Added CAST to integrate multi slice

README.md

@@ -142,7 +142,7 @@ The table contains the tools have been published
   </tr>
 
   <tr>
-    <td align="center">COMPOSITE<br><a href="https://github.com/wanglab-broad/CAST">📦</a> <a href="https://www.nature.com/articles/s41592-024-02410-7">📖</a></td>
+    <td align="center">CAST<br><a href="https://github.com/wanglab-broad/CAST">📦</a> <a href="https://www.nature.com/articles/s41592-024-02410-7">📖</a></td>
   </tr>
 </table>
 </div>

omicverse/space/__init__.py

@@ -4,4 +4,5 @@
 from ._spaceflow import pySpaceFlow
 from ._spatrio import CellMap
 from ._stt import STT
-from ._svg import svg
+from ._svg import svg
+from ._cast import CAST

omicverse/space/_cast.py

@@ -15,7 +15,7 @@ def CAST(adata,sample_key=None,basis='spatial',layer='norm_1e4',
     # Get the coordinates and expression data for each sample
     samples = np.unique(adata.obs[sample_key]) # used samples in adata
     coords_raw = {sample_t: np.array(adata.obs[['x','y']])[adata.obs[sample_key] == sample_t] for sample_t in samples}
-    exp_dict = {sample_t: adata[adata.obs[sample_key] == sample_t].layers['norm_1e4'] for sample_t in samples}
+    exp_dict = {sample_t: adata[adata.obs[sample_key] == sample_t].layers[layer] for sample_t in samples}
 
 
     os.makedirs(output_path, exist_ok=True)

omicverse_guide/docs/Release_notes.md

@@ -491,4 +491,8 @@ Support Raw Windows platform
 
 ### Bulk Module
 
-- Fixed the error of log_init in gsea_obj.enrichment (#184)
+- Fixed the error of log_init in gsea_obj.enrichment (#184)
+
+### Space Module
+
+- Added CAST to integrate multi slice

pyproject.toml

@@ -54,7 +54,7 @@ dependencies = [
     'graphtools>=1.5',
     'phate>=1.0',
     'tqdm>=4.64',
-    'pydeseq2>=0.3',
+    'pydeseq2==0.4.1',
     'mofax>=0.3',
     'adjustText>=0.8',
     'scikit-misc>=0.1',
@@ -68,7 +68,7 @@ dependencies = [
     'plotly',
     'numba>=0.56',
     'tqdm',
-    'transformers',
+    'transformers>=0.30',
     #'cvxpy>=1.3',
 
 ]