v0.99.2

New features

• enrichment_CTD() now supports four enrichment methods through a unified
  interface, selectable via the method argument:
  • "ORA" (default) — Over-Representation Analysis via
    clusterProfiler::enricher() (unchanged).
  • "GSEA" — rank-based Gene Set Enrichment Analysis via fgsea::fgsea()
    (unchanged).
  • "CAMERA" — competitive gene-set test accounting for inter-gene
    correlation, via limma::camera(). Input: a numeric expression matrix
    (genes x samples) plus a design matrix and a contrast.
  • "GSVA" — per-sample Gene Set Variation Analysis via GSVA::gsva(),
    returning a chemical x sample score matrix.
• New first argument x (polymorphic): a data frame for ORA/GSEA, a numeric
  matrix for CAMERA/GSVA. Auto-detects identifier type (Entrez vs HGNC SYMBOL)
  from rownames(x); an explicit id_type override is also accepted.
• plot_CTD() now dispatches on input class and method-specific columns:
  bar/dot plots of fold enrichment for ORA/GSEA, bar/dot plots of
  -log10(padj) coloured by direction of enrichment for CAMERA, and a
  sample-level heatmap of the top-variance chemicals for GSVA.

Deprecation

• The first argument of enrichment_CTD() was renamed entrez_ids -> x.
  Calls using the old name still work but emit a deprecation warning and will
  be removed in a future release.

Dependencies

• New Imports: limma, GSVA, stats.