Longitudinal multi-omic study of treatment response and immune recovery in newly diagnosed multiple myeloma (NDMM).

• Cohort: FH1 NDMM patients sampled at Pre-Treatment, End Induction, and Post-Transplant (60d, 90d, 1y, 2y), with matched healthy donors and flu vaccination subcohorts.
• Tissue compartments: BMMC (bone marrow) and PBMC (peripheral blood).

2025-mm-project/
├── rna/                    # scRNA-seq analysis (Python + R)
├── flow/                   # Flow cytometry QC and composition analysis (R + Python)
├── olink/                  # Olink proteomics cleaning and analysis (R)
├── msd/                    # MSD cytokine assay data cleaning for Flu analyses (Python)
├── manuscript-figures/     # Publication-ready figure notebooks ordered by figure number
└── setup/                  # Environment setup files

Raw and processed data are stored in Zenodo and HISE and downloaded locally to ../../data/ (relative to each modality directory). See each modality README for file paths and download instructions.

• Longitudinal: Pre-Treatment → Post Induction 2 Cycles (PBMC only) → End Induction → Post-Transplant (60d, 90d, 1y, 2y)
• Cross-sectional: MM patients vs. Healthy donors
• Responder groups: Responders vs. Non-responders
• Flu response: Pre-flu → Day 0 → Day 7 → Day 90 (SA/Y1/Y2 series)

Each modality directory contains a README with environment setup, input/output documentation, and run order.

• RNA: rna/README.md and rna/00-utilities/README.md
• Flow: flow/README.md
• Olink: olink/README.md
• MSD: msd/README.md
• Figures: manuscript-figures/README.md