Changes in version 0.99.6 (2025-09-29)                 

Dependency Changes

  - Moved SingleCellExperiment from Suggests to Imports

                 Changes in version 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

                 Changes in version 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

                 Changes in version 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