Archive 4 checkpoints (1-4)
Browse files- paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/arms/scsemi__raw/labels/labels.parquet +3 -0
- paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/contrast.csv +14 -0
- paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/per_donor.csv +25 -0
- paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/summary.json +529 -0
paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/arms/scsemi__raw/labels/labels.parquet
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size 832952
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paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/contrast.csv
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arm,celltype,statistic,n_genes,r_generated,r_broadcast,partial_r_generated_given_broadcast,r_generated_vs_broadcast,n_case_donors_obs,n_control_donors_obs,n_case_donors_gen,n_control_donors_gen,n_cells_obs,n_cells_gen,deg_scored,top50_overlap,top50_jaccard,obs_top_list_size,gen_top_list_size,n_sig_obs,n_sig_gen,top50_overlap_broadcast,top50_jaccard_broadcast,broadcast_top_list_size,n_sig_broadcast
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scsemi__raw,T cell,mean_cp10k,2972,0.5638545251068595,0.6672341944769086,0.44136683141588146,0.39173265626095427,15,7,15,7,54682,20785,,,,,,,,,,,
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scsemi__raw,T cell,pseudobulk_log1p_cpm,2972,0.2551184506161339,0.6085495669711263,0.07351997842347938,0.32868401370890377,15,7,15,7,54682,20785,,,,,,,,,,,
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scsemi__raw,B cell,mean_cp10k,3082,0.21689273018683167,0.4089627988580942,0.07213783741108218,0.38155951211284267,15,7,15,7,7674,3433,,,,,,,,,,,
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scsemi__raw,B cell,pseudobulk_log1p_cpm,3082,0.008765702537975829,0.16272668271280388,-0.030770314714843268,0.23520514635180478,15,7,15,7,7674,3433,,,,,,,,,,,
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scsemi__raw,Monocyte,mean_cp10k,2800,0.5935198281085698,0.6597688312759369,0.4497434985006958,0.4394475366216848,15,7,15,7,9065,3776,,,,,,,,,,,
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scsemi__raw,Monocyte,pseudobulk_log1p_cpm,2800,0.24835016756278497,0.4554672311515457,0.13663640960389556,0.28964426185777103,15,7,15,7,9065,3776,,,,,,,,,,,
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| 8 |
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scsemi__raw,NK cell,mean_cp10k,2913,0.5370064311799259,0.6254055500074935,0.3551156070323869,0.4668273561012516,15,7,15,7,12190,3572,,,,,,,,,,,
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| 9 |
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scsemi__raw,NK cell,pseudobulk_log1p_cpm,2913,0.19787837747821874,0.47893765390113907,0.08408751239159543,0.2645264822176829,15,7,15,7,12190,3572,,,,,,,,,,,
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| 10 |
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scsemi__raw,T cell,welch_top50_deg,5927,,,,,15,7,15,7,54682,20785,True,0,,0,0,0,0,0,,0,0
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scsemi__raw,B cell,welch_top50_deg,5927,,,,,15,7,15,7,7674,3433,True,0,0.0,0,1,0,1,0,,0,0
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scsemi__raw,Monocyte,welch_top50_deg,5927,,,,,15,7,15,7,9065,3776,True,0,,0,0,0,0,0,,0,0
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scsemi__raw,NK cell,welch_top50_deg,5927,,,,,15,7,15,7,12190,3572,True,0,,0,0,0,0,0,,0,0
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scsemi__raw,DC,welch_top50_deg,5927,,,,,15,7,15,7,2742,1139,True,0,,0,0,0,0,0,,0,0
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paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/per_donor.csv
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arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
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scsemi__raw,C60_2504,covid_positive,1500,1837,150,0.7966666666666666,0.8911268372346217,0.10733333333333334,0.05443658138268917,0.04666666666666667,0.00979858464888405,0.034,0.032117583015786606,0.012666666666666666,0.009254218835057159,0.0026666666666666666,0.00326619488296135,0.19011939756849947,0.6734773678189332,0.5516133780828769,12,False,0.4866666666666667,0.07333333333333333,0.5733333333333334,0.05333333333333334,4.666666666666667,0.979858464888405,1351.0,1187.0
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scsemi__raw,C69_1804,covid_negative,1500,6901,150,0.6253333333333333,0.819591363570497,0.04133333333333333,0.028546587451094046,0.15066666666666667,0.0585422402550355,0.126,0.04637009129111723,0.024,0.03231415736849732,0.03266666666666666,0.014635560063758875,0.40514437521132207,0.5283124449896214,0.5969520270692538,7,False,0.8733333333333333,0.11333333333333333,0.5866666666666667,0.3333333333333333,15.066666666666666,5.85422402550355,1350.0,1211.0
