stgp 0.1.0__py3-none-any.whl

stgp/README.md

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+# stGP: Characterizing dynamic tissue architectures by identifying cell-type-specific spatiotemporal gene programs
+
+## Introduction
+
+stGP is a statistical framework for identifying interpretable cell-type-specific spatiotemporal gene programs (stGPs) from multi-sample spatiotemporal transcriptomic data measured across biological time by deciphering temporal trajectory and dynamic spatial patterns.
+
+stGP's effectiveness relies on our innovations in the integration of Gaussian process priors and interpretable matrix factorization:
+
+- stGP represents gene expression within each cell type as a small set of latent programs with non-negative gene loadings, making each program interpretable as a weighted gene set shared across samples. Variance components quantify the relative contributions of time and space to each program.
+- stGP decomposes per-cell program activity into a sample-level temporal component that captures coordinated responses over biological time (e.g., age or stage), and a within-section spatial component that characterizes dynamic program deployment across tissue coordinates without requiring cross-section registration.
+- For multi-program inference, stGP adopts a blockwise backfitting scheme that sequentially extracts rank-1 components from residuals, with automatic model selection to determine the number of programs.
+
+
+## Reference
+
+If you find `stGP` useful for your work, please cite:
+> Characterizing dynamic tissue architectures by identifying cell-type-specific spatiotemporal gene programs with stGP.
+> Baichen Yu, Ziyue Tan, Xiaomeng Wan, Hansheng Wang, and Can Yang.
+> Working paper, 2026.
+
+## Development
+
+The software is developed and maintained by [Baichen Yu](mailto:mabyu@ust.hk).
+
+## Contact
+
+Please feel free to contact [Baichen Yu](mailto:mabyu@ust.hk) or [Prof. Can Yang](mailto:macyang@ust.hk) if any inquiries.

stgp/__init__.py

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+from stgp.estimation import (
+    fit_rank1,
+    fit_pfactor,
+    fit_pfactor_auto,
+    project_simplex,
+    project_simplex_topk,
+    recover_low_rank_signal,
+    align_programs_and_mse,
+)
+
+from stgp.kernels import (
+    build_K_age,
+    build_K_spa,
+    build_K_spa_list,
+    build_K_spa_list_from_stacked,
+    rbf_kernel_1d,
+    ar1_kernel_1d,
+)
+
+from stgp.preprocessing import (
+    log1p_normalize,
+    log1p_norm_centered_list,
+    demean_genes,
+    library_normalize,
+)
+
+__version__ = "0.1.0"
+
+__all__ = [
+    "__version__",
+    "fit_rank1",
+    "fit_pfactor",
+    "fit_pfactor_auto",
+    "project_simplex",
+    "project_simplex_topk",
+    "recover_low_rank_signal",
+    "align_programs_and_mse",
+    "build_K_age",
+    "build_K_spa",
+    "build_K_spa_list",
+    "build_K_spa_list_from_stacked",
+    "rbf_kernel_1d",
+    "ar1_kernel_1d",
+    "log1p_normalize",
+    "log1p_norm_centered_list",
+    "demean_genes",
+    "library_normalize",
+]