add lisi score calculation and annotations

Noble-Lab · Dec 2, 2024 · 3e3a517 · 3e3a517
1 parent 2d0f203
commit 3e3a517
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diff --git a/bin/run.sh b/bin/run.sh
@@ -1,14 +1,12 @@
 #!/bin/bash
-#
-#conda activate tf_gpu
 
 input_h5ad=../data/example.h5ad
 outdir=./
 
 ## train the model
 for learning_rate in 0.001 0.0001
 do
-	python ./run_pred.py --input_h5ad $input_h5ad --outdir $outdir --train train --predict embedding --learning_rate $learning_rate 
-	python ./run_pred.py --input_h5ad $input_h5ad --outdir $outdir --train train --predict embedding --learning_rate $learning_rate --dis dis
+	python ./run_pred.py --input_h5ad $input_h5ad --outdir $outdir --train train --predict embedding --learning_rate $learning_rate --group celltype
+	python ./run_pred.py --input_h5ad $input_h5ad --outdir $outdir --train train --predict embedding --learning_rate $learning_rate --group celltype --dis dis
 done