Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/data/liu2021/training_excluded.txt

@@ -0,0 +1,14 @@
+HGR0000042_T0
+HGR0000051_T2
+HGR0000069_T2
+HGR0000092_T1
+HGR0000094_T1
+HGR0000101_T0
+HGR0000124_T1
+HGR0000134_T1
+HGR0000142_T0
+HGR0000144_T0
+HGR0000392_T3
+HGR0000430_T1
+SHD2_HC
+SHD6_HC

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/data/liu2021/usable_samples.txt

@@ -0,0 +1,58 @@
+AA220014_HC
+AA220534_HC
+AA220907_HC
+HGR0000071_T0
+HGR0000074_T0
+HGR0000083_T1
+HGR0000089_T1
+HGR0000091_T0
+HGR0000093_T0
+HGR0000098_T0
+HGR0000136_T0
+HGR0000137_T0
+HGR0000141_T0
+HGR0000143_T0
+IM000040_HC
+HGR0000042_T0
+HGR0000042_T1
+HGR0000069_T0
+HGR0000069_T1
+HGR0000069_T2
+HGR0000092_T0
+HGR0000092_T1
+HGR0000094_T0
+HGR0000094_T1
+HGR0000115_T1
+HGR0000124_T0
+HGR0000124_T1
+HGR0000144_T0
+HGR0000144_T2
+HGR0000391_T0
+HGR0000395_T0
+HGR0000418_T1
+SHD2_HC
+SHD4_HC
+SHD7_HC
+HGR0000051_T0
+HGR0000051_T1
+HGR0000051_T2
+HGR0000051_T3
+HGR0000101_T0
+HGR0000101_T1
+HGR0000101_T3
+HGR0000102_T0
+HGR0000102_T1
+HGR0000134_T0
+HGR0000134_T1
+HGR0000135_T0
+HGR0000135_T1
+HGR0000142_T0
+HGR0000392_T0
+HGR0000392_T3
+HGR0000429_T1
+HGR0000429_T2
+HGR0000430_T1
+SHD1_HC
+SHD3_HC
+SHD5_HC
+SHD6_HC

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/liu2021/folds.csv

@@ -0,0 +1,66 @@
+row,sample_id,donor_id,group,fold,inner_val_f0,inner_val_f1,inner_val_f2,inner_val_f3,inner_val_f4
+0,AA220014_HC,AA220014,HC,4,False,False,False,False,False
+1,AA220534_HC,AA220534,HC,0,False,False,True,False,True
+2,AA220907_HC,AA220907,HC,2,False,False,False,False,False
+3,HGR0000071_T0,HGR0000071,COVID,2,False,False,False,True,False
+4,HGR0000074_T0,HGR0000074,COVID,1,False,False,False,False,False
+5,HGR0000078_T0,HGR0000078,COVID,-1,False,False,False,False,False
+6,HGR0000078_T1,HGR0000078,COVID,-1,False,False,False,False,False
+7,HGR0000079_T0,HGR0000079,COVID,-1,False,False,False,False,False
+8,HGR0000079_T1,HGR0000079,COVID,-1,False,False,False,False,False
+9,HGR0000083_T0,HGR0000083,COVID,-1,False,False,False,False,False
+10,HGR0000083_T1,HGR0000083,COVID,3,False,False,False,False,False
+11,HGR0000089_T1,HGR0000089,COVID,0,False,False,False,False,False
+12,HGR0000091_T0,HGR0000091,COVID,4,False,False,False,False,False
+13,HGR0000093_T0,HGR0000093,COVID,2,False,False,False,False,False
+14,HGR0000093_T1,HGR0000093,COVID,-1,False,False,False,False,False
+15,HGR0000098_T0,HGR0000098,COVID,0,False,False,False,False,False
+16,HGR0000110_T0,HGR0000110,COVID,-1,False,False,False,False,False
+17,HGR0000136_T0,HGR0000136,COVID,3,False,False,False,False,False
+18,HGR0000137_T0,HGR0000137,COVID,0,False,False,False,False,False
+19,HGR0000141_T0,HGR0000141,COVID,1,False,False,False,False,False
+20,HGR0000143_T0,HGR0000143,COVID,1,True,False,False,False,False
+21,IM000040_HC,IM000040,HC,1,False,False,False,False,False
+22,HGR0000042_T0,HGR0000042,COVID,4,False,False,False,False,False
+23,HGR0000042_T1,HGR0000042,COVID,4,False,False,False,False,False
+24,HGR0000069_T0,HGR0000069,COVID,4,False,False,False,False,False
+25,HGR0000069_T1,HGR0000069,COVID,4,False,False,False,False,False
+26,HGR0000069_T2,HGR0000069,COVID,4,False,False,False,False,False
+27,HGR0000092_T0,HGR0000092,COVID,4,False,False,False,False,False
+28,HGR0000092_T1,HGR0000092,COVID,4,False,False,False,False,False
+29,HGR0000094_T0,HGR0000094,COVID,2,False,False,False,False,False
+30,HGR0000094_T1,HGR0000094,COVID,2,False,False,False,False,False
+31,HGR0000115_T1,HGR0000115,COVID,4,False,False,False,False,False
+32,HGR0000124_T0,HGR0000124,COVID,2,False,True,False,False,True
+33,HGR0000124_T1,HGR0000124,COVID,2,False,True,False,False,True
+34,HGR0000144_T0,HGR0000144,COVID,0,False,False,False,False,False
+35,HGR0000144_T2,HGR0000144,COVID,0,False,False,False,False,False
+36,HGR0000391_T0,HGR0000391,COVID,2,False,False,False,False,False
+37,HGR0000395_T0,HGR0000395,COVID,0,False,False,True,True,False
+38,HGR0000418_T1,HGR0000418,COVID,3,False,False,False,False,False
+39,SHD2_HC,SHD2,HC,3,False,False,False,False,False
+40,SHD4_HC,SHD4,HC,2,False,False,False,True,False
+41,SHD7_HC,SHD7,HC,1,False,False,False,False,False
+42,HGR0000051_T0,HGR0000051,COVID,2,False,False,False,False,False
+43,HGR0000051_T1,HGR0000051,COVID,2,False,False,False,False,False
+44,HGR0000051_T2,HGR0000051,COVID,2,False,False,False,False,False
+45,HGR0000051_T3,HGR0000051,COVID,2,False,False,False,False,False
+46,HGR0000101_T0,HGR0000101,COVID,1,False,False,False,False,False
+47,HGR0000101_T1,HGR0000101,COVID,1,False,False,False,False,False
+48,HGR0000101_T3,HGR0000101,COVID,1,False,False,False,False,False
+49,HGR0000102_T0,HGR0000102,COVID,1,False,False,False,False,False
+50,HGR0000102_T1,HGR0000102,COVID,1,False,False,False,False,False
+51,HGR0000134_T0,HGR0000134,COVID,3,False,False,False,False,False
+52,HGR0000134_T1,HGR0000134,COVID,3,False,False,False,False,False
+53,HGR0000135_T0,HGR0000135,COVID,0,False,False,False,False,False
+54,HGR0000135_T1,HGR0000135,COVID,0,False,False,False,False,False
+55,HGR0000142_T0,HGR0000142,COVID,4,False,False,False,False,False
+56,HGR0000392_T0,HGR0000392,COVID,1,True,False,True,False,False
+57,HGR0000392_T3,HGR0000392,COVID,1,True,False,True,False,False
+58,HGR0000429_T1,HGR0000429,COVID,3,False,True,False,False,False
+59,HGR0000429_T2,HGR0000429,COVID,3,False,True,False,False,False
+60,HGR0000430_T1,HGR0000430,COVID,3,False,False,False,False,True
+61,SHD1_HC,SHD1,HC,0,False,True,False,False,False
+62,SHD3_HC,SHD3,HC,0,False,False,False,False,False
+63,SHD5_HC,SHD5,HC,4,False,False,False,False,False
+64,SHD6_HC,SHD6,HC,3,True,False,False,False,False

paper-releases/pbisc-diffusion/updates/20261002T124820Z-crosscohort-liu-default/diffusion/dataset/server_1/model8/plans/paired_finetune_intradataset_20260927/data/liu2021/pairs.csv

@@ -0,0 +1,66 @@
+sample_id,bulk_gsm,sc_sample,donor_id,row,bulk_title,bulk_count_column,id_match,group,timepoint,batch,geo_bulk_timepoint,severity,outcome,status_meta,days_since_onset,days_since_hospitalized,sex_meta,age_meta,n_cells_object_sample,n_sorted_dropped,n_unsorted,n_hto_doublet_dropped,n_hto_negative_dropped,n_cells_library,n_cells_retained,below_200_cells,bulk_assigned_counts,bulk_canonical_counts,sc_retained_umis_canonical,bulk_XIST_cpm,bulk_Ysum_cpm,bulk_sex_score,bulk_sex_call,sc_XIST_cpm,sc_Ysum_cpm,sc_sex_score,sc_sex_call_pseudobulk,sc_frac_cells_XIST,sc_frac_cells_Y,sc_sex_call_cells,sc_sex_call_method,sc_sex_call,sex_concordant,bulk_possible_mixture,expr_rho_own,expr_rho_best,expr_own_rank_among_sc,expr_best_is_own,expr_best_sc_sample,expr_centred_own_rank_among_sc,expr_centred_best_is_own,expr_reverse_own_rank_among_bulk,expr_reverse_best_is_own,expr_centred_own_day_rank_within_subject_bulk_to_sc,expr_centred_own_day_rank_within_subject_sc_to_bulk,expr_isg_score_bulk,expr_isg_score_sc,expr_isg_peak_day_bulk,expr_isg_peak_day_sc,expr_resid_k5_own_rank_bulk_to_sc,expr_resid_k5_own_rank_sc_to_bulk,expr_resid_k5_own_subject_rank_bulk_to_sc,expr_resid_k5_own_subject_rank_sc_to_bulk,expr_resid_k5_best_subject_bulk_to_sc,expr_resid_k5_best_subject_sc_to_bulk,expr_resid_k5_best_sc_sample,expr_resid_k5_r_own,expr_resid_k5_r_best,expr_resid_k5_own_day_rank_within_subject_bulk_to_sc,expr_resid_k5_own_day_rank_within_subject_sc_to_bulk,expr_resid_k5_subject_paired_days,expr_resid_k3_own_rank_bulk_to_sc,expr_resid_k3_own_rank_sc_to_bulk,expr_resid_k3_own_subject_rank_bulk_to_sc,expr_resid_k3_own_subject_rank_sc_to_bulk,expr_resid_k3_best_subject_bulk_to_sc,expr_resid_k3_best_subject_sc_to_bulk,expr_resid_k3_best_sc_sample,expr_resid_k3_r_own,expr_resid_k3_r_best,expr_resid_k3_own_day_rank_within_subject_bulk_to_sc,expr_resid_k3_own_day_rank_within_subject_sc_to_bulk,expr_resid_k3_subject_paired_days,expr_resid_k10_own_rank_bulk_to_sc,expr_resid_k10_own_rank_sc_to_bulk,expr_resid_k10_own_subject_rank_bulk_to_sc,expr_resid_k10_own_subject_rank_sc_to_bulk,expr_resid_k10_best_subject_bulk_to_sc,expr_resid_k10_best_subject_sc_to_bulk,expr_resid_k10_best_sc_sample,expr_resid_k10_r_own,expr_resid_k10_r_best,expr_resid_k10_own_day_rank_within_subject_bulk_to_sc,expr_resid_k10_own_day_rank_within_subject_sc_to_bulk,expr_resid_k10_subject_paired_days,identity_check,identity_pass,identity_notes
