Changes in version 0.1.0                        

  - Initial release of the MMRF CoMMpass data analysis pipeline.
  - GDC data acquisition for RNA-seq, clinical, and biospecimen data.
  - Cytogenetic marker extraction (t(4;14), del(17p), etc.).
  - Differential expression via DESeq2, edgeR, and limma with consensus
    analysis.
  - Paired-sample DE analysis with apeglm shrinkage.
  - Pathway enrichment: GSEA and ORA using local MSigDB gene sets
    (hallmark, KEGG).
  - Survival analysis: Kaplan-Meier and Cox regression with cytogenetic
    stratification.
  - Reproducible targets pipeline with crew parallelism.
  - Nix-based development environment for full reproducibility.
  - Shiny dashboard with QC, DE, survival, and pathway modules.