Minor fix in .onAttach() to avoid errors when checking ggplot2 version and ensure the startup warning works correctly.
markeR 0.99.4 (17 Sep, 2025)
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.
markeR 0.99.3 (21 Aug, 2025)
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.
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
markeR 0.99.0 (18 Jul, 2025)
First submission to Bioconductor
markeR 0.9.5 (18 Jul, 2025)
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
markeR 0.9.4 (09 Jul, 2025)
Minor bug fix: corrected p-value rounding in PlotScores
markeR 0.9.3 (03 Jul, 2025)
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.
markeR 0.9.2 (25 Jun, 2025)
Fixed broken links in README and vignettes
Added GitHub Actions workflows:
R-CMD-check
Matrix-based check for minimal supported R versions