NEWS
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/