NEWS

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scCertify 0.99.7

Changes in response to Bioconductor review

New features

• Added support for both Seurat and SingleCellExperiment objects across the package.
• Expanded unit test coverage for exported functions.
• Added package-level documentation (?scCertify).
• Added executable examples for exported functions.
• Expanded the vignette with an introduction, workflow overview, methodology, and interpretation of confidence scores.
• Improved compatibility with Bioconductor documentation standards.
• Updated README installation instructions.
• Improved documentation throughout the package.

Bug fixes

• Improved handling of metadata for both supported object classes.
• Improved dimensionality reduction handling for SingleCellExperiment objects.
• Improved marker score computation for SingleCellExperiment inputs.
• Improved neighborhood agreement compatibility across supported object types.
• Improved runnable examples in package documentation.
• Updated vignette formatting and chunk labels.
• Addressed Bioconductor documentation review feedback.

Documentation

• Updated function documentation for Seurat and SingleCellExperiment compatibility.
• Added additional usage examples.
• Revised vignette formatting using BiocStyle.