Changes in version 0.99.0                        

New features

  - Initial release submitted to Bioconductor.

  - compoundDE(): main function that decomposes pseudo-bulk DE signals
    into transcriptional and compositional components. Automatically
    detects paired vs unpaired designs. Returns a CDEResult S4 object.

  - filterGenesBySource(): convenience function to extract
    transcriptional, compositional, or mixed gene lists from a
    CDEResult, with optional FDR filtering.

  - plotDecomposition(): scatter plot of z-scored transcriptional (T) vs
    compositional (C) scores for all tested genes, coloured by source
    classification.

  - plotProportion(): stacked bar chart of mean subtype proportions per
    condition with individual sample points overlaid.

  - plotTCRatio(): histogram of TC_ratio values with classification
    threshold lines.

  - CDEResult S4 class with slots for deTable, subtypeProportions,
    subtypeDE, and params. Accessor methods: deTable(),
    subtypeProportions(), subtypeDE(), tcRatio().