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1. project-1-rnaseq-pipeline project-1-rnaseq-pipeline Public

   Bulk RNA-seq differential expression pipeline (STAR → DESeq2 → GSEA). Snakemake + Docker. POC: ER+/ER− DE on Van't Veer 2002 — 34 probes at BH padj<0.05, ER signature AUC 0.868.

   R

2. project-2-scrnaseq-analysis project-2-scrnaseq-analysis Public

   Single-cell RNA-seq analysis workflow (Seurat + Scanpy). QC → HVG → PCA → UMAP → Leiden → marker annotation. POC: 10x PBMC 3k — 2,643 cells post-QC, 7 Leiden clusters mapped to canonical T/B/Monocy…

   Python

3. project-3-ml-classification project-3-ml-classification Public

   Genomic classification ML pipeline (Logistic Regression, Random Forest, Gradient Boosting, SHAP, PyTorch). POC: GDSC Olaparib sensitivity — RandomForest 5-fold CV AUC 0.711 on 704-feature full geno…

   Python

4. project-4-ddr-biomarker-pipeline project-4-ddr-biomarker-pipeline Public

   DDR biomarker and PARP/ATR inhibitor response pipeline. Full GDSC v17 mutations + CNV + MSI + tissue context. POC: Talazoparib HRD Spearman ρ=+0.12 (p=3e-4, n=912); per-drug CV AUC 0.68–0.77.

   Python

5. project-5-phenomics-profiling project-5-phenomics-profiling Public

   Phenomics perturbation profiling and MoA retrieval from morphological cell-painting profiles (UMAP + HDBSCAN + cosine similarity). POC: LINCS Cell Painting — recall@5 = 3.0× random baseline on 111 …

   Python

6. project-6-gea-survival-pipeline project-6-gea-survival-pipeline Public

   GEA survival risk stratifier (Cox PH + Kaplan-Meier). Snakemake + DuckDB feature store + Streamlit patient risk calculator. POC: GBSG2 breast cancer trial — 5-fold CV C-index 0.682 (matches Schumac…

   Python