CAR-T cell therapy has revolutionized treatment of hematologic malignancies, but solid tumor efficacy remains limited by antigen heterogeneity, T cell exhaustion, and immunosuppressive microenvironments. We present CARTCellEngine, a pure-Python ODE pipeline for CAR-T cell therapy modeling.
Tumor immune evasion is a major barrier to immunotherapy. We present ImmuneEvasionEngine, a pure-Python pipeline for comprehensive tumor immune evasion analysis.
We present BulkDeconv, a complete bulk RNA-seq cell type deconvolution pipeline implemented entirely in Python using NumPy, SciPy, pandas, and matplotlib — no CIBERSORT, TIMER, EPIC, quanTIseq, or R required. BulkDeconv provides five analysis modules: (1) a built-in LM22-inspired signature matrix covering 22 immune cell types and 50 marker genes, (2) quantile normalization preprocessing, (3) Non-Negative Least Squares (NNLS) deconvolution with fraction normalization, (4) bootstrap confidence intervals (95% CI, n=100 resamples), and (5) per-cell-type quality metrics (Pearson r, Spearman r, RMSE).
Single-cell RNA sequencing has revolutionized our understanding of cancer biology and tumor microenvironment.