add new feature

Author: hutaobo

README.md

@@ -7,6 +7,9 @@ Utilities for loading and analyzing 10x Genomics Xenium exports in Python.
 Install:
 
 ```bash
+# 稳定用法（本地开发/CI）
+pip install -U "git+https://github.com/hutaobo/pyXenium@main"
+# 或
 pip install pyXenium
 ```
 
@@ -56,6 +59,38 @@ adata = load_anndata_from_partial(
 )
 ```
 
+### Protein + RNA correlation (Xenium)
+
+Compute spatial correlation between **mean protein intensity** and **gene transcript density** on a user-defined grid.
+
+```python
+from pyXenium.io.partial_xenium_loader import load_anndata_from_partial
+from pyXenium.analysis import protein_gene_correlation
+
+# 1) Load data (RNA counts + optional cells/analysis attachments)
+BASE = "https://huggingface.co/datasets/<your-dataset>/resolve/main"
+adata = load_anndata_from_partial(
+    base_url=BASE,
+    # or base_dir="/path/to/Xenium_Export"
+    # If you also have analysis/cells zarr, pass them here to attach clusters & spatial centroids
+)
+
+# 2) Run protein–gene correlation
+#    transcripts_zarr_path 可为 .zarr 或 .zarr.zip（本地或远程，fsspec 透明读）
+pairs = [("CD3E", "CD3E"), ("E-Cadherin", "CDH1")]   # (protein, gene)
+summary = protein_gene_correlation(
+    adata=adata,
+    transcripts_zarr_path=BASE + "/transcripts.zarr.zip",
+    pairs=pairs,
+    output_dir="./protein_gene_corr",
+    grid_size=(50, 50),     # 可自定义网格
+    pixel_size_um=0.2125,   # Xenium 常见像素尺寸
+    qv_threshold=20,
+    overwrite=False
+)
+print(summary)
+```
+
 ### Troubleshooting
 - **FileNotFoundError: MEX missing files** → Ensure the three files exist in `cell_feature_matrix/`:
   `matrix.mtx.gz`, `features.tsv.gz`, `barcodes.tsv.gz`.

src/pyXenium/__init__.py

@@ -1,6 +1,12 @@
 from ._version import __version__
 from .io.partial_xenium_loader import load_anndata_from_partial
 from .io.xenium_gene_protein_loader import load_xenium_gene_protein
+from .analysis import protein_gene_correlation
 
 # src/pyXenium/__init__.py
-__all__ = []
+__all__ = [
+    "__version__",
+    "load_xenium_gene_protein",
+    "load_anndata_from_partial",
+    "protein_gene_correlation",
+]

src/pyXenium/analysis/__init__.py

@@ -0,0 +1,6 @@
+# 新增/补充
+from .protein_gene_correlation import protein_gene_correlation
+
+__all__ = [
+    "protein_gene_correlation",
+]