NEWS

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OrnTx 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