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popV
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tabula_muris_Spleen_Smart-seq2

Joblib
popV
biology
genomics
single-cell
AnnData:0.12.2
scikit_learn:1.7.2
organism:Mus musculus
Python:3.12.8
popV:0.6.0
tissue: spleen
Model card Files
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 Community
canergen commited on
Commit
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1 Parent(s): 53c0c3a

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Files changed (16) 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 +2 -2
  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 +1 -1
  12. scvi/model.pt +1 -1
  13. scvi_knn_classifier.joblib +2 -2
  14. svm_classifier.joblib +3 -0
  15. svm_classifier_cuml.joblib +2 -2
  16. 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| B cell | 294 | 1.00 | 0.99 | 1.00 | 0.91 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 44 | 0.94 | 0.96 | 0.95 | 0.32 | 0.00 | 0.90 | 0.97 | 0.96 | 0.99 |\n| CD8-positive, alpha-beta T cell | 24 | 0.94 | 0.94 | 0.90 | 0.18 | 0.00 | 0.77 | 0.90 | 0.92 | 0.94 |\n| proerythroblast | 11 | 0.95 | 0.84 | 0.84 | 0.27 | 0.00 | 0.92 | 1.00 | 0.92 | 1.00 |\n| natural killer cell | 10 | 0.89 | 0.95 | 0.95 | 0.12 | 0.00 | 0.95 | 0.95 | 1.00 | 0.95 |\n| granulocyte | 1 | 1.00 | 1.00 | 0.67 | 0.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |",
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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| B cell | 2557 | 1.00 | 1.00 | 1.00 | 0.99 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| CD4-positive, alpha-beta T cell | 370 | 0.94 | 0.94 | 0.96 | 0.68 | 0.00 | 0.95 | 1.00 | 1.00 | 0.99 |\n| CD8-positive, alpha-beta T cell | 330 | 0.93 | 0.93 | 0.95 | 0.65 | 0.00 | 0.93 | 1.00 | 1.00 | 0.99 |\n| proerythroblast | 96 | 0.84 | 0.88 | 0.96 | 0.71 | 0.00 | 0.90 | 0.98 | 0.96 | 0.98 |\n| natural killer cell | 77 | 0.96 | 0.97 | 0.99 | 0.51 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |\n| granulocyte | 20 | 0.98 | 0.98 | 0.93 | 0.80 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |"
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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| B cell | 293 | 1.00 | 0.99 | 1.00 | 0.99 | 0.00 | 0.99 | 1.00 | 0.99 | 1.00 |\n| CD4-positive, alpha-beta T cell | 42 | 0.94 | 0.95 | 0.98 | 0.66 | 0.00 | 0.81 | 0.98 | 0.95 | 0.99 |\n| CD8-positive, alpha-beta T cell | 24 | 0.93 | 0.92 | 0.94 | 0.42 | 0.00 | 0.77 | 0.92 | 0.91 | 0.94 |\n| proerythroblast | 13 | 0.96 | 0.82 | 0.92 | 0.78 | 0.00 | 0.88 | 1.00 | 0.89 | 1.00 |\n| natural killer cell | 11 | 0.90 | 0.91 | 0.95 | 0.27 | 0.00 | 0.95 | 0.95 | 0.96 | 0.95 |\n| granulocyte | 1 | 1.00 | 1.00 | 1.00 | 0.00 | 0.00 | 0.67 | 1.00 | 1.00 | 1.00 |",
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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| B cell | 2558 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| CD4-positive, alpha-beta T cell | 372 | 0.94 | 0.95 | 0.96 | 0.70 | 0.00 | 0.89 | 1.00 | 1.00 | 0.99 |\n| CD8-positive, alpha-beta T cell | 330 | 0.93 | 0.94 | 0.96 | 0.68 | 0.00 | 0.89 | 1.00 | 1.00 | 0.99 |\n| proerythroblast | 94 | 0.91 | 0.87 | 0.96 | 0.76 | 0.00 | 0.94 | 0.98 | 0.93 | 0.99 |\n| natural killer cell | 76 | 0.97 | 0.98 | 1.00 | 0.24 | 0.00 | 0.97 | 1.00 | 1.00 | 1.00 |\n| granulocyte | 20 | 0.98 | 0.98 | 0.93 | 0.60 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |"
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190
  "ENSMUSG00000003559",
191
  "ENSMUSG00000003581",
 
341
  "ENSMUSG00000007038",
342
  "ENSMUSG00000007041",
343
  "ENSMUSG00000007338",
344
+ "ENSMUSG00000007570",
345
  "ENSMUSG00000007589",
346
  "ENSMUSG00000007603",
347
  "ENSMUSG00000007613",
 
