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1. windowCNV windowCNV Public

   A window-based refinement of inferCNV for more accurate CNV detection from single-cell RNA-seq data, featuring customizable smoothing, cell type annotations, and event-level evaluation tools.

   Jupyter Notebook

2. cross-species-immune-transfer-learning cross-species-immune-transfer-learning Public

   Transfer learning framework (CoGAPS + projectR) quantifying cross-species conservation of tumor microenvironment transcriptional programs between mouse models and human melanoma, with immunotherapy…

   Jupyter Notebook

3. melatonin-pbpkpd-model melatonin-pbpkpd-model Public

   Physiologically based pharmacokinetic-pharmacodynamic (PBPK/PD) model of oral melatonin with circadian oscillator coupling, virtual population simulation, and interactive Shiny app for personalized…

   MATLAB

4. danielchen05/scRNA-cross-donor-generalization danielchen05/scRNA-cross-donor-generalization Public

   scRNA-seq cell type classification benchmark showing that random cell-level splits inflate performance due to donor-level leakage

   Jupyter Notebook 1