+AA220014_HC,GSM4929233,B1_AA220014_HC,AA220014,0,Batch 1 bulkRNAseq AA220014,AA220014,exact_subject_timepoint,HC,HC,B1,Healthy Control,HC,HC,na,,,Male,67,2665,2212,453,25,0,428,419,False,12664363.0,11891066.0,2102818.0,0.0,968.9393773693947,-9.92175076934081,male,3.213279105423097,810.664414311027,-7.589796063513166,male,0.014319809069212411,0.8687350835322196,male,pseudobulk,male,True,False,0.33363197128864475,0.33363197128864475,1,True,B1_AA220014_HC,1,True,1,True,1,1,4.791870029800825,4.472953804558001,HC,HC,1,1,1,1,AA220014,AA220014,B1_AA220014_HC,0.4840933616978335,0.4840933616978335,1,1,1,1,1,1,1,AA220014,AA220014,B1_AA220014_HC,0.5541421270327175,0.5541421270327175,1,1,1,1,1,1,1,AA220014,AA220014,B1_AA220014_HC,0.39461162156578367,0.39461162156578367,1,1,1,pass,True,
+AA220534_HC,GSM4929234,B1_AA220534_HC,AA220534,1,Batch1 bulkRNAseq AA220534,AA220534,exact_subject_timepoint,HC,HC,B1,Healthy Control,HC,HC,na,,,Male,47,2000,1630,370,17,0,353,353,False,15421579.0,14461083.0,1449568.0,0.0,1484.6080287887512,-10.53683780193983,male,0.0,1118.2087586433981,-10.128263442486427,male,0.0,0.943342776203966,male,pseudobulk,male,True,False,0.25840193643911663,0.30204767229580687,13,False,B3_SHD5_HC,3,False,3,False,1,1,5.5322734473000095,4.660268956615205,HC,HC,1,1,1,1,AA220534,AA220534,B1_AA220534_HC,0.5071624970549011,0.5071624970549011,1,1,1,1,1,1,1,AA220534,AA220534,B1_AA220534_HC,0.5458207262265085,0.5458207262265085,1,1,1,1,1,1,1,AA220534,AA220534,B1_AA220534_HC,0.40470168193208683,0.40470168193208683,1,1,1,pass,True,
+AA220907_HC,GSM4929235,B1_AA220907_HC,AA220907,2,Batch 1 bulk RNAseq AA220907,AA220907,exact_subject_timepoint,HC,HC,B1,Healthy Control,HC,HC,na,,,Female,32,1820,1418,402,18,0,384,381,False,15090297.0,14107858.0,1631559.0,1009.5891419499563,0.0,9.980980869098188,female,47.69304052554198,15.897680175180659,1.5268903917864058,ambiguous,0.1679790026246719,0.06824146981627296,female,per-cell (pseudobulk ambiguous),female,True,False,0.2518010950981389,0.3086197953948131,12,False,B3_SHD5_HC,3,False,4,False,1,1,4.840480275353389,4.077328734863998,HC,HC,1,1,1,1,AA220907,AA220907,B1_AA220907_HC,0.5153183878862712,0.5153183878862712,1,1,1,1,1,1,1,AA220907,AA220907,B1_AA220907_HC,0.558988473116742,0.558988473116742,1,1,1,1,1,1,1,AA220907,AA220907,B1_AA220907_HC,0.40663342391298685,0.40663342391298685,1,1,1,pass,True,"sc sex from per-cell detection (pseudobulk ambiguous: ambient pool-mate RNA / low 5' XIST capture; 0.068 of cells with Y UMIs, 0.168 with XIST)"
+HGR0000071_T0,GSM4929237,B1_HGR0000071_T0,HGR0000071,3,Batch 1 bulk RNAseq HGR0000071,HGR0000071_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,deceased,Deceased,8,2,Female,71,2510,2143,367,20,0,347,341,False,15192136.0,14430660.0,1208046.0,664.949286920549,0.06582352869932181,9.28729992084296,female,85.64508991941432,14.274181653235718,2.5040229091236474,female,0.2404692082111437,0.05278592375366569,female,pseudobulk,female,True,False,0.27531946244177125,0.27531946244177125,1,True,B1_HGR0000071_T0,1,True,4,False,1,1,5.676697124560118,5.226931335971307,T0,T0,1,1,1,1,HGR0000071,HGR0000071,B1_HGR0000071_T0,0.5318774241981559,0.5318774241981559,1,1,1,1,1,1,1,HGR0000071,HGR0000071,B1_HGR0000071_T0,0.6961058927032604,0.6961058927032604,1,1,1,1,1,1,1,HGR0000071,HGR0000071,B1_HGR0000071_T0,0.5052647259868666,0.5052647259868666,1,1,1,pass,True,
+HGR0000074_T0,GSM4929238,B1_HGR0000074_T0,HGR0000074,4,Batch 1 bulk RNAseq HGR0000074,PHGR0000074_T0,subject_timepoint; bulk column name corrected,COVID,T0,B1,Timepoint 0,Critical,alive,Alive,18,9,Male,52,1796,1433,363,16,0,347,335,False,12817133.0,11879019.0,1243809.0,0.0,1073.1729162832282,-10.069010536257501,male,0.7703560816916403,925.1976541116601,-9.03113672586433,male,0.0029850746268656717,0.8865671641791045,male,pseudobulk,male,True,False,0.2545207387524255,0.33598273362278214,17,False,B3_HGR0000135_T1,2,False,6,False,1,1,3.909648293219625,3.1967396882953842,T0,T0,1,1,1,1,HGR0000074,HGR0000074,B1_HGR0000074_T0,0.5910098632485511,0.5910098632485511,1,1,1,1,1,1,1,HGR0000074,HGR0000074,B1_HGR0000074_T0,0.6144593205382577,0.6144593205382577,1,1,1,1,1,1,1,HGR0000074,HGR0000074,B1_HGR0000074_T0,0.46545002653989614,0.46545002653989614,1,1,1,pass,True,subject_timepoint; bulk column name corrected
+HGR0000078_T0,GSM4929239,B1_HGR0000078_T0,HGR0000078,5,Batch 1 bulk RNAseq HGR0000078_T0,HGR0000078_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,alive,Alive,18,13,Female,40,899,691,208,22,0,186,184,True,13247240.0,12236577.0,696114.0,1334.3911637442968,0.0,10.383046683753962,female,44.00367430680462,11.000918576701155,1.9068979573931557,ambiguous,0.16304347826086957,0.03260869565217391,female,per-cell (pseudobulk ambiguous),female,True,False,0.206903703969843,0.30892460522289017,30,False,B2_HGR0000115_T1,6,False,4,False,1,2,4.6804559044662035,3.945567515492103,T0,T1,4,2,4,1,HGR0000110,HGR0000078,B1_HGR0000110_T0,0.23434219948943846,0.3050690398589066,1,2,2,2,1,2,1,SHD5,HGR0000078,B3_SHD5_HC,0.3993492050940758,0.41699248666168254,1,1,2,4,1,4,1,HGR0000430,HGR0000078,B3_HGR0000430_T1,0.17029510179210144,0.35177046927718286,1,1,2,borderline: own subject rank 4 (bulk->sc) and 1 (sc->bulk),False,"sc sex from per-cell detection (pseudobulk ambiguous: ambient pool-mate RNA / low 5' XIST capture; 0.033 of cells with Y UMIs, 0.163 with XIST); within subject, another timepoint beats the own one in some tests (residualised 1/2, centred 1/2); not a timepoint failure; subject ISG peak timepoint differs between assays (bulk T0, sc T1); only 184 retained cells (< 200; excluded by prepare_dataset)"
+HGR0000078_T1,GSM4929240,B1_HGR0000078_T1,HGR0000078,6,Batch 1 bulk RNAseq HGR0000078_T1,HGR0000078_T1,exact_subject_timepoint,COVID,T1,B1,Timepoint 1,Critical,alive,Alive,23,18,Female,40,1125,908,217,13,0,204,199,True,11714462.0,10857757.0,773275.0,1370.4427911414114,0.0,10.421478727002851,female,53.400692718753454,16.14439547311151,1.6658879879110557,ambiguous,0.1658291457286432,0.06030150753768844,female,per-cell (pseudobulk ambiguous),female,True,False,0.18656952757878492,0.2908629941314997,43,False,B2_HGR0000115_T1,27,False,19,False,2,1,4.640105320194252,4.166696344584951,T0,T1,1,1,1,1,HGR0000078,HGR0000078,B1_HGR0000078_T1,0.2954119670056332,0.2954119670056332,1,1,2,1,1,1,1,HGR0000078,HGR0000078,B1_HGR0000078_T1,0.4309694406453747,0.4309694406453747,1,1,2,1,1,1,1,HGR0000078,HGR0000078,B1_HGR0000078_T1,0.3283887613714895,0.3283887613714895,1,1,2,pass,True,"sc sex from per-cell detection (pseudobulk ambiguous: ambient pool-mate RNA / low 5' XIST capture; 0.060 of cells with Y UMIs, 0.166 with XIST); within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 2/1); not a timepoint failure; subject ISG peak timepoint differs between assays (bulk T0, sc T1); only 199 retained cells (< 200; excluded by prepare_dataset)"
+HGR0000079_T0,GSM4929241,B1_HGR0000079_T0,HGR0000079,7,Batch 1 bulk RNAseq HGR0000079_T0,HGR0000079_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,alive,Alive,30,6,Female,37,1405,1282,123,4,0,119,114,True,13224826.0,12550056.0,383848.0,0.0,950.7875566756038,-9.894495783126096,male,2.4682155542007798,972.4769283551071,-8.13280941013656,male,0.008771929824561403,0.8157894736842105,male,pseudobulk,male,False,False,0.17161455447183366,0.3528212523543739,50,False,B3_HGR0000135_T1,39,False,27,False,2,1,8.24878565909279,6.296753626865088,T0,T0,5,1,5,1,HGR0000144,HGR0000079,B2_HGR0000144_T0,0.29949884561374407,0.4275944569225654,1,1,2,5,1,5,1,HGR0000144,HGR0000079,B2_HGR0000144_T0,0.2832381044427507,0.443444330853057,1,1,2,55,46,4,35,HGR0000392,HGR0000110,B3_HGR0000392_T0,-0.056661195515506156,0.21336357841339992,2,1,2,fail: sex bulk=male sc=male meta=female,False,"bulk and sc agree (male) but the author metadata says Female; the sc cells were assigned by demuxlet with SNPs called from this subject's bulk RNA-seq, so the metadata sex is the likely error; within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 2/1); not a timepoint failure; only 114 retained cells (< 200; excluded by prepare_dataset)"
