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markeR 1.1.2 (12 Mar, 2026)

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 (11 Mar, 2026)

  • 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 (31 Oct, 2025)

  • Official Bioconductor Release.

markeR 0.99.5 (17 Sep, 2025)

  • 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.

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 (23 Jul, 2025)

  • Minor fixes in documentation

markeR 0.99.1 (23 Jul, 2025)

  • 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
  • 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 (20 Jun, 2025)

  • 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 (21 Apr, 2025)

  • 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/