NEWS

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markeR 1.1.2

Minor Changes

• Moved Python bridge scripts from inst/python/ to a top-level python/ directory, as these are supplementary scripts not part of the R package itself.
• Added requirements.txt to the python/ directory listing all needed Python dependencies (rpy2, pandas, numpy, and optionally ipython and jupyter) for easier environment setup.
• Removed redundant code snippets from the Python bridge scripts.

markeR 1.1.1

• Added p.adjust.method parameter across all functions performing or depending on multiple testing correction, allowing users to specify any correction method supported by stats::p.adjust(), beyond the default Benjamini-Hochberg FDR.
• Added Python bridge scripts in inst/python/ for users who wish to call markeR from a Python environment via rpy2. Includes a tutorial workflow script and a generic command-line wrapper capable of invoking any exported markeR function. See inst/python/README.md for installation and usage.

markeR 1.0.0

• Official Bioconductor Release.

markeR 0.99.5

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

markeR 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.

markeR 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().

markeR 0.99.2

• Minor fixes in documentation

markeR 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

markeR 0.99.0

• First submission to Bioconductor

markeR 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

markeR 0.9.4

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

markeR 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.

markeR 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)

markeR 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

markeR 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/