+HGR0000079_T1,GSM4929242,B1_HGR0000079_T1,HGR0000079,8,Batch 1 bulk RNAseq HGR0000079_T1,HGR0000079_T1,exact_subject_timepoint,COVID,T1,B1,Timepoint 1,Critical,alive,Alive,36,12,Female,37,955,799,156,11,0,145,141,True,13601543.0,12698313.0,614964.0,0.0,980.4034733412232,-9.938702567114522,male,0.0,612.5670486048392,-9.261077195283606,male,0.0,0.8723404255319149,male,pseudobulk,male,False,False,0.4092719512366083,0.4092719512366083,1,True,B1_HGR0000079_T1,1,True,2,False,1,1,4.373311954947451,3.764613805506304,T0,T0,1,1,1,1,HGR0000079,HGR0000079,B1_HGR0000079_T1,0.37743834876442406,0.37743834876442406,1,1,2,1,1,1,1,HGR0000079,HGR0000079,B1_HGR0000079_T1,0.36409521259845795,0.36409521259845795,1,1,2,1,1,1,1,HGR0000079,HGR0000079,B1_HGR0000079_T1,0.3342389947327462,0.3342389947327462,1,1,2,fail: sex bulk=male sc=male meta=female,False,"bulk and sc agree (male) but the author metadata says Female; the sc cells were assigned by demuxlet with SNPs called from this subject's bulk RNA-seq, so the metadata sex is the likely error; only 141 retained cells (< 200; excluded by prepare_dataset)"
+HGR0000083_T0,GSM4929243,B1_HGR0000083_T0,HGR0000083,9,Batch 1 bulk RNAseq HGR0000083_T0,HGR0000083_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Moderate,alive,Alive,6,1,Male,55,2240,2063,177,12,0,165,158,True,13311038.0,12537801.0,558611.0,0.0,1304.33103714376,-10.3502000110601,male,1.703687802617546,1115.9155107144925,-8.690375769791576,male,0.006329113924050633,0.8544303797468354,male,pseudobulk,male,True,False,0.15701511392764006,0.3155630305809251,56,False,B3_HGR0000051_T2,32,False,26,False,2,2,4.291872406245575,4.080986811366844,T1,T1,1,1,1,1,HGR0000083,HGR0000083,B1_HGR0000083_T0,0.5064968909285001,0.5064968909285001,1,1,2,1,1,1,1,HGR0000083,HGR0000083,B1_HGR0000083_T0,0.4739585014708595,0.4739585014708595,1,1,2,5,1,3,1,HGR0000101,HGR0000083,B3_HGR0000101_T3,0.20066334867204233,0.2753006978646358,1,1,2,pass,True,"within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 2/2); not a timepoint failure; only 158 retained cells (< 200; excluded by prepare_dataset)"
+HGR0000083_T1,GSM4929244,B1_HGR0000083_T1,HGR0000083,10,Batch 1 bulk RNAseq HGR0000083_T1,HGR0000083_T1,exact_subject_timepoint,COVID,T1,B1,Timepoint 1,Moderate,alive,Alive,13,8,Male,55,1680,1365,315,11,0,304,299,False,12456228.0,11845211.0,1293298.0,0.0,1087.3275601570556,-10.08789712276788,male,0.7384291839028345,690.4312869491503,-8.635657777044953,male,0.0033444816053511705,0.8461538461538461,male,pseudobulk,male,True,False,0.2945901787943319,0.2945901787943319,1,True,B1_HGR0000083_T1,1,True,1,True,1,1,9.127617028763131,8.509534391654437,T1,T1,1,1,1,1,HGR0000083,HGR0000083,B1_HGR0000083_T1,0.6942513008055402,0.6942513008055402,1,1,2,1,1,1,1,HGR0000083,HGR0000083,B1_HGR0000083_T1,0.8065315402829264,0.8065315402829264,1,1,2,1,1,1,1,HGR0000083,HGR0000083,B1_HGR0000083_T1,0.4489707035375605,0.4489707035375605,1,1,2,pass,True,
+HGR0000089_T1,GSM4929245,B1_HGR0000089_T1,HGR0000089,11,Batch 1 bulk RNAseq HGR0000089,HGR0000089_T1,subject_timepoint; GEO bulk timepoint characteristic differs,COVID,T1,B1,Timepoint 0,Critical,alive,Alive,20,8,Male,78,2476,2102,374,9,0,365,358,False,13949392.0,13144916.0,1497775.0,0.0,913.3731419978734,-9.83663921747897,male,0.0,665.7575897649241,-9.381018531978967,male,0.0,0.8016759776536313,male,pseudobulk,male,True,False,0.4624357720698913,0.4624357720698913,1,True,B1_HGR0000089_T1,1,True,1,True,1,1,3.097731131129418,2.9994049622856895,T1,T1,1,1,1,1,HGR0000089,HGR0000089,B1_HGR0000089_T1,0.410596459108106,0.410596459108106,1,1,1,1,1,1,1,HGR0000089,HGR0000089,B1_HGR0000089_T1,0.5584664547405632,0.5584664547405632,1,1,1,1,1,1,1,HGR0000089,HGR0000089,B1_HGR0000089_T1,0.3889627730244914,0.3889627730244914,1,1,1,pass,True,subject_timepoint; GEO bulk timepoint characteristic differs
+HGR0000091_T0,GSM4929246,B1_HGR0000091_T0,HGR0000091,12,Batch 1 bulk RNAseq HGR0000091,HGR0000091_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Moderate,alive,Alive,20,3,Male,35,1764,1383,381,13,0,368,362,False,14237881.0,13391489.0,1445581.0,0.0,1229.0452490788482,-10.264495672926538,male,0.0,1020.8440569496994,-9.996959328852142,male,0.0,0.8922651933701657,male,pseudobulk,male,True,False,0.26358351057115426,0.28125550462885596,16,False,B3_HGR0000142_T0,1,True,2,False,1,1,7.4410412397634635,6.5176068724057785,T0,T0,1,1,1,1,HGR0000091,HGR0000091,B1_HGR0000091_T0,0.7127298369770455,0.7127298369770455,1,1,1,1,1,1,1,HGR0000091,HGR0000091,B1_HGR0000091_T0,0.7327761152414642,0.7327761152414642,1,1,1,1,1,1,1,HGR0000091,HGR0000091,B1_HGR0000091_T0,0.4746476595789147,0.4746476595789147,1,1,1,pass,True,
+HGR0000093_T0,GSM4929247,B1_HGR0000093_T0,HGR0000093,13,Batch 1 bulk RNAseq HGR0000093_T0,HGR0000093_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,alive,Alive,11,1,Male,70,1773,1288,485,28,0,457,451,False,14237409.0,13247358.0,1748846.0,0.0,978.1976481816318,-9.935456282771822,male,0.0,1057.3073723258956,-10.047542985958584,male,0.0,0.8381374722838137,male,pseudobulk,male,True,False,0.1944298970403941,0.29140071273927654,65,False,B3_HGR0000051_T0,6,False,7,False,1,1,6.944860757755792,4.843544475690307,T0,T0,1,1,1,1,HGR0000093,HGR0000093,B1_HGR0000093_T0,0.5014150659599409,0.5014150659599409,1,1,2,1,1,1,1,HGR0000093,HGR0000093,B1_HGR0000093_T0,0.48426764135291955,0.48426764135291955,1,1,2,1,1,1,1,HGR0000093,HGR0000093,B1_HGR0000093_T0,0.3820685873347586,0.3820685873347586,1,1,2,pass,True,
+HGR0000093_T1,GSM4929248,B1_HGR0000093_T1,HGR0000093,14,Batch 1 bulk RNAseq HGR0000093_T1,HGR0000093_T1,exact_subject_timepoint,COVID,T1,B1,Timepoint 1,Critical,alive,Alive,17,7,Male,70,981,812,169,15,0,154,152,True,13015283.0,12047173.0,562442.0,0.0,749.0424910468716,-9.550828518564785,male,1.7073936976683832,505.38853450984146,-7.547196236482485,male,0.006578947368421052,0.4605263157894737,male,pseudobulk,male,True,False,0.29408432719151906,0.3513679144512859,9,False,B3_HGR0000135_T1,2,False,4,False,1,1,3.7296568554448157,3.333774819465179,T0,T0,1,1,1,1,HGR0000093,HGR0000093,B1_HGR0000093_T1,0.43154569593601194,0.43154569593601194,1,1,2,2,1,2,1,HGR0000135,HGR0000093,B3_HGR0000135_T1,0.3912184232399747,0.3957952024149206,1,1,2,16,12,9,11,HGR0000051,HGR0000134,B3_HGR0000051_T3,0.07169934165180916,0.27236746806383955,2,1,2,pass,True,only 152 retained cells (< 200; excluded by prepare_dataset)
+HGR0000098_T0,GSM4929249,B1_HGR0000098_T0,HGR0000098,15,Batch 1 bulk RNAseq HGR0000098,HGR0000098_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,alive,Alive,,1,Male,60,2552,2128,424,17,0,407,390,False,12676607.0,11862112.0,1561702.0,0.0,1113.8627236767693,-10.122650362463842,male,1.2315718366615536,945.2313846377423,-8.727988953561587,male,0.005128205128205128,0.8205128205128205,male,pseudobulk,male,True,False,0.28108693720937217,0.305973492853984,3,False,B3_HGR0000051_T0,1,True,1,True,1,1,5.042010307724511,4.446735628731321,T0,T0,1,1,1,1,HGR0000098,HGR0000098,B1_HGR0000098_T0,0.6668172763633873,0.6668172763633873,1,1,1,1,1,1,1,HGR0000098,HGR0000098,B1_HGR0000098_T0,0.6818322031431205,0.6818322031431205,1,1,1,1,1,1,1,HGR0000098,HGR0000098,B1_HGR0000098_T0,0.5136971901874888,0.5136971901874888,1,1,1,pass,True,
