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popV
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tabula_sapiens_Testis

Joblib
popV
biology
genomics
single-cell
AnnData:0.12.2
scikit_learn:1.7.2
organism:Homo sapiens
Python:3.12.8
popV:0.6.0
tissue: Testis
Model card Files
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Community
canergen commited on
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1 Parent(s): b4a3bbe

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Files changed (15) hide show
  1. OnClass.data-00000-of-00001 +1 -1
  2. OnClass.index +0 -0
  3. OnClass.meta +0 -0
  4. OnClass.npz +2 -2
  5. accuracies.json +2 -2
  6. celltypist.pkl +1 -1
  7. harmony_knn_classifier.joblib +2 -2
  8. popv_output/predictions.csv +0 -0
  9. preprocessing.json +22 -22
  10. pynndescent_index.joblib +2 -2
  11. scanvi/model.pt +2 -2
  12. scvi/model.pt +1 -1
  13. scvi_knn_classifier.joblib +2 -2
  14. svm_classifier_cuml.joblib +1 -1
  15. xgboost_classifier.model +2 -2
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accuracies.json CHANGED
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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| spermatid | 405 | 0.99 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| spermatocyte | 299 | 0.98 | 0.98 | 0.98 | 0.99 | 0.00 | 0.96 | 0.99 | 0.97 | 0.99 |\n| male germ cell | 12 | 1.00 | 1.00 | 1.00 | 0.96 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| peritubular myoid cell | 11 | 0.80 | 0.91 | 0.82 | 0.74 | 0.00 | 0.83 | 0.87 | 0.92 | 0.91 |\n| spermatogonium | 7 | 0.93 | 0.93 | 0.93 | 0.93 | 0.00 | 0.88 | 0.93 | 0.88 | 0.93 |\n| stromal cell | 6 | 0.86 | 0.60 | 0.80 | 0.67 | 0.00 | 0.86 | 0.77 | 0.92 | 0.86 |\n| tissue-resident macrophage | 4 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.86 | 1.00 | 1.00 | 1.00 |\n| endothelial cell | 7 | 0.83 | 0.92 | 0.92 | 0.92 | 0.00 | 0.92 | 0.92 | 0.92 | 0.92 |\n| Leydig cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| CD8-positive, alpha-beta T cell | 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 | 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| macrophage | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| B cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| monocyte | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |",
3
- "ref_accuracy": "| Cell Type | N cells | celltypist | knn bbknn | knn harmony | knn on scvi | onclass | scanvi | svm | xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| spermatid | 3604 | 0.98 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| spermatocyte | 2771 | 0.97 | 0.98 | 0.99 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |\n| male germ cell | 104 | 0.97 | 0.99 | 0.99 | 0.97 | 0.00 | 0.98 | 1.00 | 1.00 | 1.00 |\n| peritubular myoid cell | 56 | 0.75 | 0.76 | 0.87 | 0.73 | 0.00 | 0.91 | 0.99 | 0.98 | 0.95 |\n| spermatogonium | 57 | 0.86 | 0.85 | 0.92 | 0.89 | 0.00 | 0.83 | 0.91 | 0.87 | 0.93 |\n| stromal cell | 55 | 0.81 | 0.65 | 0.87 | 0.80 | 0.00 | 0.96 | 0.99 | 1.00 | 0.93 |\n| tissue-resident macrophage | 50 | 0.91 | 0.93 | 0.97 | 0.96 | 0.00 | 0.99 | 1.00 | 1.00 | 0.99 |\n| endothelial cell | 46 | 1.00 | 1.00 | 1.00 | 0.95 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| Leydig cell | 9 | 0.00 | 0.11 | 0.33 | 0.38 | 0.00 | 0.94 | 1.00 | 1.00 | 0.71 |\n| CD8-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.50 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |\n| CD4-positive, alpha-beta T cell | 2 | 0.00 | 0.50 | 0.57 | 0.40 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |\n| mast cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| macrophage | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| B cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |"
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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| spermatid | 406 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| spermatocyte | 298 | 0.96 | 0.97 | 0.99 | 0.98 | 0.00 | 0.96 | 0.98 | 0.98 | 0.98 |\n| male germ cell | 11 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 0.88 | 1.00 | 1.00 | 1.00 |\n| peritubular myoid cell | 11 | 0.83 | 0.83 | 0.91 | 0.73 | 0.00 | 0.70 | 0.87 | 0.96 | 0.87 |\n| spermatogonium | 7 | 0.88 | 0.93 | 0.93 | 0.86 | 0.00 | 0.70 | 0.93 | 1.00 | 0.93 |\n| stromal cell | 6 | 0.86 | 0.60 | 0.86 | 0.71 | 0.00 | 0.67 | 0.77 | 0.92 | 0.86 |\n| tissue-resident macrophage | 5 | 1.00 | 1.00 | 1.00 | 0.89 | 0.00 | 1.00 | 1.00 | 0.89 | 1.00 |\n| endothelial cell | 7 | 0.83 | 0.92 | 0.92 | 0.77 | 0.00 | 0.92 | 0.92 | 0.92 | 0.92 |\n| Leydig cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| CD8-positive, alpha-beta T cell | 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 | 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| macrophage | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| B cell | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |\n| 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| spermatid | 3603 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.99 | 0.99 |\n| spermatocyte | 2772 | 0.97 | 0.98 | 0.99 | 0.98 | 0.00 | 0.97 | 0.98 | 0.98 | 0.99 |\n| male germ cell | 105 | 0.98 | 0.98 | 0.99 | 0.97 | 0.00 | 0.91 | 1.00 | 1.00 | 1.00 |\n| peritubular myoid cell | 56 | 0.76 | 0.83 | 0.88 | 0.77 | 0.00 | 0.96 | 0.99 | 1.00 | 0.95 |\n| spermatogonium | 57 | 0.85 | 0.86 | 0.92 | 0.85 | 0.00 | 0.71 | 0.93 | 0.88 | 0.94 |\n| stromal cell | 55 | 0.81 | 0.71 | 0.82 | 0.77 | 0.00 | 0.98 | 1.00 | 1.00 | 0.92 |\n| tissue-resident macrophage | 49 | 0.91 | 0.97 | 0.98 | 0.88 | 0.00 | 1.00 | 1.00 | 0.99 | 0.99 |\n| endothelial cell | 46 | 1.00 | 1.00 | 1.00 | 0.85 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| Leydig cell | 9 | 0.00 | 0.14 | 0.00 | 0.14 | 0.00 | 0.95 | 1.00 | 1.00 | 0.50 |\n| CD8-positive, alpha-beta T cell | 3 | 0.00 | 0.00 | 0.50 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| CD4-positive, alpha-beta T cell | 2 | 0.00 | 0.57 | 0.50 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| mast cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| macrophage | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| B cell | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| monocyte | 1 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |"
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3656
  "ENSG00000231889",
3657
  "ENSG00000232040",
@@ -3687,6 +3688,7 @@
3687
  "ENSG00000234665",
3688
  "ENSG00000234707",
3689
  "ENSG00000234715",
 