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scsemi__raw,C113_0605,covid_positive,1500,3274,150,0.702,0.6053756872327428,0.056,0.14141722663408673,0.13466666666666666,0.032376298106292,0.0026666666666666666,0.03512522907758094,0.104,0.030849114233353694,0.0006666666666666666,0.1548564447159438,0.5441311341885562,0.4699938177421493,0.548116137789877,2,False,0.41333333333333333,0.14,0.8933333333333333,0.2733333333333333,13.466666666666665,3.2376298106292003,1349.0,2026.0
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scsemi__raw,C126_2504,covid_positive,1500,8159,150,0.628,0.5618335580340728,0.13933333333333334,0.056992278465498224,0.10466666666666667,0.2332393675695551,0.09066666666666667,0.11177840421620297,0.03333333333333333,0.028925113371736734,0.004,0.0072312783429341835,0.3058314335907178,0.211109210228439,0.7228953039803039,3,False,0.8533333333333334,0.1,0.44,0.34,10.466666666666667,23.32393675695551,1352.0,1410.0
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scsemi__raw,C126_3004,covid_positive,1500,7181,150,0.698,0.743629021027712,0.138,0.05848767581116836,0.07466666666666667,0.05082857540732488,0.06933333333333333,0.1211530427517059,0.018666666666666668,0.0181033282272664,0.0013333333333333333,0.007798356774822448,0.20782750777514739,0.3667911311371116,0.5964726283590828,6,False,0.8133333333333334,0.07333333333333333,0.7266666666666667,0.25333333333333335,7.466666666666668,5.082857540732489,1350.0,1641.0
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scsemi__raw,C126_0605,covid_positive,1500,6577,150,0.5586666666666666,0.5716892200091227,0.07933333333333334,0.11023262885814201,0.138,0.08712178804926259,0.17933333333333334,0.16618519081648167,0.042666666666666665,0.055648471947696516,0.002,0.009122700319294512,0.1280527089351782,0.09271373910350957,0.6628824064812847,2,False,0.8933333333333333,0.1,0.6266666666666667,0.26,13.8,8.712178804926259,1350.0,1620.0
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scsemi__raw,C132_0205,covid_positive,1500,4671,150,0.5873333333333334,0.6112181545707557,0.094,0.11432241490044959,0.156,0.08948833226289873,0.148,0.13680154142581888,0.014,0.046242774566473986,0.0006666666666666666,0.0019267822736030828,0.15542025262256468,0.18543146907811653,0.5829472852840993,9,False,0.7666666666666667,0.09333333333333334,0.6466666666666666,0.16,15.6,8.948833226289873,1351.0,1457.0
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scsemi__raw,C132_1105,covid_positive,1500,4699,150,0.6726666666666666,0.6814215790593743,0.058,0.19472228133645456,0.030666666666666665,0.04618003830602256,0.20133333333333334,0.06873802936795063,0.018,0.007022770802298362,0.019333333333333334,0.001915301127899553,0.32198113073703627,0.47001316111739216,0.6844297075476911,15,False,0.86,0.02,0.36,0.35333333333333333,3.0666666666666664,4.618003830602256,1349.0,1737.0
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scsemi__raw,C168_2001,covid_positive,1500,2751,150,0.598,0.3300617957106507,0.18266666666666667,0.31842966194111233,0.052,0.18684114867320975,0.13066666666666665,0.11959287531806616,0.03133333333333333,0.03744093057070156,0.005333333333333333,0.007633587786259542,0.5580239912758996,0.7007174883902608,0.7445536826794203,1,True,0.8266666666666667,0.36666666666666664,0.4266666666666667,0.12666666666666668,5.2,18.684114867320975,1350.0,945.0
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scsemi__raw,C168_0202,covid_positive,1500,651,150,0.5326666666666666,0.2903225806451613,0.10666666666666667,0.18125960061443933,0.21266666666666667,0.3302611367127496,0.12133333333333333,0.09984639016897082,0.024,0.09831029185867896,0.0026666666666666666,0.0,0.532995391705069,0.8349560643919492,0.5729472713948683,19,False,0.8533333333333334,0.2866666666666667,0.6333333333333333,0.08666666666666667,21.266666666666666,33.026113671274956,1352.0,670.0
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scsemi__raw,C168_0403,recovery,1500,2526,150,0.498,0.29493269992082344,0.24933333333333332,0.08036421219319081,0.05533333333333333,0.4398258115597783,0.13133333333333333,0.1421219319081552,0.004666666666666667,0.0344418052256532,0.06133333333333333,0.00831353919239905,0.8501124307205066,0.7245576639774581,0.6058363091644977,4,False,0.7733333333333333,0.17333333333333334,0.09333333333333334,0.13333333333333333,5.533333333333333,43.982581155977826,1351.0,1080.0
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scsemi__raw,C170_0202,covid_positive,1500,5621,150,0.554,0.4090019569471624,0.14666666666666667,0.10745418964597046,0.11933333333333333,0.13271659847002312,0.09533333333333334,0.26845756982743285,0.06666666666666667,0.07987902508450453,0.018,0.0024906600249066002,0.3994397200972544,0.38261694647394334,0.5948792841059968,11,False,0.86,0.3,0.6533333333333333,0.12666666666666668,11.933333333333334,13.271659847002311,1351.0,840.0
