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().