Changes in version 0.1.0                        

New features

  - importCustomAtlas() - universal import for any plant species
  - buildRosaAtlas() - curated Rosa chinensis atlas import
  - normalizeCounts() - CPM, TMM, DESeq2-VST normalization
  - buildAtlas() + plotAtlas() - expression atlas construction
  - plotPCA() - PCA visualization with botanical theme
  - runDE() - DESeq2-based differential expression analysis
  - plotVolcano() - publication-quality volcano plot
  - annotateGenes() + annotateDEResults() - Rosa chinensis annotation
  - getRosaAnnotation() - access 51,302-gene annotation database
  - ornTheme() - botanical ggplot2 theme

Built-in data

  - rosa_annotation - 51,302 Rosa chinensis gene annotations
    (RchiOBHm-V2)
  - rosa_example - 500 genes x 6 samples example dataset

First release

  - First Bioconductor package for ornamental plant transcriptomics
  - 270-sample Rosa chinensis expression atlas from 10+ NCBI BioProjects
  - Validated on Tagetes erecta (marigold) as second species
  - 0 errors, 0 warnings on R CMD check