added files

rsinghlab · Sep 26, 2024 · df2dd95 · df2dd95
1 parent df40220
commit df2dd95
Show file tree

Hide file tree

Showing 1,424 changed files with 177,771 additions and 1 deletion.
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,2 @@
+*.h5ad
+*.npy
diff --git a/Analysis.ipynb b/Analysis.ipynb
diff --git a/Analysis/.DS_Store b/Analysis/.DS_Store
diff --git a/Analysis/batch_corrected/.DS_Store b/Analysis/batch_corrected/.DS_Store
diff --git a/Analysis/batch_corrected/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/Stats.JSON b/Analysis/batch_corrected/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/Stats.JSON
@@ -0,0 +1,15 @@
+{
+    "Test": {
+        "Accuracy": "57.72%",
+        "Precision": "52.83%",
+        "Recall": "54.14%",
+        "F1": "53.37%",
+        "AUC": "80.10%"
+    },
+    "Baseline": {
+        "Accuracy": "33.58%",
+        "Precision": "8.39%",
+        "Recall": "25.00%",
+        "F1": "12.57%"
+    }
+}
diff --git a/...d/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/confusion_matrix.png b/...d/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/confusion_matrix.png
diff --git a/...orrected/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/roc_curve.png b/...orrected/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/roc_curve.png
diff --git a/...d/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/training_metrics.png b/...d/body/CNN/age/full_data/celltype_all/sextype_all/Analysis/training_metrics.png
diff --git a/...corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_30.png b/...corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_30.png
diff --git a/..._corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_5.png b/..._corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_5.png
diff --git a/...corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_50.png b/...corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_50.png
diff --git a/...corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_70.png b/...corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_70.png
diff --git a/...cted/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_Overall.png b/...cted/head/CNN/age/full_data/celltype_all/Analysis/SHAP/SHAP_Summary_Overall.png
diff --git a/Analysis/batch_corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/Stats.JSON b/Analysis/batch_corrected/head/CNN/age/full_data/celltype_all/Analysis/SHAP/Stats.JSON
@@ -0,0 +1,15 @@
+{
+    "Test": {
+        "Accuracy": "89.17%",
+        "Precision": "88.22%",
+        "Recall": "88.27%",
+        "F1": "88.24%",
+        "AUC": "98.35%"
+    },
+    "Baseline": {
+        "Accuracy": "33.78%",
+        "Precision": "8.44%",
+        "Recall": "25.00%",
+        "F1": "12.62%"
+    }
+}
diff --git a/Analysis/batch_corrected/head/CNN/age/full_data/celltype_all/Analysis/Stats.JSON b/Analysis/batch_corrected/head/CNN/age/full_data/celltype_all/Analysis/Stats.JSON
@@ -0,0 +1,15 @@
+{
+    "Test": {
+        "Accuracy": "89.17%",
+        "Precision": "88.22%",
+        "Recall": "88.27%",
+        "F1": "88.24%",
+        "AUC": "98.35%"
+    },
+    "Baseline": {
+        "Accuracy": "33.78%",
+        "Precision": "8.44%",
+        "Recall": "25.00%",
+        "F1": "12.62%"
+    }
+}
diff --git a/...tch_corrected/head/CNN/age/full_data/celltype_all/Analysis/confusion_matrix.png b/...tch_corrected/head/CNN/age/full_data/celltype_all/Analysis/confusion_matrix.png
diff --git a/...ysis/batch_corrected/head/CNN/age/full_data/celltype_all/Analysis/roc_curve.png b/...ysis/batch_corrected/head/CNN/age/full_data/celltype_all/Analysis/roc_curve.png
diff --git a/...tch_corrected/head/CNN/age/full_data/celltype_all/Analysis/training_metrics.png b/...tch_corrected/head/CNN/age/full_data/celltype_all/Analysis/training_metrics.png
diff --git a/Analysis/umaps/UMAP_after_correction.png b/Analysis/umaps/UMAP_after_correction.png
diff --git a/Analysis/umaps/UMAP_before_correction.png b/Analysis/umaps/UMAP_before_correction.png
diff --git a/Analysis/uncorrected/.DS_Store b/Analysis/uncorrected/.DS_Store
diff --git a/Analysis/uncorrected/all/CNN/age/full_data/celltype_all/sextype_all/Results/Stats.JSON b/Analysis/uncorrected/all/CNN/age/full_data/celltype_all/sextype_all/Results/Stats.JSON
@@ -0,0 +1,15 @@
+{
+    "Test": {
+        "Accuracy": "90.78%",
+        "Precision": "89.61%",
+        "Recall": "89.54%",
+        "F1": "89.56%",
+        "AUC": "98.61%"
+    },
+    "Baseline": {
+        "Accuracy": "33.77%",
+        "Precision": "8.44%",
+        "Recall": "25.00%",
+        "F1": "12.62%"
+    }
+}
diff --git a/...ted/all/CNN/age/full_data/celltype_all/sextype_all/Results/confusion_matrix.png b/...ted/all/CNN/age/full_data/celltype_all/sextype_all/Results/confusion_matrix.png