Shiny_dev

Shiny App - dev

Adds an interactive Shiny app to the package, launched with markeR::markeRapp() from the source code in the ShinyApp branch.

Also added a Dockerfile and GitHub Actions workflow to publish the app to Docker Hub (diseasetranscriptomicslab/marker), and exported markeRapp() so it can be called directly.

Development version

1.2

General

• Official Bioconductor Release 3.23

Full Changelog: v1.1.2...v1.2

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.

Full Changelog: v1.1.1...v1.1.2

1.1.1

Improvements

• 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.

Full Changelog: v1.0.0...v1.1.1

1.0.0

General

• Official Bioconductor Release

Full Changelog: v0.99.3...v1.0.0

0.99.5

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.

Full Changelog: v0.99.3...v0.99.5

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().

Full Changelog: v0.99.2...v0.99.3

0.99.2

• Minor fixes in documentation

Full Changelog: v0.99.1...v0.99.2

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

Full Changelog: v0.99.0...v0.99.1

0.99.0

0.99.0

• First submission to Bioconductor

Full Changelog: v0.9.5...v0.99.0