3690
  "ENSG00000234745",
3691
  "ENSG00000234776",
3692
  "ENSG00000234840",
@@ -3706,6 +3708,7 @@
3706
  "ENSG00000236107",
3707
  "ENSG00000236197",
3708
  "ENSG00000236202",
 
3709
  "ENSG00000236404",
3710
  "ENSG00000236532",
3711
  "ENSG00000236548",
@@ -3826,7 +3829,6 @@
3826
  "ENSG00000249797",
3827
  "ENSG00000249816",
3828
  "ENSG00000249835",
3829
- "ENSG00000249853",
3830
  "ENSG00000249917",
3831
  "ENSG00000249937",
3832
  "ENSG00000249961",
@@ -3839,7 +3841,6 @@
3839
  "ENSG00000250326",
3840
  "ENSG00000250328",
3841
  "ENSG00000250337",
3842
- "ENSG00000250423",
3843
  "ENSG00000250548",
3844
  "ENSG00000250582",
3845
  "ENSG00000250722",
@@ -3863,7 +3864,6 @@
3863
  "ENSG00000253276",
3864
  "ENSG00000253301",
3865
  "ENSG00000253438",
3866
- "ENSG00000253582",
3867
  "ENSG00000253626",
3868
  "ENSG00000253633",
3869
  "ENSG00000253729",
 
107
  "ENSG00000033122",
108
  "ENSG00000033170",
109
  "ENSG00000033178",
 
110
  "ENSG00000033867",
111
  "ENSG00000034053",
112
  "ENSG00000034510",
 
165
  "ENSG00000054938",
166
  "ENSG00000054965",
167
  "ENSG00000055147",
 
168
  "ENSG00000055332",
169
  "ENSG00000055917",
170
  "ENSG00000055950",
 
182
  "ENSG00000058668",
183
  "ENSG00000058729",
184
  "ENSG00000058804",
 
185
  "ENSG00000059588",
186
  "ENSG00000060138",
187
  "ENSG00000060237",
 
262
  "ENSG00000071054",
263
  "ENSG00000071205",
264
  "ENSG00000071462",
265
+ "ENSG00000071553",
266
  "ENSG00000071564",
267
  "ENSG00000071626",
268
  "ENSG00000071794",
 
