Fixed metacell

Drug digicash Burn Cable & Wireless SWS Small Pox red noise NORAD
Albright SURVIAC Resistant E911 Chemical fire analyzer Axis of Evil

benj/metacell.py

@@ -38,7 +38,7 @@ def _mc_prepare(adata, idx, neighbors_key:str=None):
         method = P.get("method", "umap")
         metric = P.get("metric", "euclidean")
         n_neighbors = P.get("n_neighbors", 15)
-        n_pcs = P.get("n_pcs", 50)
+        n_pcs = P.get("n_pcs", adata.obsm[rep].shape[1])
         sc.pp.neighbors(xdata, n_neighbors=n_neighbors,
                         n_pcs=n_pcs, use_rep=rep,
                         metric=metric, method=method)
@@ -98,3 +98,4 @@ def metacell(data, niter:int=100,
         out = pd.concat(out, axis=1)
         out.columns = list(range(out.shape[1]))
         return out
+

conda/chrombpnet.yml

@@ -0,0 +1,21 @@
+
+name: chrombpnet
+
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - conda-forge::python==3.8
+  - conda-forge::h5py>=2.10.0
+  - conda-forge::numpy==1.23.4
+  - conda-forge::cudatoolkit=11.2
+  - conda-forge::tensorflow==2.8.0=*cuda112py*
+  - bioconda::samtools
+  - bioconda::bedtools
+  - bioconda::ucsc-bedgraphtobigwig
+  - bioconda::pybigwig
+  - bioconda::meme
+  - conda-forge::pip
+  - pip:
+    - chrombpnet