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scsemi__raw,C170_0402,covid_positive,1500,808,150,0.6086666666666667,0.5742574257425742,0.1,0.054455445544554455,0.13,0.017326732673267328,0.118,0.3193069306930693,0.043333333333333335,0.03094059405940594,0.0,0.0037128712871287127,0.4100396039603962,0.3888156893006302,0.5458783548224794,22,False,0.6133333333333333,0.11333333333333333,0.62,0.05333333333333334,13.0,1.7326732673267329,1349.0,907.0
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scsemi__raw,C170_0403,recovery,1500,3745,150,0.5973333333333334,0.6101468624833111,0.10133333333333333,0.015487316421895861,0.146,0.06809078771695594,0.12866666666666668,0.2809078771695594,0.026,0.021628838451268357,0.0006666666666666666,0.003738317757009346,0.33625278148642623,0.36301854875971346,0.5987404146011082,16,False,0.5,0.18,0.5933333333333334,0.04666666666666667,14.6,6.809078771695594,1351.5,984.0
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scsemi__raw,C237_2805,covid_negative,1500,5071,150,0.6166666666666667,0.5912048905541314,0.086,0.08913429303884836,0.16466666666666666,0.15519621376454348,0.11,0.14789982252021297,0.018,0.014198382961940446,0.004666666666666667,0.0023663971603234074,0.08206823111812261,0.10307828202378862,0.6035254554398575,3,False,0.6933333333333334,0.14666666666666667,0.6133333333333333,0.26,16.466666666666665,15.519621376454348,1351.0,1379.0
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paper-releases/pbisc-diffusion/updates/20261008T050202Z-scsemi-imperial-deck/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3/summary.json
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|
|
| 1 |
+
{
|
| 2 |
+
"schema": "paired_ft_scores.v1",
|
| 3 |
+
"dataset": "imperial_eskd",
|
| 4 |
+
"written_utc": "2026-10-08T04:47:12.426326+00:00",
|
| 5 |
+
"command": [
|
| 6 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/tools/score_ft.py",
|
| 7 |
+
"--dataset",
|
| 8 |
+
"imperial_eskd",
|
| 9 |
+
"--out",
|
| 10 |
+
"/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scores/imperial_eskd/scsemi_cv_20261002/fold3",
|
| 11 |
+
"--threads",
|
| 12 |
+
"8",
|
| 13 |
+
"--arm",
|
| 14 |
+
"scsemi__raw=/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/generated/imperial_eskd/fold3/scsemi__raw.npz",
|
| 15 |
+
"--case-groups",
|
| 16 |
+
"covid_positive",
|
| 17 |
+
"--control-groups",
|
| 18 |
+
"covid_negative"
|
| 19 |
+
],
|
| 20 |
+
"arms": [
|
| 21 |
+
"scsemi__raw"
|
| 22 |
+
],
|
| 23 |
+
"donors": [
|
| 24 |
+
"C60_2504",
|
| 25 |
+
"C69_1804",
|
| 26 |
+
"C85_2004",
|
| 27 |
+
"C113_0605",
|
| 28 |
+
"C126_2504",
|
| 29 |
+
"C126_3004",
|
| 30 |
+
"C126_0605",
|
| 31 |
+
"C132_2804",
|
| 32 |
+
"C132_0205",
|
| 33 |
+
"C132_1105",
|
| 34 |
+
"C164_1105",
|
| 35 |
+
"C168_1205",
|
| 36 |
+
"C168_2001",
|
| 37 |
+
"C168_2301",
|
| 38 |
+
"C168_3001",
|
| 39 |
+
"C168_0202",
|
| 40 |
+
"C168_0403",
|
| 41 |
+
"C170_1205",
|
| 42 |
+
"C170_2301",
|
| 43 |
+
"C170_0202",
|
| 44 |
+
"C170_0402",
|
| 45 |
+
"C170_0403",
|
| 46 |
+
"C195_2605",
|
| 47 |
+
"C237_2805"
|
| 48 |
+
],
|
| 49 |
+
"n_donors": 24,
|
| 50 |
+
"reference": {
|
| 51 |
+
"cache": "/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/imperial_eskd",
|
| 52 |
+
"reference_sha256": "34b4caa3f8a60b46d5faf58f09cdaa5622bcce19e4c45d9902a711fead96375e",
|
| 53 |
+
"features_sha256": "e46e5bb1a24eae045efe75125d20e3accaa8f68a1006eb2f60d24159013d4aa7",
|
| 54 |
+
"n_r1_cells": 3600,
|
| 55 |
+
"pca": {
|
| 56 |
+
"n_components": 50,
|
| 57 |
+
"explained_variance_ratio_sum": 0.2543349266052246,
|
| 58 |
+
"n_fit_cells": 3600
|
| 59 |
+
},
|
| 60 |
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"r2_control": {
|
| 61 |
+
"precision": 0.9958333333333333,
|
| 62 |
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"coverage": 1.0,
|
| 63 |
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"density": 2.5191944444444445,
|
| 64 |
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"n_query": 3600,
|
| 65 |
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"depth_matched": {
|
| 66 |
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"precision": 0.9966666666666667,
|
| 67 |
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"coverage": 1.0,
|
| 68 |
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"density": 2.4921944444444444
|
| 69 |
+
}
|
| 70 |
+
},
|
| 71 |
+
"observed_l1_loo_null_mean": 0.43074713408214976
|
| 72 |
+
},
|
| 73 |
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"contrast_definition": {
|
| 74 |
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"enabled": true,
|
| 75 |
+
"rule": "explicit --case-groups / --control-groups",
|
| 76 |
+
"group_source": "features groups",
|
| 77 |
+
"case_groups": [
|
| 78 |
+
"covid_positive"
|
| 79 |
+
],
|
| 80 |
+
"control_groups": [
|
| 81 |
+
"covid_negative"
|
| 82 |
+
],
|
| 83 |
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"n_case_donors": 15,
|
| 84 |
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"n_control_donors": 7,
|
| 85 |
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"n_donors_in_neither": 2,
|
| 86 |
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"case": [