281
  "ENSG00000072958",
282
  "ENSG00000073060",
283
  "ENSG00000073282",
284
+ "ENSG00000073331",
285
  "ENSG00000073417",
286
  "ENSG00000073711",
287
  "ENSG00000073734",
 
350
  "ENSG00000079308",
351
  "ENSG00000079385",
352
  "ENSG00000079387",
353
+ "ENSG00000079432",
354
  "ENSG00000079459",
355
  "ENSG00000079462",
356
  "ENSG00000079482",
 
437
  "ENSG00000088356",
438
  "ENSG00000088387",
439
  "ENSG00000088538",
440
+ "ENSG00000088727",
441
  "ENSG00000088826",
442
  "ENSG00000089012",
443
  "ENSG00000089041",
 
459
  "ENSG00000090376",
460
  "ENSG00000090470",
461
  "ENSG00000090621",
462
+ "ENSG00000090863",
463
  "ENSG00000090889",
464
  "ENSG00000090905",
465
  "ENSG00000090924",
 
471
  "ENSG00000091592",
472
  "ENSG00000091732",
473
  "ENSG00000091879",
 
474
  "ENSG00000092068",
475
  "ENSG00000092108",
476
  "ENSG00000092140",
 
665
  "ENSG00000105011",
666
  "ENSG00000105171",
667
  "ENSG00000105185",
668
+ "ENSG00000105227",
669
  "ENSG00000105278",
670
  "ENSG00000105281",
671
  "ENSG00000105289",
 
674
  "ENSG00000105464",
675
  "ENSG00000105467",
676
  "ENSG00000105479",
677
+ "ENSG00000105538",
678
  "ENSG00000105640",
679
  "ENSG00000105662",
680
  "ENSG00000105707",
 
942
  "ENSG00000115129",
943
  "ENSG00000115137",
944
  "ENSG00000115159",
945
+ "ENSG00000115170",
946
  "ENSG00000115183",
947
  "ENSG00000115233",
948
  "ENSG00000115306",
 
997
  "ENSG00000116580",
998
  "ENSG00000116641",
999
  "ENSG00000116678",
1000
+ "ENSG00000116703",
1001
  "ENSG00000116729",
1002
  "ENSG00000116731",
1003
  "ENSG00000116741",
 
1362
  "ENSG00000132300",
1363
  "ENSG00000132334",
1364
  "ENSG00000132341",
1365
+ "ENSG00000132383",
1366
  "ENSG00000132386",
1367
  "ENSG00000132424",
1368
+ "ENSG00000132432",
1369
  "ENSG00000132466",
1370
  "ENSG00000132475",
1371
  "ENSG00000132549",
 
1375
  "ENSG00000132681",
1376
  "ENSG00000132694",
1377
  "ENSG00000132749",
1378
+ "ENSG00000132763",
1379
  "ENSG00000132773",
1380
  "ENSG00000132780",
1381
  "ENSG00000132912",
 
1417
  "ENSG00000133943",
1418
  "ENSG00000133958",
1419
  "ENSG00000133962",
1420
+ "ENSG00000134013",
1421
  "ENSG00000134046",
1422
  "ENSG00000134057",
1423
  "ENSG00000134058",
 
1609
  "ENSG00000138640",
1610
  "ENSG00000138646",
1611
  "ENSG00000138650",
1612
+ "ENSG00000138668",
1613
  "ENSG00000138670",
1614
  "ENSG00000138696",
1615
  "ENSG00000138709",
 
1743
  "ENSG00000143398",
1744
  "ENSG00000143401",
1745
  "ENSG00000143437",
1746
+ "ENSG00000143443",
1747
  "ENSG00000143452",
1748
  "ENSG00000143469",
1749
  "ENSG00000143476",
 
1762
  "ENSG00000143799",
1763
  "ENSG00000143815",
1764
  "ENSG00000143878",
 
1765
  "ENSG00000143919",
1766
  "ENSG00000143924",
1767
  "ENSG00000143933",
 
1846
  "ENSG00000145779",
1847
  "ENSG00000145781",
1848
  "ENSG00000145808",
 
1849
  "ENSG00000145826",
1850
  "ENSG00000145832",
1851
  "ENSG00000145833",
 
2178
  "ENSG00000156970",
2179
  "ENSG00000156973",
2180
  "ENSG00000156976",
 
2181
  "ENSG00000157036",
2182
  "ENSG00000157060",
2183
  "ENSG00000157106",
 
2194
  "ENSG00000157554",
2195
  "ENSG00000157557",
2196
  "ENSG00000157578",
2197
+ "ENSG00000157625",
2198
  "ENSG00000157680",
2199
  "ENSG00000157703",
2200
  "ENSG00000157764",
 
