NEWS

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SETA 0.99.6 (2025-09-29)

Dependency Changes

• Moved SingleCellExperiment from Suggests to Imports

SETA 0.99.5 (2025-09-19)

Bioconductor Preparation

• Updated package for Stefano's review
• Included direct access of SCE and Seurat objects with SetaCounts
• removed direct accessors from tests and mockup of these objects

SETA 0.99.3 (2025-09-15)

Bioconductor Preparation

• Updated package for Bioconductor review
• Added package-level documentation (?SETA)
• Bioconductor installation instructions
• Added proper error handling for optional dependencies
• Created NEWS file for change tracking

Documentation Improvements

• Added detailed motivation and comparison sections to introductory vignette
• Vignette descriptions with step-by-step explanations
• Added backticks for code formatting throughout vignettes
• Added BiocStyle dependency for proper vignette formatting

Package Structure

• Created R/SETA-package.R with roxygen2 documentation
• Added proper error handling for SeuratObject and SingleCellExperiment dependencies
• Updated DESCRIPTION with BiocStyle dependency
• package-level help with overview

SETA 0.99.1 (2025-08-26)

New Features

• Initial submission of SETA package for compositional analysis of single-cell RNA-seq data
• Added compositional transform functions (CLR, ALR, ILR, balance)
• Implemented latent space analysis methods (PCA, PCoA, NMDS)
• Created multi-resolution analysis capabilities with hierarchical taxonomies
• Added distance calculation functions for compositional data
• Included vignettes with educational content

Functions Added

• setaCounts(): Extract cell-type count matrices from single-cell objects
• setaTransform(): Apply various compositional transforms
• setaCLR(): Centered log-ratio transformation
• setaALR(): Additive log-ratio transformation
• setaILR(): Isometric log-ratio transformation
• setaBalance(): User-defined balance transformations
• setaPercent(): Percentage transformation
• setaLogCPM(): Log counts-per-million transformation
• setaLatent(): Dimensionality reduction methods
• setaDistances(): Calculate compositional distances
• setaTaxonomyDF(): Create hierarchical taxonomies
• taxonomy_to_tbl_graph(): Convert taxonomies to graph objects
• setaMetadata(): Extract sample-level metadata
• resolveGroup(): Resolve group specifications for balance transforms

Documentation

• Added package documentation
• Created three detailed vignettes:
  • Introductory vignette with basic workflow
  • Comparing samples vignette with statistical analysis
  • Reference frames vignette with multi-resolution analysis
• Added function-level documentation with examples
• Included mathematical foundations and references

Data

• Added mock data functions for testing and examples:
  • mockSeurat(): Mock Seurat object
  • mockSCE(): Mock SingleCellExperiment object
  • mockCount(): Mock count matrix
  • mockLong(): Mock long-form data frame

Dependencies

• Core dependencies: dplyr, MASS, Matrix, stats, tidygraph, rlang
• Suggested dependencies: BiocStyle, caret, corrplot, ggplot2, ggraph, knitr, methods, patchwork, reshape2, rmarkdown, SeuratObject, Seurat, SummarizedExperiment, SingleCellExperiment, TabulaMurisSenisData, tidyr, tidytext, testthat

Bioconductor Integration

• Prepared package for Bioconductor submission
• Added BiocStyle dependency for vignette formatting
• Updated README with Bioconductor installation instructions
• Created package-level documentation for ?SETA
• Added NEWS file for change tracking

Testing

• Test suite covering all major functions
• Tests for error handling and edge cases
• Validation of mathematical correctness for transforms
• Mock data testing for integration with single-cell objects