+HGR0000110_T0,GSM4929250,B1_HGR0000110_T0,HGR0000110,16,Batch 1 bulk RNAseq HGR0000110,HGR0000110_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,deceased,Alive,3,0,Male,73,561,427,134,5,0,129,128,True,11314446.0,11031949.0,540237.0,0.0,391.71162246918675,-8.617326485590425,male,0.0,394.08724513130517,-8.626027461342543,male,0.0,0.4140625,male,pseudobulk,male,True,False,0.3127482752616742,0.32494676296253167,2,False,B3_HGR0000101_T0,3,False,1,True,1,1,7.652598521687934,6.2251082259360695,T0,T0,17,19,14,13,HGR0000051,HGR0000092,B3_HGR0000051_T0,0.15304943089255424,0.47459416700073165,1,1,1,5,5,5,5,HGR0000101,HGR0000083,B3_HGR0000101_T0,0.24869746237199422,0.4037868066529876,1,1,1,5,2,5,2,HGR0000079,HGR0000094,B1_HGR0000079_T0,0.17701012868076324,0.35912665655246734,1,1,1,fail: expression: own subject rank 14 (bulk->47 sc subjects) and 13 (sc->48 bulk subjects); bulk best subject = HGR0000051,False,only 128 retained cells (< 200; excluded by prepare_dataset)
+HGR0000136_T0,GSM4929251,B1_HGR0000136_T0,HGR0000136,17,Batch 1 bulk RNAseq HGR0000136,HGR0000136_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Moderate,alive,Alive,17,1,Female,57,1956,1626,330,10,0,320,317,False,13772408.0,12737223.0,1401756.0,1267.8247696408646,0.0,10.309277124979,female,87.01616102511889,10.27749933367546,2.964321246685067,female,0.2744479495268139,0.03785488958990536,female,pseudobulk,female,True,False,0.22014179617467522,0.32227246962731015,32,False,B2_HGR0000115_T1,11,False,4,False,1,1,4.507866623309185,3.9753842404986224,T0,T0,1,1,1,1,HGR0000136,HGR0000136,B1_HGR0000136_T0,0.4317229500919729,0.4317229500919729,1,1,1,1,1,1,1,HGR0000136,HGR0000136,B1_HGR0000136_T0,0.45985019122278903,0.45985019122278903,1,1,1,1,1,1,1,HGR0000136,HGR0000136,B1_HGR0000136_T0,0.5001290529692503,0.5001290529692503,1,1,1,pass,True,
+HGR0000137_T0,GSM4929252,B1_HGR0000137_T0,HGR0000137,18,Batch 1 bulk RNAseq HGR0000137,HGR0000137_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Severe,alive,Alive,4,1,Female,79,1980,1635,345,16,0,329,314,False,13611474.0,12590950.0,1219077.0,1164.605684880271,0.0,10.186864103491988,female,78.19317467416904,8.601249214158594,3.0440820643069086,female,0.2356687898089172,0.03503184713375796,female,pseudobulk,female,True,False,0.22788852080681204,0.30826696575407003,34,False,B2_HGR0000094_T0,6,False,4,False,1,1,4.906862496667871,4.368474873473017,T0,T0,1,1,1,1,HGR0000137,HGR0000137,B1_HGR0000137_T0,0.5119649304371529,0.5119649304371529,1,1,1,1,1,1,1,HGR0000137,HGR0000137,B1_HGR0000137_T0,0.531830183041812,0.531830183041812,1,1,1,1,1,1,1,HGR0000137,HGR0000137,B1_HGR0000137_T0,0.4884041384905634,0.4884041384905634,1,1,1,pass,True,
+HGR0000141_T0,GSM4929253,B1_HGR0000141_T0,HGR0000141,19,Batch 1 bulk RNAseq HGR0000141,HGR0000141_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,deceased,Deceased,20,6,Male,76,1807,1534,273,15,0,258,240,False,12687948.0,11955616.0,957742.0,0.0,520.4151214995522,-9.026288612686695,male,0.0,512.630074835918,-9.004585869544766,male,0.0,0.45,male,pseudobulk,male,True,False,0.3528132356078283,0.4274234984306115,10,False,B3_HGR0000135_T1,2,False,1,True,1,1,4.49651757194116,3.919599306172293,T0,T0,1,1,1,1,HGR0000141,HGR0000141,B1_HGR0000141_T0,0.5197111475734897,0.5197111475734897,1,1,1,1,1,1,1,HGR0000141,HGR0000141,B1_HGR0000141_T0,0.541292739872988,0.541292739872988,1,1,1,1,1,1,1,HGR0000141,HGR0000141,B1_HGR0000141_T0,0.4328293098755704,0.4328293098755704,1,1,1,pass,True,
+HGR0000143_T0,GSM4929254,B1_HGR0000143_T0,HGR0000143,20,Batch 1 bulk RNAseq HGR0000143,HGR0000143_T0,exact_subject_timepoint,COVID,T0,B1,Timepoint 0,Critical,alive,Alive,8,1,Female,54,1636,1336,300,11,0,289,280,False,12297944.0,11510725.0,857145.0,1072.8622605534713,0.0,10.068593241895936,female,100.03077870113881,15.389350569405973,2.623964278668809,female,0.2571428571428571,0.05,female,pseudobulk,female,True,False,0.2663030022161347,0.30800241654210336,3,False,B2_HGR0000094_T0,1,True,3,False,1,1,7.276301969658072,5.794457396952421,T0,T0,1,1,1,1,HGR0000143,HGR0000143,B1_HGR0000143_T0,0.3516549273472461,0.3516549273472461,1,1,1,1,1,1,1,HGR0000143,HGR0000143,B1_HGR0000143_T0,0.5924043977329667,0.5924043977329667,1,1,1,1,1,1,1,HGR0000143,HGR0000143,B1_HGR0000143_T0,0.4485625387590445,0.4485625387590445,1,1,1,pass,True,
+IM000040_HC,GSM4929255,B1_IM000040_HC,IM000040,21,Batch 1 bulk RNAseq IM000040,IM000040,exact_subject_timepoint,HC,HC,B1,Healthy Control,HC,HC,na,,,Male,37,2352,1958,394,15,0,379,373,False,14728828.0,13799982.0,1665075.0,0.0,1110.271638721017,-10.117995796199978,male,1.1529597052112626,921.7912843164045,-8.743539249449654,male,0.005361930294906166,0.9276139410187667,male,pseudobulk,male,True,False,0.31205927342098516,0.31205927342098516,1,True,B1_IM000040_HC,1,True,1,True,1,1,5.148590272052938,4.4541508860134345,HC,HC,1,1,1,1,IM000040,IM000040,B1_IM000040_HC,0.6246278729890282,0.6246278729890282,1,1,1,1,1,1,1,IM000040,IM000040,B1_IM000040_HC,0.6978494370027345,0.6978494370027345,1,1,1,1,1,1,1,IM000040,IM000040,B1_IM000040_HC,0.5244347825984544,0.5244347825984544,1,1,1,pass,True,
+HGR0000042_T0,GSM4929261,B2_HGR0000042_T0,HGR0000042,22,Batch 2 bulk RNAseq HGR0000042_T0,HGR0000042_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Critical,alive,Alive,12,7,Male,53,4551,1141,3410,5,1099,2306,2213,False,18084223.0,17013195.0,11010971.0,0.0,1294.996196408328,-10.339845768755847,male,0.3465691559689432,915.635710069948,-9.410916356278813,male,0.0018075011296882061,0.9136918210573881,male,pseudobulk,male,True,False,0.2676925950682796,0.30155732612593783,8,False,B2_HGR0000042_T1,13,False,7,False,2,1,5.208408709797022,4.891334811355696,T0,T0,1,1,1,1,HGR0000042,HGR0000042,B2_HGR0000042_T0,0.739976887415458,0.739976887415458,1,1,2,1,1,1,1,HGR0000042,HGR0000042,B2_HGR0000042_T0,0.7790675236528766,0.7790675236528766,1,1,2,1,1,1,1,HGR0000042,HGR0000042,B2_HGR0000042_T0,0.7197569174956042,0.7197569174956042,1,1,2,pass,True,"within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 2/1); not a timepoint failure"
+HGR0000042_T1,GSM4929262,B2_HGR0000042_T1,HGR0000042,23,Batch 2 bulk RNAseq HGR0000042_T1,HGR0000042_T1,exact_subject_timepoint,COVID,T1,B2,Timepoint 1,Critical,alive,Alive,18,13,Male,53,6641,1944,4697,2,32,4663,4514,False,19086930.0,18010219.0,19375025.0,0.0,1576.2094794710306,-10.623158571248064,male,0.6363310677826217,1156.996726859833,-9.46695079161119,male,0.0028799291094373063,0.9297740363314134,male,pseudobulk,male,True,False,0.3193114407190615,0.3193114407190615,1,True,B2_HGR0000042_T1,1,True,4,False,1,1,4.85355394714584,4.123977938018881,T0,T0,1,1,1,1,HGR0000042,HGR0000042,B2_HGR0000042_T1,0.730364791987348,0.730364791987348,1,1,2,1,1,1,1,HGR0000042,HGR0000042,B2_HGR0000042_T1,0.717942560289948,0.717942560289948,1,1,2,1,1,1,1,HGR0000042,HGR0000042,B2_HGR0000042_T1,0.7124175832904901,0.7124175832904901,1,1,2,pass,True,
+HGR0000069_T0,GSM4929263,B2_HGR0000069_T0,HGR0000069,24,Batch 2 bulk RNAseq HGR0000069_T0,HGR0000069_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Severe,alive,Alive,13,1,Male,54,6909,2351,4558,3,31,4524,4419,False,18052155.0,16811824.0,16939904.0,0.0,1349.8665394796355,-10.39966943353603,male,0.6098851403315213,1181.014852200158,-9.520074687207243,male,0.0024892509617560534,0.9106132609187599,male,pseudobulk,male,True,False,0.33779078059306866,0.33779078059306866,1,True,B2_HGR0000069_T0,1,True,2,False,1,1,5.961438521048012,4.800275459170987,T0,T0,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T0,0.575724822392058,0.575724822392058,1,1,3,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T0,0.6514492621566557,0.6514492621566557,1,1,3,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T0,0.6168427787606269,0.6168427787606269,1,1,3,pass,True,