2242
  "ENSG00000159592",
2243
  "ENSG00000159593",
2244
  "ENSG00000159685",
 
2245
  "ENSG00000159788",
2246
  "ENSG00000159885",
2247
  "ENSG00000159915",
 
2289
  "ENSG00000162520",
2290
  "ENSG00000162521",
2291
  "ENSG00000162592",
2292
+ "ENSG00000162594",
2293
  "ENSG00000162599",
2294
  "ENSG00000162604",
2295
  "ENSG00000162607",
 
2427
  "ENSG00000164329",
2428
  "ENSG00000164330",
2429
  "ENSG00000164331",
2430
+ "ENSG00000164342",
2431
  "ENSG00000164366",
2432
  "ENSG00000164398",
2433
  "ENSG00000164418",
 
2597
  "ENSG00000168070",
2598
  "ENSG00000168078",
2599
  "ENSG00000168079",
 
 
2600
  "ENSG00000168209",
2601
  "ENSG00000168214",
2602
  "ENSG00000168263",
 
2617
  "ENSG00000168779",
2618
  "ENSG00000168781",
2619
  "ENSG00000168785",
 
2620
  "ENSG00000168843",
2621
  "ENSG00000168887",
2622
  "ENSG00000168916",
 
2774
  "ENSG00000172765",
2775
  "ENSG00000172818",
2776
  "ENSG00000172831",
 
2777
  "ENSG00000172889",
2778
  "ENSG00000172915",
2779
  "ENSG00000172936",
 
2830
  "ENSG00000174628",
2831
  "ENSG00000174640",
2832
  "ENSG00000174652",
 
2833
  "ENSG00000174718",
2834
  "ENSG00000174720",
2835
  "ENSG00000174744",
 
2859
  "ENSG00000175471",
2860
  "ENSG00000175497",
2861
  "ENSG00000175575",
 
2862
  "ENSG00000175600",
2863
  "ENSG00000175606",
2864
  "ENSG00000175611",
 
2874
  "ENSG00000175928",
2875
  "ENSG00000175931",
2876
  "ENSG00000176029",
 
2877
  "ENSG00000176101",
2878
  "ENSG00000176102",
2879
  "ENSG00000176105",
 
2880
  "ENSG00000176160",
2881
  "ENSG00000176165",
2882
  "ENSG00000176177",
 
3030
  "ENSG00000182389",
3031
  "ENSG00000182463",
3032
  "ENSG00000182481",
 
3033
  "ENSG00000182578",
3034
  "ENSG00000182580",
3035
  "ENSG00000182583",
 
3165
  "ENSG00000186088",
3166
  "ENSG00000186094",
3167
  "ENSG00000186111",
3168
+ "ENSG00000186132",
3169
  "ENSG00000186153",
3170
  "ENSG00000186185",
3171
  "ENSG00000186197",
 
3224
  "ENSG00000188033",
3225
  "ENSG00000188039",
3226
  "ENSG00000188042",
 
3227
  "ENSG00000188107",
3228
  "ENSG00000188158",
3229
  "ENSG00000188177",
 
3572
  "ENSG00000224825",
3573
  "ENSG00000224897",
3574
  "ENSG00000224957",
3575
+ "ENSG00000225361",
3576
  "ENSG00000225434",
3577
  "ENSG00000225470",
3578
  "ENSG00000225484",
 
3653
  "ENSG00000231646",
3654
  "ENSG00000231672",
3655
  "ENSG00000231689",
 
3656
  "ENSG00000231806",
3657
  "ENSG00000231889",
3658
  "ENSG00000232040",
 
3688
  "ENSG00000234665",
3689
  "ENSG00000234707",
3690
  "ENSG00000234715",
3691
+ "ENSG00000234719",
3692
  "ENSG00000234745",
3693
  "ENSG00000234776",
3694
  "ENSG00000234840",
 
3708
  "ENSG00000236107",
3709
  "ENSG00000236197",
3710
  "ENSG00000236202",
3711
+ "ENSG00000236384",
3712
  "ENSG00000236404",
3713
  "ENSG00000236532",
3714
  "ENSG00000236548",
 
3829
  "ENSG00000249797",
3830
  "ENSG00000249816",
3831
  "ENSG00000249835",
 
3832
  "ENSG00000249917",
3833
  "ENSG00000249937",
3834
  "ENSG00000249961",
 
3841
  "ENSG00000250326",
3842
  "ENSG00000250328",
3843
  "ENSG00000250337",
 
3844
  "ENSG00000250548",
3845
  "ENSG00000250582",
3846
  "ENSG00000250722",
 
3864
  "ENSG00000253276",
3865
  "ENSG00000253301",
3866
  "ENSG00000253438",
 
3867
  "ENSG00000253626",
3868
  "ENSG00000253633",
3869
  "ENSG00000253729",
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