popV version: 0.6.0

.gitattributes

@@ -35,3 +35,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
 OnClass.data-00000-of-00001 filter=lfs diff=lfs merge=lfs -text
 minified_ref_adata.h5ad filter=lfs diff=lfs merge=lfs -text
+faiss_index.index filter=lfs diff=lfs merge=lfs -text
+harmony_knn_classifier.index filter=lfs diff=lfs merge=lfs -text
+scvi_knn_classifier.index filter=lfs diff=lfs merge=lfs -text

OnClass.data-00000-of-00001

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OnClass.npz

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accuracies.json

@@ -1,4 +1,4 @@
 {
-    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| neutrophil | 3205 | 1.00 | 1.00 | 0.98 | 0.99 | 0.00 | 0.96 | 0.99 | 0.99 | 1.00 |\n| erythrocyte | 1174 | 1.00 | 1.00 | 0.99 | 1.00 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| classical monocyte | 1091 | 0.79 | 0.67 | 0.84 | 0.70 | 0.00 | 0.61 | 0.65 | 0.77 | 0.83 |\n| monocyte | 953 | 0.81 | 0.29 | 0.81 | 0.58 | 0.00 | 0.40 | 0.69 | 0.81 | 0.81 |\n| CD4-positive, alpha-beta T cell | 468 | 0.83 | 0.87 | 0.89 | 0.89 | 0.00 | 0.70 | 0.80 | 0.88 | 0.89 |\n| CD8-positive, alpha-beta T cell | 434 | 0.53 | 0.66 | 0.65 | 0.65 | 0.00 | 0.62 | 0.61 | 0.64 | 0.65 |\n| B cell | 390 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| natural killer cell | 321 | 0.69 | 0.64 | 0.59 | 0.59 | 0.00 | 0.67 | 0.63 | 0.68 | 0.70 |\n| macrophage | 117 | 0.47 | 0.43 | 0.46 | 0.39 | 0.00 | 0.37 | 0.28 | 0.40 | 0.52 |\n| intermediate monocyte | 90 | 0.45 | 0.00 | 0.60 | 0.15 | 0.00 | 0.20 | 0.41 | 0.48 | 0.62 |\n| plasma cell | 90 | 0.98 | 0.98 | 0.96 | 0.97 | 0.00 | 0.92 | 0.95 | 0.97 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 54 | 0.47 | 0.20 | 0.41 | 0.30 | 0.00 | 0.31 | 0.47 | 0.61 | 0.48 |\n| platelet | 46 | 0.97 | 0.96 | 0.93 | 0.99 | 0.00 | 0.80 | 0.98 | 0.96 | 0.98 |\n| non-classical monocyte | 43 | 0.71 | 0.72 | 0.72 | 0.31 | 0.00 | 0.82 | 0.73 | 0.78 | 0.80 |\n| mature NK T cell | 13 | 0.48 | 0.48 | 0.45 | 0.20 | 0.00 | 0.47 | 0.36 | 0.54 | 0.60 |\n| hematopoietic precursor cell | 10 | 0.69 | 0.55 | 0.67 | 0.70 | 0.00 | 0.64 | 0.62 | 0.64 | 0.82 |\n| hematopoietic stem cell | 7 | 0.00 | 0.22 | 0.57 | 0.40 | 0.00 | 0.71 | 0.73 | 0.22 | 0.60 |\n| basophil | 9 | 0.80 | 0.00 | 0.50 | 0.80 | 0.00 | 0.12 | 0.60 | 0.71 | 0.80 |\n| regulatory T cell | 6 | 0.00 | 0.00 | 0.25 | 0.00 | 0.00 | 0.30 | 0.25 | 0.50 | 0.29 |\n| plasmacytoid dendritic cell | 2 | 0.80 | 0.00 | 0.50 | 0.67 | 0.00 | 0.80 | 0.80 | 0.50 | 0.80 |\n| common myeloid progenitor | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
-    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| neutrophil | 28993 | 1.00 | 1.00 | 0.99 | 0.99 | 0.00 | 0.96 | 0.99 | 0.99 | 1.00 |\n| erythrocyte | 10374 | 1.00 | 0.99 | 1.00 | 1.00 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| classical monocyte | 9500 | 0.76 | 0.65 | 0.88 | 0.84 | 0.00 | 0.81 | 0.66 | 0.77 | 0.87 |\n| monocyte | 8649 | 0.80 | 0.25 | 0.88 | 0.85 | 0.00 | 0.82 | 0.71 | 0.80 | 0.88 |\n| CD4-positive, alpha-beta T cell | 4432 | 0.84 | 0.89 | 0.93 | 0.92 | 0.00 | 