+HGR0000069_T1,GSM4929264,B2_HGR0000069_T1,HGR0000069,25,Batch 2 bulk RNAseq HGR0000069_T1,HGR0000069_T1,exact_subject_timepoint,COVID,T1,B2,Timepoint 1,Severe,alive,Alive,20,8,Male,54,6981,1534,5447,3,774,4670,4418,False,18008732.0,16884255.0,21143736.0,0.0,1131.1179487817355,-10.144808556664017,male,1.2647420364388442,893.5854181024877,-8.625728701480469,male,0.004074241738343142,0.901765504753282,male,pseudobulk,male,True,False,0.30712510075266075,0.30712510075266075,1,True,B2_HGR0000069_T1,1,True,10,False,1,1,3.852693338417073,3.735968689548564,T0,T0,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T1,0.8069232763990125,0.8069232763990125,1,1,3,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T1,0.7698977053537568,0.7698977053537568,1,1,3,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T1,0.7163265177108233,0.7163265177108233,1,1,3,pass,True,
+HGR0000069_T2,GSM4929265,B2_HGR0000069_T2,HGR0000069,26,Batch 2 bulk RNAseq HGR0000069_T2,HGR0000069_T2,exact_subject_timepoint,COVID,T2,B2,Timepoint 2,Severe,alive,Alive,33,21,Male,54,5944,1658,4286,7,1866,2413,2351,False,20860514.0,19705277.0,12572105.0,0.0,1362.286662735156,-10.4128732388979,male,0.8330826511901115,971.6015756470856,-9.051433282076525,male,0.0038281582305401958,0.9438536792854104,male,pseudobulk,male,True,False,0.2569974718886929,0.2921944775051895,7,False,B2_HGR0000042_T1,3,False,23,False,1,1,4.323511037075209,4.121319396579765,T0,T0,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T2,0.6046122899103675,0.6046122899103675,1,1,3,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T2,0.761556229064104,0.761556229064104,1,1,3,1,1,1,1,HGR0000069,HGR0000069,B2_HGR0000069_T2,0.5382814626855451,0.5382814626855451,1,1,3,pass,True,
+HGR0000092_T0,GSM4929266,B2_HGR0000092_T0,HGR0000092,27,Batch 2 bulk RNAseq HGR0000092_T0,HGR0000092_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Critical,alive,Alive,11,2,Male,45,7743,2134,5609,9,198,5402,5316,False,22959289.0,21619116.0,23167075.0,0.0,1299.1255957447115,-10.344435282997152,male,0.6164281048805572,1073.5300922529864,-9.376680829687833,male,0.002069224981188864,0.9319036869826938,male,pseudobulk,male,True,False,0.25978377953748477,0.28554155420437977,6,False,B3_HGR0000051_T3,1,True,11,False,1,1,6.594821281730951,5.606481772426682,T0,T0,1,1,1,1,HGR0000092,HGR0000092,B2_HGR0000092_T0,0.7628833792553888,0.7628833792553888,1,1,2,1,1,1,1,HGR0000092,HGR0000092,B2_HGR0000092_T0,0.7715537668387222,0.7715537668387222,1,1,2,1,1,1,1,HGR0000092,HGR0000092,B2_HGR0000092_T0,0.6217988574775817,0.6217988574775817,1,1,2,pass,True,
+HGR0000092_T1,GSM4929267,B2_HGR0000092_T1,HGR0000092,28,Batch 2 bulk RNAseq HGR0000092_T1,HGR0000092_T1,exact_subject_timepoint,COVID,T1,B2,Timepoint 1,Critical,alive,Alive,18,9,Male,45,6429,1938,4491,9,1467,3015,2917,False,18069822.0,16709925.0,17216506.0,0.0,1222.0374943372437,-10.256252917525947,male,1.285106095286147,770.2814186789053,-8.398852394621711,male,0.005142269454919438,0.9338361330133699,male,pseudobulk,male,True,False,0.32533270548298276,0.3323060496649007,2,False,B2_HGR0000069_T1,2,False,9,False,1,1,3.956621121945107,3.6690651548937985,T0,T0,1,1,1,1,HGR0000092,HGR0000092,B2_HGR0000092_T1,0.7654923808174036,0.7654923808174036,1,1,2,1,1,1,1,HGR0000092,HGR0000092,B2_HGR0000092_T1,0.8051457467091533,0.8051457467091533,1,1,2,1,1,1,1,HGR0000092,HGR0000092,B2_HGR0000092_T1,0.5760739179578245,0.5760739179578245,1,1,2,pass,True,
+HGR0000094_T0,GSM4929268,B2_HGR0000094_T0,HGR0000094,29,Batch 2 bulk RNAseq HGR0000094_T0,HGR0000094_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Critical,alive,Alive,6,1,Male,61,4591,1418,3173,2,23,3148,3045,False,15344157.0,14146287.0,11479346.0,0.0,1390.4967213252576,-10.442421794026279,male,0.5742720855199427,1147.9698989543654,-9.511440379885341,male,0.0019704433497536944,0.9004926108374385,male,pseudobulk,male,True,False,0.3727907083422181,0.3727907083422181,1,True,B2_HGR0000094_T0,1,True,1,True,1,1,5.548570620770715,4.53904792408391,T0,T0,1,1,1,1,HGR0000094,HGR0000094,B2_HGR0000094_T0,0.4755554466659166,0.4755554466659166,1,1,2,1,1,1,1,HGR0000094,HGR0000094,B2_HGR0000094_T0,0.7333013383827479,0.7333013383827479,1,1,2,1,1,1,1,HGR0000094,HGR0000094,B2_HGR0000094_T0,0.48195176404752804,0.48195176404752804,1,1,2,pass,True,
+HGR0000094_T1,GSM4929269,B2_HGR0000094_T1,HGR0000094,30,Batch 2 bulk RNAseq HGR0000094_T1,HGR0000094_T1,exact_subject_timepoint,COVID,T1,B2,Timepoint 1,Critical,alive,Alive,13,8,Male,61,2554,671,1883,2,914,967,908,False,16597065.0,15392794.0,4493549.0,0.0,1328.8494080128023,-10.377047169024781,male,0.6391743571770225,791.0847960660949,-8.916541754536164,male,0.003303964757709251,0.8711453744493393,male,pseudobulk,male,True,False,0.25176877500589695,0.27300441433272266,8,False,B3_HGR0000051_T3,15,False,26,False,1,1,4.0358062296798884,3.6543115160354707,T0,T0,1,1,1,1,HGR0000094,HGR0000094,B2_HGR0000094_T1,0.6299326121343625,0.6299326121343625,1,1,2,1,1,1,1,HGR0000094,HGR0000094,B2_HGR0000094_T1,0.7374057182321906,0.7374057182321906,1,1,2,1,1,1,1,HGR0000094,HGR0000094,B2_HGR0000094_T1,0.5625178252975893,0.5625178252975893,1,1,2,pass,True,
+HGR0000115_T1,GSM4929270,B2_HGR0000115_T1,HGR0000115,31,Batch 2 bulk RNAseq HGR0000115_T1,HGR0000115_T1,exact_subject_timepoint,COVID,T1,B2,Timepoint 1,Severe,alive,Alive,11,8,Male,24,8138,2823,5315,1,29,5285,5186,False,17362517.0,16308343.0,23488709.0,0.0,1361.553742467178,-10.412097419110768,male,0.5672443456070694,1254.7039750295799,-9.646050557192522,male,0.0023139220979560356,0.9544928654068646,male,pseudobulk,male,True,False,0.2745380618028078,0.31925416652786365,8,False,B3_HGR0000051_T3,2,False,11,False,1,1,5.442014099983955,4.31843217878939,T1,T1,1,1,1,1,HGR0000115,HGR0000115,B2_HGR0000115_T1,0.5012253043916323,0.5012253043916323,1,1,1,1,1,1,1,HGR0000115,HGR0000115,B2_HGR0000115_T1,0.5223633779229611,0.5223633779229611,1,1,1,1,1,1,1,HGR0000115,HGR0000115,B2_HGR0000115_T1,0.5304443714238375,0.5304443714238375,1,1,1,pass,True,
+HGR0000124_T0,GSM4929271,B2_HGR0000124_T0,HGR0000124,32,Batch 2 bulk RNAseq HGR0000124_T0,HGR0000124_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Critical,alive,Alive,36,28,Male,79,14056,4842,9214,6,73,9135,8731,False,20169871.0,19099902.0,39533365.0,0.0,459.84428953462316,-8.848135563719627,male,0.6029024931826801,663.337439099312,-8.695085743360158,male,0.0025197571870347038,0.5685488489291032,male,pseudobulk,male,True,False,0.2706342916400125,0.30470787657522347,10,False,B3_HGR0000051_T3,12,False,21,False,2,1,4.260333179021862,3.898035408765686,T1,T1,1,1,1,1,HGR0000124,HGR0000124,B2_HGR0000124_T0,0.6836604134152865,0.6836604134152865,1,1,2,1,1,1,1,HGR0000124,HGR0000124,B2_HGR0000124_T0,0.6004004742797254,0.6004004742797254,1,1,2,1,1,1,1,HGR0000124,HGR0000124,B2_HGR0000124_T0,0.6563489368740208,0.6563489368740208,1,1,2,pass,True,"within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 2/1); not a timepoint failure"
+HGR0000124_T1,GSM4929272,B2_HGR0000124_T1,HGR0000124,33,Batch 2 bulk RNAseq HGR0000124_T1,HGR0000124_T1,exact_subject_timepoint,COVID,T1,B2,Timepoint 1,Critical,alive,Alive,49,41,Male,79,5969,1928,4041,1,1423,2617,2515,False,17824077.0,16885347.0,14654971.0,0.0,658.4913204762299,-9.365209862157837,male,1.1142850756786373,507.3929865193136,-7.909630404784134,male,0.005964214711729622,0.5411530815109344,male,pseudobulk,male,True,False,0.2963418713087741,0.30734542213485655,2,False,B3_HGR0000051_T3,1,True,10,False,1,2,4.696863913415172,4.323093077661307,T1,T1,1,1,1,1,HGR0000124,HGR0000124,B2_HGR0000124_T1,0.705607381533158,0.705607381533158,1,1,2,1,1,1,1,HGR0000124,HGR0000124,B2_HGR0000124_T1,0.7637590945946582,0.7637590945946582,1,1,2,1,1,1,1,HGR0000124,HGR0000124,B2_HGR0000124_T1,0.6049785615996934,0.6049785615996934,1,1,2,pass,True,"within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 1/2); not a timepoint failure"
