NEWS

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coMMpass 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.