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Browse files- OnClass.data-00000-of-00001 +1 -1
- OnClass.index +0 -0
- OnClass.meta +0 -0
- OnClass.npz +2 -2
- accuracies.json +2 -2
- celltypist.pkl +1 -1
- harmony_knn_classifier.joblib +2 -2
- popv_output/predictions.csv +0 -0
- preprocessing.json +11 -11
- pynndescent_index.joblib +2 -2
- scanvi/model.pt +1 -1
- scvi/model.pt +1 -1
- scvi_knn_classifier.joblib +2 -2
- svm_classifier.joblib +3 -0
- svm_classifier_cuml.joblib +1 -1
- xgboost_classifier.model +2 -2
OnClass.data-00000-of-00001
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OnClass.index
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OnClass.meta
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OnClass.npz
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accuracies.json
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{
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"query_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| pancreatic acinar cell |
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"ref_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| pancreatic acinar cell |
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}
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{
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"query_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| pancreatic acinar cell | 545 | 0.97 | 0.96 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.98 | 0.98 |\n| pancreatic ductal cell | 271 | 0.94 | 0.93 | 0.96 | 0.95 | 0.00 | 0.96 | 0.97 | 0.96 | 0.97 |\n| endothelial cell | 239 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.99 | 1.00 |\n| macrophage | 163 | 0.94 | 0.88 | 0.93 | 0.93 | 0.00 | 0.90 | 0.95 | 0.93 | 0.95 |\n| CD8-positive, alpha-beta T cell | 59 | 0.98 | 0.96 | 0.98 | 0.95 | 0.00 | 0.97 | 0.98 | 0.98 | 0.98 |\n| pancreatic stellate cell | 42 | 0.96 | 0.95 | 0.98 | 0.96 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |\n| classical monocyte | 38 | 0.76 | 0.00 | 0.75 | 0.78 | 0.00 | 0.83 | 0.83 | 0.80 | 0.80 |\n| fibroblast | 17 | 0.97 | 1.00 | 0.97 | 0.97 | 0.00 | 1.00 | 1.00 | 0.94 | 1.00 |\n| type B pancreatic cell | 14 | 1.00 | 0.96 | 1.00 | 0.93 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| B cell | 2 | 1.00 | 1.00 | 0.80 | 0.80 | 0.00 | 0.80 | 1.00 | 0.80 | 1.00 |\n| natural killer cell | 4 | 0.89 | 0.86 | 1.00 | 1.00 | 0.00 | 0.80 | 1.00 | 1.00 | 1.00 |\n| pancreatic A cell | 7 | 1.00 | 0.44 | 0.92 | 0.83 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| intermediate monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| CD4-positive, alpha-beta T cell | 4 | 0.00 | 0.00 | 0.00 | 0.33 | 0.00 | 0.55 | 0.40 | 0.40 | 0.00 |\n| monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| plasma cell | 3 | 0.86 | 1.00 | 1.00 | 0.86 | 0.00 | 0.86 | 1.00 | 1.00 | 1.00 |\n| pancreatic D cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| neutrophil | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 0.00 | 0.00 | 0.00 |\n| mature NK T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| mast cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| pancreatic PP cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| T cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| non-classical monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