|
| 87 |
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true,
|
| 88 |
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false,
|
| 89 |
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false,
|
| 90 |
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true,
|
| 91 |
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|
| 92 |
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|
| 93 |
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|
| 94 |
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|
| 95 |
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|
| 96 |
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|
| 97 |
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|
| 98 |
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| 99 |
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| 100 |
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| 101 |
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| 104 |
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|
| 106 |
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|
| 107 |
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|
| 108 |
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|
| 109 |
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|
| 110 |
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false
|
| 111 |
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],
|
| 112 |
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"ctrl": [
|
| 113 |
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false,
|
| 114 |
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true,
|
| 115 |
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true,
|
| 116 |
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false,
|
| 117 |
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|
| 118 |
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|
| 119 |
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|
| 120 |
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|
| 121 |
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|
| 122 |
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|
| 123 |
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|
| 124 |
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true,
|
| 125 |
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|
| 126 |
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|
| 127 |
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|
| 128 |
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|
| 129 |
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false,
|
| 130 |
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true,
|
| 131 |
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|
| 132 |
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|
| 133 |
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false,
|
| 134 |
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false,
|
| 135 |
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true,
|
| 136 |
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true
|
| 137 |
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],
|
| 138 |
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"groups": [
|
| 139 |
+
"covid_positive",
|
| 140 |
+
"covid_negative",
|
| 141 |
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"covid_negative",
|
| 142 |
+
"covid_positive",
|
| 143 |
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"covid_positive",
|
| 144 |
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"covid_positive",
|
| 145 |
+
"covid_positive",
|
| 146 |
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"covid_positive",
|
| 147 |
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"covid_positive",
|
| 148 |
+
"covid_positive",
|
| 149 |
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"covid_negative",
|
| 150 |
+
"covid_negative",
|
| 151 |
+
"covid_positive",
|
| 152 |
+
"covid_positive",
|
| 153 |
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"covid_positive",
|
| 154 |
+
"covid_positive",
|
| 155 |
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"recovery",
|
| 156 |
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"covid_negative",
|
| 157 |
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"covid_positive",
|
| 158 |
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"covid_positive",
|
| 159 |
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"covid_positive",
|
| 160 |
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"recovery",
|
| 161 |
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"covid_negative",
|
| 162 |
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"covid_negative"
|
| 163 |
+
]
|
| 164 |
+
},
|
| 165 |
+
"deg_definition": {
|
| 166 |
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"enabled": true,
|
| 167 |
+
"score": "top-50 DEG overlap per cell type (benchmark total_top50_overlap, Welch backend)",
|
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