes
  - Added GitHub Actions workflows:
      - R-CMD-check
      - Matrix-based check for minimal supported R versions
  - Unified VariableAssociation() function by modularly integrating
    GSEA_VariableAssociation() and Score_VariableAssociation()
  - Added scripts to fully reproduce all analyses from the original
    markeR manuscript (inst/Paper)

                        Changes in version 0.9.1                        

  - Added package logo
  - Updated and simplified README file with concise installation
    instructions and main usage workflow
  - Creation of dedicated tutorials:
      - Benchmarking mode
      - Discovery mode
      - Gene set similarity
  - Improved function documentation
  - Minor bug fixes and internal cleanup
  - Published full codebase for reproducing analyses shown in markeR's
    paper

                        Changes in version 0.9.0                        

  - Initial release of the package.
  - Implementation of score-based and enrichment-based methods to
    evaluate gene signatures as phenotype markers.
  - Visualization of individual genes' expression, scores, and
    enrichment results
  - Add pkgdown documentation site:
    https://diseasetranscriptomicslab.github.io/markeR/