+HGR0000144_T0,GSM4929273,B2_HGR0000144_T0,HGR0000144,34,Batch 2 bulk RNAseq HGR0000144_T0,HGR0000144_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Severe,alive,Alive,15,3,Female,84,5288,999,4289,5,2001,2283,2243,False,17791383.0,16785185.0,11825415.0,460.054173416423,0.16862095543668526,8.623985400955133,female,85.83281366665102,30.602668278138047,1.4581939593783497,ambiguous,0.3290236290682122,0.1506910387873384,female,per-cell (pseudobulk ambiguous),female,True,False,0.30403731681043794,0.3238172847527492,6,False,B3_HGR0000051_T3,1,True,1,True,1,1,6.701207186075185,6.109214781189526,T0,T0,1,1,1,1,HGR0000144,HGR0000144,B2_HGR0000144_T0,0.7857593018803359,0.7857593018803359,1,1,2,1,1,1,1,HGR0000144,HGR0000144,B2_HGR0000144_T0,0.8099598625577668,0.8099598625577668,1,1,2,1,1,1,1,HGR0000144,HGR0000144,B2_HGR0000144_T0,0.7057987195068303,0.7057987195068303,1,1,2,pass,True,"sc sex from per-cell detection (pseudobulk ambiguous: ambient pool-mate RNA / low 5' XIST capture; 0.151 of cells with Y UMIs, 0.329 with XIST)"
+HGR0000144_T2,GSM4929274,B2_HGR0000144_T2,HGR0000144,35,Batch 2 bulk RNAseq HGR0000144_T2,HGR0000144_T2,exact_subject_timepoint,COVID,T2,B2,Timepoint 2,Severe,alive,Alive,28,16,Female,84,8949,1691,7258,8,816,6434,6257,False,19361566.0,18233544.0,28446740.0,672.6728612757872,0.10329742955709265,9.254082603162821,female,103.5850598569128,33.346562698528274,1.6064391442426498,ambiguous,0.3442544350327633,0.1382451654147355,female,per-cell (pseudobulk ambiguous),female,True,False,0.32801018310873387,0.32801018310873387,1,True,B2_HGR0000144_T2,1,True,1,True,1,1,3.9246104896340497,3.569519682119731,T0,T0,1,1,1,1,HGR0000144,HGR0000144,B2_HGR0000144_T2,0.6612392802730919,0.6612392802730919,1,1,2,1,1,1,1,HGR0000144,HGR0000144,B2_HGR0000144_T2,0.7067419717343971,0.7067419717343971,1,1,2,1,1,1,1,HGR0000144,HGR0000144,B2_HGR0000144_T2,0.6519867256608174,0.6519867256608174,1,1,2,pass,True,"sc sex from per-cell detection (pseudobulk ambiguous: ambient pool-mate RNA / low 5' XIST capture; 0.138 of cells with Y UMIs, 0.344 with XIST)"
+HGR0000391_T0,GSM4929275,B2_HGR0000391_T0,HGR0000391,36,Batch 2 bulk RNAseq HGR0000391_T0,HGR0000391_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Critical,alive,Alive,6,1,Male,66,9292,2382,6910,5,59,6846,6728,False,20341160.0,19432977.0,25940444.0,0.0,1065.2784796933902,-10.0583685602865,male,0.726051508635203,941.398386096404,-9.092717740356392,male,0.002526753864447087,0.9014565992865636,male,pseudobulk,male,True,False,0.24254739406011439,0.26856791882220116,9,False,B2_HGR0000395_T0,3,False,13,False,1,1,8.490362068250137,7.604654564798312,T0,T0,1,1,1,1,HGR0000391,HGR0000391,B2_HGR0000391_T0,0.7299440633678598,0.7299440633678598,1,1,1,1,1,1,1,HGR0000391,HGR0000391,B2_HGR0000391_T0,0.7844722681529462,0.7844722681529462,1,1,1,1,1,1,1,HGR0000391,HGR0000391,B2_HGR0000391_T0,0.5616541285487228,0.5616541285487228,1,1,1,pass,True,
+HGR0000395_T0,GSM4929276,B2_HGR0000395_T0,HGR0000395,37,Batch 2 bulk RNAseq HGR0000395_T0,HGR0000395_T0,exact_subject_timepoint,COVID,T0,B2,Timepoint 0,Severe,alive,Alive,14,2,Male,50,5628,1557,4071,3,1197,2871,2786,False,19193734.0,18114961.0,14328140.0,0.0,1229.8284429699818,-10.265413972784506,male,1.404297900534516,908.1126423456536,-8.562699588549712,male,0.005025125628140704,0.9185211773151472,male,pseudobulk,male,True,False,0.31938413127778675,0.31938413127778675,1,True,B2_HGR0000395_T0,1,True,1,True,1,1,5.257907260693159,4.872435146026965,T0,T0,1,1,1,1,HGR0000395,HGR0000395,B2_HGR0000395_T0,0.7033195970240774,0.7033195970240774,1,1,1,1,1,1,1,HGR0000395,HGR0000395,B2_HGR0000395_T0,0.7386869222614314,0.7386869222614314,1,1,1,1,1,1,1,HGR0000395,HGR0000395,B2_HGR0000395_T0,0.6058268739334889,0.6058268739334889,1,1,1,pass,True,
+HGR0000418_T1,GSM4929277,B2_HGR0000418_T1,HGR0000418,38,Batch 2 bulk RNAseq HGR0000418_T1,HGR0000418_T1,exact_subject_timepoint,COVID,T1,B2,Timepoint 1,Critical,alive,Alive,32,11,Male,50,8474,1828,6646,5,328,6313,6151,False,20418731.0,19266210.0,28989868.0,0.0,1320.650142263983,-10.368124612173208,male,0.691004526112551,1105.8375766221193,-9.354347292136321,male,0.003251503820516989,0.9370834010729963,male,pseudobulk,male,True,False,0.29762968392743194,0.3083149351493736,2,False,B3_HGR0000051_T3,1,True,9,False,1,1,4.07030672242495,3.767027334061614,T1,T1,1,1,1,1,HGR0000418,HGR0000418,B2_HGR0000418_T1,0.6578307719731754,0.6578307719731754,1,1,1,1,1,1,1,HGR0000418,HGR0000418,B2_HGR0000418_T1,0.7735049299996565,0.7735049299996565,1,1,1,1,1,1,1,HGR0000418,HGR0000418,B2_HGR0000418_T1,0.5781086444368281,0.5781086444368281,1,1,1,pass,True,
+SHD2_HC,GSM4929278,B2_SHD2_HC,SHD2,39,Batch 2 bulk RNAseq SHD2,SHD2,exact_subject_timepoint,HC,HC,B2,Healthy Control,HC,HC,na,,,Male,53,8603,2885,5718,1,2179,3538,3484,False,28220948.0,26661675.0,19831531.0,0.0,1183.2699596058928,-10.209782271871052,male,0.675951014795602,975.3973143500538,-9.186344534538966,male,0.0037313432835820895,0.9466130884041332,male,pseudobulk,male,True,False,0.28249693733228237,0.28249693733228237,1,True,B2_SHD2_HC,1,True,3,False,1,1,3.9486183012345872,3.754711689336466,HC,HC,1,1,1,1,SHD2,SHD2,B2_SHD2_HC,0.7471081447929092,0.7471081447929092,1,1,1,1,1,1,1,SHD2,SHD2,B2_SHD2_HC,0.7383202959536468,0.7383202959536468,1,1,1,1,1,1,1,SHD2,SHD2,B2_SHD2_HC,0.6674833941169087,0.6674833941169087,1,1,1,pass,True,
+SHD4_HC,GSM4929279,B2_SHD4_HC,SHD4,40,Batch 2 bulk RNAseq SHD4,SHD4,exact_subject_timepoint,HC,HC,B2,Healthy Control,HC,HC,na,,,Male,63,10177,2890,7287,7,40,7240,7126,False,21978808.0,20863808.0,34387241.0,0.0,1192.3758558698908,-10.220832778659211,male,0.9690790681025575,968.6360605285678,-8.943778499433906,male,0.0030872859949480774,0.9469548133595285,male,pseudobulk,male,True,False,0.2746137121784326,0.2746137121784326,1,True,B2_SHD4_HC,1,True,4,False,1,1,4.356944911433897,4.026826123874041,HC,HC,1,1,1,1,SHD4,SHD4,B2_SHD4_HC,0.8053307170046947,0.8053307170046947,1,1,1,1,1,1,1,SHD4,SHD4,B2_SHD4_HC,0.796098412070074,0.796098412070074,1,1,1,1,1,1,1,SHD4,SHD4,B2_SHD4_HC,0.6928978007759055,0.6928978007759055,1,1,1,pass,True,
+SHD7_HC,GSM4929280,B2_SHD7_HC,SHD7,41,Batch 2 bulk RNAseq SHD7,SHD7,exact_subject_timepoint,HC,HC,B2,Healthy Control,HC,HC,na,,,Male,77,9502,2989,6513,2,23,6488,6375,False,19163297.0,18041521.0,31254749.0,0.0,1312.1959128431815,-10.358866449486069,male,0.6099965068550035,1015.2781860094678,-9.302022091817078,male,0.002980392156862745,0.9383529411764706,male,pseudobulk,male,True,False,0.3091985211222013,0.3091985211222013,1,True,B2_SHD7_HC,1,True,1,True,1,1,4.399216982993381,3.9372281460875853,HC,HC,1,1,1,1,SHD7,SHD7,B2_SHD7_HC,0.693872198046374,0.693872198046374,1,1,1,1,1,1,1,SHD7,SHD7,B2_SHD7_HC,0.6768114216977228,0.6768114216977228,1,1,1,1,1,1,1,SHD7,SHD7,B2_SHD7_HC,0.5647107350570535,0.5647107350570535,1,1,1,pass,True,
+HGR0000051_T0,GSM4929283,B3_HGR0000051_T0,HGR0000051,42,Batch 3 bulk RNAseq HGR0000051_T0,HGR0000051_T0,exact_subject_timepoint,COVID,T0,B3,Timepoint 0,Critical,alive,Alive,10,3,Male,55,4378,1153,3225,67,0,3158,2947,False,17519627.0,15356413.0,12815466.0,0.0,949.7348316833458,-9.892899206612679,male,0.5209662882714859,852.1520001012162,-9.131670812517923,male,0.0023752969121140144,0.836443841194435,male,pseudobulk,male,True,False,0.36130672766287786,0.36130672766287786,1,True,B3_HGR0000051_T0,1,True,1,True,1,1,4.906982327469576,4.522210208996498,T3,T3,1,3,1,3,HGR0000051,HGR0000110,B3_HGR0000051_T0,0.35176738675281677,0.35176738675281677,1,1,4,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T0,0.7797525150575447,0.7797525150575447,1,1,4,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T0,0.5569785464459329,0.5569785464459329,1,1,4,pass,True,
+HGR0000051_T1,GSM4929284,B3_HGR0000051_T1,HGR0000051,43,Batch 3 bulk RNAseq HGR0000051_T1,HGR0000051_T1,exact_subject_timepoint,COVID,T1,B3,Timepoint 1,Critical,alive,Alive,14,7,Male,55,6772,1715,5057,0,0,5057,4888,False,18482172.0,17190164.0,21840946.0,0.0,1044.682410703677,-10.030229034837262,male,0.611356167893775,951.7068802197807,-9.207613180520756,male,0.0028641571194762683,0.8938216039279869,male,pseudobulk,male,True,False,0.29912408418892206,0.32558080401715095,3,False,B3_HGR0000051_T3,1,True,5,False,1,1,4.347548221282799,3.960133912254287,T3,T3,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T1,0.832853671056365,0.832853671056365,1,1,4,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T1,0.8568236992641609,0.8568236992641609,1,1,4,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T1,0.6412236997879359,0.6412236997879359,1,1,4,pass,True,