443
  "ENSMUSG00000014846",
444
  "ENSMUSG00000014859",
445
  "ENSMUSG00000014873",
 
446
  "ENSMUSG00000014980",
447
  "ENSMUSG00000015023",
448
  "ENSMUSG00000015027",
 
507
  "ENSMUSG00000016933",
508
  "ENSMUSG00000016940",
509
  "ENSMUSG00000016946",
 
510
  "ENSMUSG00000017176",
511
  "ENSMUSG00000017221",
512
  "ENSMUSG00000017264",
 
580
  "ENSMUSG00000018965",
581
  "ENSMUSG00000018974",
582
  "ENSMUSG00000018983",
 
583
  "ENSMUSG00000019039",
584
  "ENSMUSG00000019082",
585
  "ENSMUSG00000019087",
 
604
  "ENSMUSG00000019699",
605
  "ENSMUSG00000019731",
606
  "ENSMUSG00000019777",
 
607
  "ENSMUSG00000019794",
608
  "ENSMUSG00000019795",
609
  "ENSMUSG00000019797",
 
752
  "ENSMUSG00000020720",
753
  "ENSMUSG00000020721",
754
  "ENSMUSG00000020733",
755
+ "ENSMUSG00000020737",
756
  "ENSMUSG00000020739",
757
  "ENSMUSG00000020740",
758
  "ENSMUSG00000020743",
 
1056
  "ENSMUSG00000022747",
1057
  "ENSMUSG00000022751",
1058
  "ENSMUSG00000022757",
 
1059
  "ENSMUSG00000022769",
1060
  "ENSMUSG00000022771",
1061
  "ENSMUSG00000022774",
 
1066
  "ENSMUSG00000022792",
1067
  "ENSMUSG00000022797",
1068
  "ENSMUSG00000022801",
 
1069
  "ENSMUSG00000022814",
1070
  "ENSMUSG00000022816",
1071
  "ENSMUSG00000022822",
 
1079
  "ENSMUSG00000022895",
1080
  "ENSMUSG00000022898",
1081
  "ENSMUSG00000022901",
1082
+ "ENSMUSG00000022911",
1083
  "ENSMUSG00000022913",
1084
  "ENSMUSG00000022946",
1085
  "ENSMUSG00000022951",
 
1106
  "ENSMUSG00000023048",
1107
  "ENSMUSG00000023051",
1108
  "ENSMUSG00000023067",
 
1109
  "ENSMUSG00000023088",
1110
  "ENSMUSG00000023104",
1111
  "ENSMUSG00000023143",
 
1265
  "ENSMUSG00000024725",
1266
  "ENSMUSG00000024726",
1267
  "ENSMUSG00000024732",
1268
+ "ENSMUSG00000024740",
1269
  "ENSMUSG00000024742",
1270
  "ENSMUSG00000024758",
1271
  "ENSMUSG00000024764",
 
1296
  "ENSMUSG00000024885",
1297
  "ENSMUSG00000024889",
1298
  "ENSMUSG00000024896",
 
1299
  "ENSMUSG00000024906",
1300
  "ENSMUSG00000024910",
1301
  "ENSMUSG00000024911",
 
1325
  "ENSMUSG00000025041",
1326
  "ENSMUSG00000025047",
1327
  "ENSMUSG00000025049",
 
1328
  "ENSMUSG00000025060",
1329
  "ENSMUSG00000025068",
1330
  "ENSMUSG00000025076",
 
1339
  "ENSMUSG00000025139",
1340
  "ENSMUSG00000025142",
1341
  "ENSMUSG00000025147",
 
1342
  "ENSMUSG00000025153",
1343
  "ENSMUSG00000025155",
1344
  "ENSMUSG00000025156",
 
1512
  "ENSMUSG00000026360",
1513
  "ENSMUSG00000026365",
1514
  "ENSMUSG00000026411",
1515
+ "ENSMUSG00000026417",
1516
  "ENSMUSG00000026421",
1517
  "ENSMUSG00000026427",
1518
  "ENSMUSG00000026433",
 
1633
  "ENSMUSG00000027291",
1634
  "ENSMUSG00000027293",
1635
  "ENSMUSG00000027305",
1636
+ "ENSMUSG00000027309",
1637
  "ENSMUSG00000027330",
1638
  "ENSMUSG00000027332",
1639
  "ENSMUSG00000027341",
 
1652
  "ENSMUSG00000027455",
1653
  "ENSMUSG00000027472",
1654
  "ENSMUSG00000027475",
1655
+ "ENSMUSG00000027487",
1656
  "ENSMUSG00000027495",
1657
  "ENSMUSG00000027498",
1658
  "ENSMUSG00000027502",
 
