NEWS
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.