+HGR0000051_T2,GSM4929285,B3_HGR0000051_T2,HGR0000051,44,Batch 3 bulk RNAseq HGR0000051_T2,HGR0000051_T2,exact_subject_timepoint,COVID,T2,B3,Timepoint 2,Critical,alive,Alive,17,10,Male,55,6060,1773,4287,71,2037,2179,2109,False,18516442.0,17326737.0,11289003.0,0.0,1125.2161727398816,-10.13726805826731,male,0.5093265328054672,696.5889213669441,-8.852328361014589,male,0.002844950213371266,0.8795637743006164,male,pseudobulk,male,True,False,0.3587043656025774,0.3587043656025774,1,True,B3_HGR0000051_T2,1,True,5,False,2,1,4.3486279238629235,4.026098680698358,T3,T3,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T2,0.6874260864221282,0.6874260864221282,1,1,4,2,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T1,0.5890611403377172,0.6601766437858136,2,1,4,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T2,0.48588678436658705,0.48588678436658705,1,1,4,pass,True,"within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 2/1); not a timepoint failure"
+HGR0000051_T3,GSM4929286,B3_HGR0000051_T3,HGR0000051,45,Batch 3 bulk RNAseq HGR0000051_T3,HGR0000051_T3,exact_subject_timepoint,COVID,T3,B3,Timepoint 3,Critical,alive,Alive,20,13,Male,55,7400,2207,5193,74,0,5119,5007,False,18317829.0,17258815.0,22974594.0,0.0,1228.693640496371,-10.26408321942273,male,1.0778279677122538,1159.4112538837044,-9.12534426462524,male,0.003395246654683443,0.902336728579988,male,pseudobulk,male,True,False,0.39283873320069734,0.39283873320069734,1,True,B3_HGR0000051_T3,1,True,1,True,1,1,5.056120465183856,4.631507896417957,T3,T3,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T3,0.7838617048632136,0.7838617048632136,1,1,4,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T3,0.8720208309003848,0.8720208309003848,1,1,4,1,1,1,1,HGR0000051,HGR0000051,B3_HGR0000051_T3,0.7364027525256175,0.7364027525256175,1,1,4,pass,True,
+HGR0000101_T0,GSM4929287,B3_HGR0000101_T0,HGR0000101,46,Batch 3 bulk RNAseq HGR0000101_T0,HGR0000101_T0,exact_subject_timepoint,COVID,T0,B3,Timepoint 0,Critical,alive,Alive,8,1,Male,73,2904,890,2014,23,1014,977,920,False,18432081.0,17229227.0,4306863.0,0.0,1019.3640099563364,-9.994868203206284,male,0.4455108985331108,734.6474716810997,-8.991291284166705,male,0.002173913043478261,0.7989130434782609,male,pseudobulk,male,True,False,0.3466572121316757,0.3466572121316757,1,True,B3_HGR0000101_T0,5,False,1,True,1,1,4.027870069877872,3.7610853803221773,T0,T0,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T0,0.6136672820086329,0.6136672820086329,1,1,3,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T0,0.8070717963417475,0.8070717963417475,1,1,3,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T0,0.3972932331976173,0.3972932331976173,1,1,3,pass,True,
+HGR0000101_T1,GSM4929288,B3_HGR0000101_T1,HGR0000101,47,Batch 3 bulk RNAseq HGR0000101_T1,HGR0000101_T1,exact_subject_timepoint,COVID,T1,B3,Timepoint 1,Critical,alive,Alive,14,7,Male,73,7872,2801,5071,61,0,5010,4781,False,18300389.0,17246997.0,21311199.0,0.0,988.9407268883738,-9.951198335588979,male,0.3593963686411214,898.8503179714447,-9.37057505773758,male,0.0016732901066722444,0.870110855469567,male,pseudobulk,male,True,False,0.2679780525569475,0.27696693939233563,2,False,B2_HGR0000069_T1,1,True,5,False,1,1,3.530518002587089,3.5085553217990118,T0,T0,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T1,0.7808292513648778,0.7808292513648778,1,1,3,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T1,0.8448257155265266,0.8448257155265266,1,1,3,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T1,0.6478139896420765,0.6478139896420765,1,1,3,pass,True,
+HGR0000101_T3,GSM4929289,B3_HGR0000101_T3,HGR0000101,48,Batch 3 bulk RNAseq HGR0000101_T3,HGR0000101_T3,exact_subject_timepoint,COVID,T3,B3,Timepoint 3,Critical,alive,Alive,27,20,Male,73,6075,1999,4076,75,0,4001,3855,False,21190725.0,20016870.0,17406010.0,0.0,1278.295103164238,-10.321133382942069,male,0.3299682075632013,971.3164136635436,-9.513890306472264,male,0.0012970168612191958,0.8671854734111544,male,pseudobulk,male,True,False,0.28952492731727447,0.3092372009027334,6,False,B3_HGR0000051_T3,1,True,1,True,1,1,3.522271677437736,3.440523535462404,T0,T0,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T3,0.8011646419299828,0.8011646419299828,1,1,3,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T3,0.812907292118485,0.812907292118485,1,1,3,1,1,1,1,HGR0000101,HGR0000101,B3_HGR0000101_T3,0.603225171477045,0.603225171477045,1,1,3,pass,True,
+HGR0000102_T0,GSM4929290,B3_HGR0000102_T0,HGR0000102,49,Batch 3 bulk RNAseq HGR0000102_T0,HGR0000102_T0,exact_subject_timepoint,COVID,T0,B3,Timepoint 0,Critical,alive,Alive,10,3,Male,58,7555,2860,4695,69,0,4626,4533,False,18323261.0,17087068.0,21032460.0,0.0,1270.2433262288846,-10.312024484906699,male,0.4989055825720488,990.917197094011,-9.370166373163958,male,0.0022060445621001545,0.9247738804323847,male,pseudobulk,male,True,False,0.25354569706850655,0.28199297211890695,15,False,B3_HGR0000142_T0,1,True,7,False,1,1,5.807557337860065,5.126904729346219,T0,T0,1,1,1,1,HGR0000102,HGR0000102,B3_HGR0000102_T0,0.6016472862027202,0.6016472862027202,1,1,2,1,1,1,1,HGR0000102,HGR0000102,B3_HGR0000102_T0,0.6699322713148765,0.6699322713148765,1,1,2,1,1,1,1,HGR0000102,HGR0000102,B3_HGR0000102_T0,0.6310787492781742,0.6310787492781742,1,1,2,pass,True,
+HGR0000102_T1,GSM4929291,B3_HGR0000102_T1,HGR0000102,50,Batch 3 bulk RNAseq HGR0000102_T1,HGR0000102_T1,exact_subject_timepoint,COVID,T1,B3,Timepoint 1,Critical,alive,Alive,17,10,Male,58,9292,3508,5784,94,0,5690,5393,False,22750759.0,21404959.0,26449724.0,0.0,1065.5468681286632,-10.05873164924457,male,0.3632314332345937,829.9838249410466,-9.251646078498915,male,0.0018542555164101613,0.9026515853884666,male,pseudobulk,male,True,False,0.34959958841659927,0.3635771169719229,3,False,B3_HGR0000051_T2,1,True,5,False,1,1,3.776633999265935,3.7037344385287976,T0,T0,1,1,1,1,HGR0000102,HGR0000102,B3_HGR0000102_T1,0.7417427608843071,0.7417427608843071,1,1,2,1,1,1,1,HGR0000102,HGR0000102,B3_HGR0000102_T1,0.7288407169118163,0.7288407169118163,1,1,2,1,1,1,1,HGR0000102,HGR0000102,B3_HGR0000102_T1,0.6403910639609836,0.6403910639609836,1,1,2,pass,True,
+HGR0000134_T0,GSM4929292,B3_HGR0000134_T0,HGR0000134,51,Batch 3 bulk RNAseq HGR0000134_T0,HGR0000134_T0,exact_subject_timepoint,COVID,T0,B3,Timepoint 0,Critical,alive,Alive,16,2,Male,53,8210,2121,6089,0,0,6089,5941,False,23343766.0,22044063.0,29475292.0,0.0,1124.5828972069032,-10.136456597327278,male,0.7149521518272389,1005.287721119264,-9.196658824014296,male,0.002861471132805925,0.9378892442349773,male,pseudobulk,male,True,False,0.26252241196882725,0.2911834599098805,10,False,B3_HGR0000051_T3,1,True,10,False,1,1,5.554847124628393,4.931586116462738,T1,T1,1,1,1,1,HGR0000134,HGR0000134,B3_HGR0000134_T0,0.8030949897125976,0.8030949897125976,1,1,2,1,1,1,1,HGR0000134,HGR0000134,B3_HGR0000134_T0,0.8250000754891376,0.8250000754891376,1,1,2,1,1,1,1,HGR0000134,HGR0000134,B3_HGR0000134_T0,0.7742211890862681,0.7742211890862681,1,1,2,pass,True,