0.84 | 0.83 | 0.88 | 0.92 |\n| CD8-positive, alpha-beta T cell | 4138 | 0.55 | 0.66 | 0.79 | 0.78 | 0.00 | 0.66 | 0.66 | 0.69 | 0.72 |\n| B cell | 3503 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| natural killer cell | 2736 | 0.68 | 0.62 | 0.74 | 0.72 | 0.00 | 0.68 | 0.64 | 0.69 | 0.74 |\n| macrophage | 1111 | 0.49 | 0.45 | 0.62 | 0.60 | 0.00 | 0.48 | 0.41 | 0.52 | 0.64 |\n| intermediate monocyte | 946 | 0.47 | 0.00 | 0.72 | 0.54 | 0.00 | 0.56 | 0.49 | 0.56 | 0.71 |\n| plasma cell | 726 | 0.97 | 0.97 | 0.97 | 0.98 | 0.00 | 0.92 | 0.96 | 0.96 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 436 | 0.41 | 0.14 | 0.56 | 0.48 | 0.00 | 0.51 | 0.50 | 0.62 | 0.66 |\n| platelet | 392 | 0.96 | 0.96 | 0.96 | 0.99 | 0.00 | 0.76 | 0.98 | 0.97 | 0.98 |\n| non-classical monocyte | 310 | 0.74 | 0.76 | 0.85 | 0.53 | 0.00 | 0.80 | 0.73 | 0.77 | 0.88 |\n| mature NK T cell | 189 | 0.69 | 0.72 | 0.75 | 0.56 | 0.00 | 0.67 | 0.69 | 0.76 | 0.81 |\n| hematopoietic precursor cell | 121 | 0.69 | 0.63 | 0.82 | 0.83 | 0.00 | 0.88 | 0.80 | 0.95 | 0.95 |\n| hematopoietic stem cell | 57 | 0.00 | 0.38 | 0.69 | 0.67 | 0.00 | 0.89 | 0.95 | 0.97 | 0.95 |\n| basophil | 32 | 0.79 | 0.00 | 0.79 | 0.74 | 0.00 | 0.07 | 0.59 | 0.65 | 0.91 |\n| regulatory T cell | 34 | 0.00 | 0.00 | 0.66 | 0.24 | 0.00 | 0.32 | 0.83 | 0.73 | 0.73 |\n| plasmacytoid dendritic cell | 27 | 0.75 | 0.44 | 0.84 | 0.79 | 0.00 | 0.68 | 0.95 | 0.98 | 0.87 |\n| common myeloid progenitor | 3 | 0.00 | 0.00 | 0.00 | 0.40 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| neutrophil | 3209 | 1.00 | 1.00 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |\n| erythrocyte | 1162 | 1.00 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| classical monocyte | 1108 | 0.81 | 0.68 | 0.83 | 0.68 | 0.00 | 0.67 | 0.66 | 0.78 | 0.83 |\n| monocyte | 948 | 0.81 | 0.28 | 0.81 | 0.59 | 0.00 | 0.49 | 0.70 | 0.80 | 0.80 |\n| CD4-positive, alpha-beta T cell | 477 | 0.78 | 0.89 | 0.90 | 0.90 | 0.00 | 0.80 | 0.79 | 0.85 | 0.90 |\n| CD8-positive, alpha-beta T cell | 438 | 0.51 | 0.65 | 0.67 | 0.66 | 0.00 | 0.60 | 0.58 | 0.60 | 0.60 |\n| B cell | 380 | 0.98 | 0.98 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| natural killer cell | 309 | 0.69 | 0.62 | 0.63 | 0.54 | 0.00 | 0.65 | 0.59 | 0.66 | 0.65 |\n| macrophage | 124 | 0.50 | 0.48 | 0.45 | 0.49 | 0.00 | 0.48 | 0.33 | 0.43 | 0.49 |\n| intermediate monocyte | 91 | 0.50 | 0.00 | 0.64 | 0.11 | 0.00 | 0.26 | 0.36 | 0.47 | 0.62 |\n| plasma cell | 86 | 0.98 | 0.97 | 0.95 | 0.97 | 0.00 | 0.98 | 0.94 | 0.97 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 52 | 0.40 | 0.30 | 0.36 | 0.21 | 0.00 | 0.39 | 0.43 | 0.53 | 0.58 |\n| platelet | 46 | 0.98 | 0.95 | 0.90 | 1.00 | 0.00 | 0.74 | 0.93 | 0.94 | 0.98 |\n| non-classical monocyte | 47 | 0.71 | 0.72 | 0.78 | 0.53 | 0.00 | 0.41 | 0.75 | 0.77 | 0.78 |\n| mature NK T cell | 13 | 0.50 | 0.52 | 0.54 | 0.55 | 0.00 | 0.35 | 0.42 | 0.43 | 0.61 |\n| hematopoietic precursor cell | 11 | 0.74 | 0.73 | 0.60 | 0.67 | 0.00 | 0.64 | 0.70 | 0.64 | 0.78 |\n| hematopoietic stem cell | 7 | 0.00 | 0.60 | 0.62 | 0.40 | 0.00 | 0.47 | 0.57 | 0.36 | 0.55 |\n| basophil | 9 | 0.80 | 0.00 | 0.80 | 0.80 | 0.00 | 0.36 | 0.67 | 0.80 | 0.80 |\n| regulatory T cell | 5 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.14 | 0.25 | 0.73 | 0.00 |\n| plasmacytoid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.50 | 0.00 | 0.50 | 0.40 | 0.00 | 0.50 |\n| common myeloid progenitor | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| myeloid dendritic cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
+    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| neutrophil | 28989 | 1.00 | 1.00 | 0.98 | 0.99 | 0.00 | 0.97 | 0.99 | 0.99 | 1.00 |\n| erythrocyte | 10386 | 1.00 | 0.99 | 1.00 | 1.00 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| classical monocyte | 9483 | 0.78 | 0.66 | 0.85 | 0.74 | 0.00 | 0.82 | 0.67 | 0.78 | 0.86 |\n| monocyte | 8654 | 0.79 | 0.30 | 0.86 | 0.73 | 0.00 | 0.84 | 0.71 | 0.81 | 0.86 |\n| CD4-positive, alpha-beta T cell | 4423 | 0.79 | 0.90 | 0.91 | 0.91 | 0.00 | 0.87 | 0.82 | 0.87 | 0.92 |\n| CD8-positive, alpha-beta T cell | 4134 | 0.54 | 0.72 | 0.72 | 0.75 | 0.00 | 0.65 | 0.65 | 0.68 | 0.71 |\n| B cell | 3513 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 0.99 |\n| natural killer cell | 2748 | 0.69 | 0.67 | 0.69 | 0.68 | 0.00 | 0.70 | 0.66 | 0.69 | 0.74 |\n| macrophage | 1104 | 0.48 | 0.48 | 0.50 | 0.51 | 0.00 | 0.52 | 0.43 | 0.52 | 0.61 |\n| intermediate monocyte | 945 | 0.52 | 0.01 | 0.66 | 0.25 | 0.00 | 0.48 | 0.49 | 0.56 | 0.70 |\n| plasma cell | 730 | 0.99 | 0.97 | 0.96 | 0.98 | 0.00 | 0.97 | 0.95 | 0.96 | 0.99 |\n| naive thymus-derived CD4-positive, alpha-beta T cell | 438 | 0.36 | 0.30 | 0.40 | 0.33 | 0.00 | 0.58 | 0.48 | 0.59 | 0.65 |\n| platelet | 392 | 0.97 | 0.97 | 0.94 | 0.98 | 0.00 | 0.75 | 0.95 | 0.96 | 0.98 |\n| non-classical monocyte | 306 | 0.77 | 0.79 | 0.83 | 0.67 | 0.00 | 0.43 | 0.76 | 0.76 | 0.86 |\n| mature NK T cell | 189 | 0.67 | 0.76 | 0.75 | 0.72 | 0.00 | 0.60 | 0.69 | 0.78 | 0.82 |\n| hematopoietic precursor cell | 120 | 0.72 | 0.77 | 0.64 | 0.79 | 0.00 | 0.72 | 0.85 | 0.91 | 0.91 |\n| hematopoietic stem cell | 57 | 0.00 | 0.53 | 0.53 | 0.59 | 0.00 | 0.71 | 0.95 | 0.97 | 0.91 |\n| basophil | 32 | 0.79 | 0.00 | 0.77 | 0.72 | 0.00 | 0.22 | 0.70 | 0.75 | 0.91 |\n| regulatory T cell | 35 | 0.00 | 0.05 | 0.36 | 0.00 | 0.00 | 0.14 | 0.68 | 0.60 | 0.36 |\n| plasmacytoid dendritic cell | 28 | 0.70 | 0.77 | 0.80 | 0.75 | 0.00 | 0.81 | 0.90 | 0.93 | 0.91 |\n| common myeloid progenitor | 3 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.10 | 1.00 | 1.00 | 0.80 |\n| myeloid dendritic cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |"
 }

celltypist.pkl

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faiss_index.index

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harmony_knn_classifier.index

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+size 15341845

preprocessing.json

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         "ENSG00000004939",
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         "ENSG00000009724",
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