2066
  "ENSMUSG00000030120",
2067
  "ENSMUSG00000030126",
2068
  "ENSMUSG00000030127",
 
2069
  "ENSMUSG00000030165",
2070
  "ENSMUSG00000030166",
2071
  "ENSMUSG00000030168",
 
2236
  "ENSMUSG00000031556",
2237
  "ENSMUSG00000031557",
2238
  "ENSMUSG00000031568",
 
2239
  "ENSMUSG00000031577",
2240
  "ENSMUSG00000031583",
2241
  "ENSMUSG00000031584",
 
2301
  "ENSMUSG00000031917",
2302
  "ENSMUSG00000031922",
2303
  "ENSMUSG00000031924",
2304
+ "ENSMUSG00000031928",
2305
  "ENSMUSG00000031930",
2306
  "ENSMUSG00000031931",
2307
  "ENSMUSG00000031933",
 
2328
  "ENSMUSG00000032123",
2329
  "ENSMUSG00000032126",
2330
  "ENSMUSG00000032171",
2331
+ "ENSMUSG00000032175",
2332
  "ENSMUSG00000032178",
2333
  "ENSMUSG00000032180",
2334
  "ENSMUSG00000032182",
 
2403
  "ENSMUSG00000032575",
2404
  "ENSMUSG00000032578",
2405
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2406
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2407
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2408
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2410
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2411
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2412
  "ENSMUSG00000032698",
 
2413
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2414
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2415
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2526
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2527
  "ENSMUSG00000034274",
2528
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2529
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2530
  "ENSMUSG00000034300",
2531
  "ENSMUSG00000034312",
2532
  "ENSMUSG00000034321",
 
2626
  "ENSMUSG00000035711",
2627
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2628
  "ENSMUSG00000035725",
 
2629
  "ENSMUSG00000035754",
2630
  "ENSMUSG00000035762",
2631
  "ENSMUSG00000035765",
 
2768
  "ENSMUSG00000037426",
2769
  "ENSMUSG00000037447",
2770
  "ENSMUSG00000037461",
2771
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2772
  "ENSMUSG00000037466",
2773
  "ENSMUSG00000037470",
2774
  "ENSMUSG00000037503",
 
2916
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2917
  "ENSMUSG00000039087",
2918
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2919
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2920
  "ENSMUSG00000039108",
2921
  "ENSMUSG00000039130",
2922
  "ENSMUSG00000039145",
 
2972
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2973
  "ENSMUSG00000039756",
2974
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2975
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2976
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2977
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3070
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3071
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3072
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3073
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3161
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3162
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3163
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3164
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3202
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3204
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3205
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  "ENSMUSG00000044199",
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3235
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3236
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3237
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3238
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3240
  "ENSMUSG00000045377",
3241
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3267
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3268
  "ENSMUSG00000046546",
3269
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3270
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3271
  "ENSMUSG00000046671",
3272
  "ENSMUSG00000046688",
3273
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3299
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3300
  "ENSMUSG00000047446",
3301
  "ENSMUSG00000047454",
3302
+ "ENSMUSG00000047557",
3303
  "ENSMUSG00000047617",
3304
  "ENSMUSG00000047635",
3305
  "ENSMUSG00000047649",
 
3423
  "ENSMUSG00000051864",
3424
  "ENSMUSG00000051977",
3425
  "ENSMUSG00000052031",
 
3426
  "ENSMUSG00000052160",
3427
  "ENSMUSG00000052305",
3428
  "ENSMUSG00000052337",
 
3490
  "ENSMUSG00000054414",
3491
  "ENSMUSG00000054452",
3492
  "ENSMUSG00000054455",
 
3493
  "ENSMUSG00000054499",
3494
  "ENSMUSG00000054675",
3495
  "ENSMUSG00000054676",
 
3734
  "ENSMUSG00000063849",
3735
  "ENSMUSG00000063856",
3736
  "ENSMUSG00000063884",
3737
+ "ENSMUSG00000063889",
3738
  "ENSMUSG00000063904",
3739
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3740
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3741
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3742
+ "ENSMUSG00000064061",
3743
  "ENSMUSG00000064065",
3744
  "ENSMUSG00000064068",
3745
  "ENSMUSG00000064090",
 
3830
  "ENSMUSG00000070738",
3831
  "ENSMUSG00000070934",
3832
  "ENSMUSG00000070953",
3833
+ "ENSMUSG00000071042",
3834
  "ENSMUSG00000071074",
3835
  "ENSMUSG00000071076",
3836
  "ENSMUSG00000071078",
 
3893
  "ENSMUSG00000075701",
3894
  "ENSMUSG00000075703",
3895
  "ENSMUSG00000075704",
3896
+ "ENSMUSG00000075705",
3897
  "ENSMUSG00000076431",
3898
  "ENSMUSG00000076435",
3899
  "ENSMUSG00000076441",
 
3945
  "ENSMUSG00000085793",
3946
  "ENSMUSG00000085887",
3947
  "ENSMUSG00000086370",
3948
+ "ENSMUSG00000086429",
3949
  "ENSMUSG00000086503",
3950
  "ENSMUSG00000086938",
3951
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