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"ref_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| pancreatic acinar cell | 4937 | 0.97 | 0.87 | 0.98 | 0.99 | 0.00 | 0.98 | 0.98 | 0.98 | 0.99 |\n| pancreatic ductal cell | 2449 | 0.95 | 0.80 | 0.97 | 0.97 | 0.00 | 0.96 | 0.97 | 0.97 | 0.97 |\n| endothelial cell | 2084 | 0.99 | 0.99 | 1.00 | 1.00 | 0.00 | 0.99 | 1.00 | 1.00 | 1.00 |\n| macrophage | 1426 | 0.93 | 0.87 | 0.95 | 0.94 | 0.00 | 0.92 | 0.96 | 0.96 | 0.96 |\n| CD8-positive, alpha-beta T cell | 559 | 0.97 | 0.95 | 0.98 | 0.96 | 0.00 | 0.98 | 1.00 | 1.00 | 0.99 |\n| pancreatic stellate cell | 395 | 0.96 | 0.93 | 0.98 | 0.98 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| classical monocyte | 352 | 0.80 | 0.00 | 0.86 | 0.80 | 0.00 | 0.88 | 0.90 | 0.90 | 0.89 |\n| fibroblast | 177 | 0.94 | 0.93 | 0.97 | 0.97 | 0.00 | 1.00 | 0.99 | 0.99 | 0.99 |\n| type B pancreatic cell | 88 | 0.94 | 0.49 | 0.96 | 0.91 | 0.00 | 0.97 | 1.00 | 1.00 | 0.99 |\n| B cell | 51 | 0.97 | 0.99 | 0.95 | 0.95 | 0.00 | 0.97 | 0.99 | 0.95 | 1.00 |\n| natural killer cell | 46 | 0.92 | 0.69 | 0.94 | 0.73 | 0.00 | 0.98 | 1.00 | 1.00 | 0.99 |\n| pancreatic A cell | 41 | 0.93 | 0.00 | 0.94 | 0.83 | 0.00 | 0.99 | 1.00 | 1.00 | 0.96 |\n| intermediate monocyte | 42 | 0.00 | 0.00 | 0.34 | 0.16 | 0.00 | 0.46 | 0.82 | 0.91 | 0.85 |\n| CD4-positive, alpha-beta T cell | 33 | 0.00 | 0.00 | 0.52 | 0.34 | 0.00 | 0.70 | 1.00 | 0.99 | 0.73 |\n| monocyte | 13 | 0.00 | 0.00 | 0.12 | 0.35 | 0.00 | 0.46 | 0.93 | 0.96 | 0.35 |\n| plasma cell | 10 | 0.53 | 0.50 | 0.95 | 0.89 | 0.00 | 0.80 | 1.00 | 1.00 | 0.95 |\n| pancreatic D cell | 9 | 0.00 | 0.00 | 0.43 | 0.33 | 0.00 | 0.94 | 1.00 | 1.00 | 0.88 |\n| neutrophil | 6 | 0.00 | 0.00 | 0.80 | 0.00 | 0.00 | 0.92 | 1.00 | 1.00 | 1.00 |\n| mature NK T cell | 2 | 0.00 | 0.00 | 0.50 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| mast cell | 2 | 0.00 | 0.00 | 0.00 | 0.67 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |\n| pancreatic PP cell | 2 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.44 | 1.00 | 1.00 | 0.67 |\n| T cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.50 | 1.00 | 1.00 | 1.00 |\n| non-classical monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.12 | 1.00 | 1.00 | 0.00 |"
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celltypist.pkl
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harmony_knn_classifier.joblib
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popv_output/predictions.csv
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preprocessing.json
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"ENSG00000144847",
|
| 1847 |
"ENSG00000144857",
|
| 1848 |
"ENSG00000144868",
|
|
|
|
| 1969 |
"ENSG00000149257",
|
| 1970 |
"ENSG00000149260",
|
| 1971 |
"ENSG00000149294",
|
| 1972 |
+
"ENSG00000149428",
|
| 1973 |
"ENSG00000149554",
|
| 1974 |
"ENSG00000149564",
|
| 1975 |
"ENSG00000149573",
|
|
|
|
| 2211 |
"ENSG00000157554",
|
| 2212 |
"ENSG00000157557",
|
| 2213 |
"ENSG00000157570",
|
| 2214 |
+
"ENSG00000157601",
|
| 2215 |
"ENSG00000157613",
|
| 2216 |
"ENSG00000157654",
|
| 2217 |
"ENSG00000157657",
|
|
|
|
| 2414 |
"ENSG00000163581",
|
| 2415 |
"ENSG00000163584",
|
| 2416 |
"ENSG00000163590",
|
|
|
|
| 2417 |
"ENSG00000163618",
|
| 2418 |
"ENSG00000163623",
|
| 2419 |
"ENSG00000163624",
|
|
|
|
| 2518 |
"ENSG00000164938",
|
| 2519 |
"ENSG00000164946",
|
| 2520 |
"ENSG00000164949",
|
|
|
|
| 2521 |
"ENSG00000165025",
|
| 2522 |
"ENSG00000165029",
|
| 2523 |
"ENSG00000165030",
|
|
|
|
| 2652 |
"ENSG00000167680",
|
| 2653 |
"ENSG00000167703",
|
| 2654 |
"ENSG00000167711",
|
|
|
|
| 2655 |
"ENSG00000167747",
|
| 2656 |
"ENSG00000167748",
|
| 2657 |
"ENSG00000167757",
|
|
|
|
| 3036 |
"ENSG00000177679",
|
| 3037 |
"ENSG00000177694",
|
| 3038 |
"ENSG00000177706",
|
|
|
|
| 3039 |
"ENSG00000177885",
|
| 3040 |
"ENSG00000177990",
|
| 3041 |
"ENSG00000178031",
|
|
|
|
| 3186 |
"ENSG00000183742",
|
| 3187 |
"ENSG00000183775",
|
| 3188 |
"ENSG00000183778",
|
|
|
|
| 3189 |
"ENSG00000183780",
|
| 3190 |
"ENSG00000183783",
|
| 3191 |
"ENSG00000183807",
|
|
|
|
| 3502 |
"ENSG00000198502",
|
| 3503 |
"ENSG00000198515",
|
| 3504 |
"ENSG00000198554",
|
| 3505 |
+
"ENSG00000198597",
|
| 3506 |
"ENSG00000198626",
|
| 3507 |
"ENSG00000198673",
|
| 3508 |
"ENSG00000198682",
|
|
|
|
| 3569 |
"ENSG00000204764",
|
| 3570 |
"ENSG00000205038",
|
| 3571 |
"ENSG00000205045",
|
| 3572 |
+
"ENSG00000205189",
|
| 3573 |
"ENSG00000205209",
|
| 3574 |
"ENSG00000205213",
|
| 3575 |
"ENSG00000205221",
|
|
|
|
| 3800 |
"ENSG00000240038",
|
| 3801 |
"ENSG00000240057",
|
| 3802 |
"ENSG00000240583",
|
|
|
|
| 3803 |
"ENSG00000240972",
|
| 3804 |
"ENSG00000241316",
|
| 3805 |
"ENSG00000241343",
|
|
|
|
| 3967 |
"ENSG00000267519",
|
| 3968 |
"ENSG00000267534",
|
| 3969 |
"ENSG00000267586",
|
| 3970 |
+
"ENSG00000267659",
|
| 3971 |
"ENSG00000267795",
|
| 3972 |
"ENSG00000267871",
|
| 3973 |
"ENSG00000268751",
|
|
|
|
| 3988 |
"ENSG00000272894",
|
| 3989 |
"ENSG00000273247",
|
| 3990 |
"ENSG00000274070",
|
| 3991 |
+
"ENSG00000274736",
|
| 3992 |
"ENSG00000275302",
|
| 3993 |
"ENSG00000275395",
|
| 3994 |
"ENSG00000276043",
|
pynndescent_index.joblib
CHANGED
|
@@ -1,3 +1,3 @@
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
-
oid sha256:
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size
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| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:cc518e69118aeaef950005e0a7f99b9d392f6add0c54488dea71049026ad3903
|
| 3 |
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size 10238623
|
scanvi/model.pt
CHANGED
|
@@ -1,3 +1,3 @@
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
-
oid sha256:
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| 3 |
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| 1 |
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| 3 |
size 11453868
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scvi/model.pt
CHANGED
|
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
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| 3 |
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| 1 |
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scvi_knn_classifier.joblib
CHANGED
|
@@ -1,3 +1,3 @@
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:
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svm_classifier.joblib
ADDED
|
@@ -0,0 +1,3 @@
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|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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|
svm_classifier_cuml.joblib
CHANGED
|
@@ -1,3 +1,3 @@
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
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size 393547
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| 1 |
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|
xgboost_classifier.model
CHANGED
|
@@ -1,3 +1,3 @@
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
-
oid sha256:
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| 3 |
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size
|
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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+
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