+HGR0000134_T1,GSM4929293,B3_HGR0000134_T1,HGR0000134,52,Batch 3 bulk RNAseq HGR0000134_T1,HGR0000134_T1,exact_subject_timepoint,COVID,T1,B3,Timepoint 1,Critical,alive,Alive,22,8,Male,53,9372,2918,6454,84,3587,2783,2705,False,20713518.0,19521263.0,13835392.0,0.0,1269.7022302054147,-10.311410280908884,male,1.876782552428442,826.6879591122763,-8.168486983460712,male,0.006654343807763401,0.8964879852125693,male,pseudobulk,male,True,False,0.2920136067977066,0.30516970647152447,6,False,B3_HGR0000051_T3,4,False,9,False,2,2,6.036257812067533,5.779285607044534,T1,T1,2,1,1,1,HGR0000134,HGR0000134,B3_HGR0000134_T0,0.6458865049552729,0.6458954622978328,2,1,2,2,1,1,1,HGR0000134,HGR0000134,B3_HGR0000134_T0,0.6674166923611318,0.6845996594380482,2,1,2,1,1,1,1,HGR0000134,HGR0000134,B3_HGR0000134_T1,0.6007771143564281,0.6007771143564281,1,1,2,pass,True,"within subject, another timepoint beats the own one in some tests (residualised 2/1, centred 2/2); not a timepoint failure"
+HGR0000135_T0,GSM4929294,B3_HGR0000135_T0,HGR0000135,53,Batch 3 bulk RNAseq HGR0000135_T0,HGR0000135_T0,exact_subject_timepoint,COVID,T0,B3,Timepoint 0,Critical,alive,Alive,10,3,Male,59,8841,2772,6069,0,0,6069,5972,False,20104322.0,19203029.0,22665348.0,0.04974054832587739,942.9315746136576,-9.812505674048897,male,0.4573262627921431,959.137898419522,-9.363773914731084,male,0.001841929002009377,0.8938379102478232,male,pseudobulk,male,True,False,0.21990113135414963,0.2921974424978109,30,False,B3_HGR0000051_T2,15,False,17,False,1,1,7.633978965095586,6.858510007990305,T0,T0,1,1,1,1,HGR0000135,HGR0000135,B3_HGR0000135_T0,0.7169162037032756,0.7169162037032756,1,1,2,1,1,1,1,HGR0000135,HGR0000135,B3_HGR0000135_T0,0.7534913714436429,0.7534913714436429,1,1,2,1,1,1,1,HGR0000135,HGR0000135,B3_HGR0000135_T0,0.7071896283355098,0.7071896283355098,1,1,2,pass,True,
+HGR0000135_T1,GSM4929295,B3_HGR0000135_T1,HGR0000135,54,Batch 3 bulk RNAseq HGR0000135_T1,HGR0000135_T1,exact_subject_timepoint,COVID,T1,B3,Timepoint 1,Critical,alive,Alive,16,9,Male,59,7509,2380,5129,110,0,5019,4829,False,24565146.0,23255702.0,23774619.0,0.0,1071.0703693761886,-10.0661838902881,male,0.24192161239786975,776.3667744534971,-9.28987751991709,male,0.0010354110581901014,0.878235659556844,male,pseudobulk,male,True,False,0.4066424332256289,0.4066424332256289,1,True,B3_HGR0000135_T1,1,True,3,False,1,1,3.908492128087822,3.638847590695397,T0,T0,1,1,1,1,HGR0000135,HGR0000135,B3_HGR0000135_T1,0.7601917286034381,0.7601917286034381,1,1,2,1,1,1,1,HGR0000135,HGR0000135,B3_HGR0000135_T1,0.7599506809469728,0.7599506809469728,1,1,2,1,1,1,1,HGR0000135,HGR0000135,B3_HGR0000135_T1,0.6751162803213754,0.6751162803213754,1,1,2,pass,True,
+HGR0000142_T0,GSM4929296,B3_HGR0000142_T0,HGR0000142,55,Batch 3 bulk RNAseq HGR0000142_T0,HGR0000142_T0,exact_subject_timepoint,COVID,T0,B3,Timepoint 0,Critical,alive,Alive,12,0,Male,49,7893,2761,5132,80,2186,2866,2766,False,19768478.0,18595766.0,12623018.0,0.0,1127.4009056235893,-10.140064013566107,male,0.6838424071495876,872.0510340950907,-9.018165057516487,male,0.0025307302964569776,0.8785249457700651,male,pseudobulk,male,True,False,0.3248911621122344,0.3248911621122344,1,True,B3_HGR0000142_T0,1,True,3,False,1,1,4.759709901069767,4.455772929581832,T0,T0,1,1,1,1,HGR0000142,HGR0000142,B3_HGR0000142_T0,0.774683433205717,0.774683433205717,1,1,1,1,1,1,1,HGR0000142,HGR0000142,B3_HGR0000142_T0,0.7734121966684366,0.7734121966684366,1,1,1,1,1,1,1,HGR0000142,HGR0000142,B3_HGR0000142_T0,0.6973775588282553,0.6973775588282553,1,1,1,pass,True,
+HGR0000392_T0,GSM4929297,B3_HGR0000392_T0,HGR0000392,56,Batch 3 bulk RNAseq HGR0000392_T0,HGR0000392_T0,exact_subject_timepoint,COVID,T0,B3,Timepoint 0,Critical,alive,Alive,2,2,Male,52,8061,2650,5411,56,0,5355,5261,False,20475556.0,19404317.0,21228357.0,0.0,1146.1959811982638,-10.163896159843578,male,0.578177619722795,976.4085741072493,-9.2745583641422,male,0.0022809351834252043,0.9207375023759742,male,pseudobulk,male,True,False,0.29666224296957194,0.29666224296957194,1,True,B3_HGR0000392_T0,1,True,1,True,1,1,8.503339313445506,7.723622417963519,T0,T0,1,1,1,1,HGR0000392,HGR0000392,B3_HGR0000392_T0,0.8226778658245268,0.8226778658245268,1,1,2,1,1,1,1,HGR0000392,HGR0000392,B3_HGR0000392_T0,0.8450869926284925,0.8450869926284925,1,1,2,1,1,1,1,HGR0000392,HGR0000392,B3_HGR0000392_T0,0.7336309198981853,0.7336309198981853,1,1,2,pass,True,
+HGR0000392_T3,GSM4929298,B3_HGR0000392_T3,HGR0000392,57,Batch 3 bulk RNAseq HGR0000392_T3,HGR0000392_T3,exact_subject_timepoint,COVID,T3,B3,Timepoint 3,Critical,alive,Alive,13,13,Male,52,7958,3106,4852,62,3345,1445,1413,False,22364432.0,20911256.0,6734906.0,0.0,1470.1915970859443,-10.52276942939607,male,1.5637294378463749,1016.2819773785213,-8.632259899906408,male,0.004953998584571833,0.9186128803963199,male,pseudobulk,male,True,False,0.23993565199606268,0.31305636504060935,13,False,B2_HGR0000144_T2,25,False,33,False,2,1,4.149785006806959,3.8646382048137475,T0,T0,1,1,1,1,HGR0000392,HGR0000392,B3_HGR0000392_T3,0.5208891275510141,0.5208891275510141,1,1,2,1,1,1,1,HGR0000392,HGR0000392,B3_HGR0000392_T3,0.5418166902354077,0.5418166902354077,1,1,2,1,1,1,1,HGR0000392,HGR0000392,B3_HGR0000392_T3,0.5207217454734491,0.5207217454734491,1,1,2,pass,True,"within subject, another timepoint beats the own one in some tests (residualised 1/1, centred 2/1); not a timepoint failure"
+HGR0000429_T1,GSM4929299,B3_HGR0000429_T1,HGR0000429,58,Batch 3 bulk RNAseq HGR0000429_T1,HGR0000429_T1,exact_subject_timepoint,COVID,T1,B3,Timepoint 1,Severe,alive,Alive,26,10,Male,54,10783,3377,7406,0,0,7406,7249,False,20637214.0,19303882.0,34372359.0,0.0,1205.5890877518643,-10.236718724635864,male,0.3604530639924524,1043.899800480911,-9.585061703876537,male,0.0015174506828528073,0.940681473306663,male,pseudobulk,male,True,False,0.2233574315823824,0.26446990139078935,18,False,B3_HGR0000051_T3,1,True,27,False,1,1,3.9920389468066246,3.6476540936174477,T2,T2,1,1,1,1,HGR0000429,HGR0000429,B3_HGR0000429_T1,0.7671181707047481,0.7671181707047481,1,1,2,1,1,1,1,HGR0000429,HGR0000429,B3_HGR0000429_T1,0.8054959992296584,0.8054959992296584,1,1,2,1,1,1,1,HGR0000429,HGR0000429,B3_HGR0000429_T1,0.626526422587601,0.626526422587601,1,1,2,pass,True,
+HGR0000429_T2,GSM4929300,B3_HGR0000429_T2,HGR0000429,59,Batch 3 bulk RNAseq HGR0000429_T2,HGR0000429_T2,exact_subject_timepoint,COVID,T2,B3,Timepoint 2,Severe,alive,Alive,28,12,Male,54,8031,2940,5091,91,0,5000,4895,False,21617613.0,20212662.0,24125127.0,0.0,1399.5069668422689,-10.451733444799814,male,0.4743372855906531,1091.25245360843,-9.53302402232718,male,0.0024514811031664963,0.9474974463738509,male,pseudobulk,male,True,False,0.2703788652311239,0.3189501414518295,10,False,B3_HGR0000051_T3,1,True,2,False,1,1,4.202568656490182,3.914464719002303,T2,T2,1,1,1,1,HGR0000429,HGR0000429,B3_HGR0000429_T2,0.7276784131455787,0.7276784131455787,1,1,2,1,1,1,1,HGR0000429,HGR0000429,B3_HGR0000429_T2,0.7698591212387607,0.7698591212387607,1,1,2,1,1,1,1,HGR0000429,HGR0000429,B3_HGR0000429_T2,0.5886381902275527,0.5886381902275527,1,1,2,pass,True,
+HGR0000430_T1,GSM4929301,B3_HGR0000430_T1,HGR0000430,60,Batch 3 bulk RNAseq HGR0000430_T1,HGR0000430_T1,exact_subject_timepoint,COVID,T1,B3,Timepoint 1,Critical,deceased,Alive,20,13,Female,77,5262,1814,3448,73,1434,1941,1875,False,19372959.0,18489797.0,10010211.0,605.3282825819225,0.2580917040086649,8.9127182231971,female,119.87744702734335,22.971684696060965,2.334141887501305,female,0.432,0.11306666666666666,female,pseudobulk,female,True,False,0.31819189028000666,0.31819189028000666,1,True,B3_HGR0000430_T1,1,True,5,False,1,1,4.898544781676722,4.175233121842385,T1,T1,1,1,1,1,HGR0000430,HGR0000430,B3_HGR0000430_T1,0.7786219402814535,0.7786219402814535,1,1,1,1,1,1,1,HGR0000430,HGR0000430,B3_HGR0000430_T1,0.8135108754571556,0.8135108754571556,1,1,1,1,1,1,1,HGR0000430,HGR0000430,B3_HGR0000430_T1,0.635554484611359,0.635554484611359,1,1,1,pass,True,
+SHD1_HC,GSM4929302,B3_SHD1_HC,SHD1,61,Batch 3 bulk RNAseq SHD1,SHD1,exact_subject_timepoint,HC,HC,B3,Healthy Control,HC,HC,na,,,Male,51,9623,3373,6250,0,0,6250,6174,False,20024244.0,18819999.0,28880475.0,0.0,1300.0740502363035,-10.345487359606713,male,0.4283382666369466,1204.553103977961,-9.721141800442002,male,0.002105604146420473,0.9564301911240687,male,pseudobulk,male,True,False,0.2453251143635771,0.24868472639677033,2,False,B2_SHD7_HC,1,True,19,False,1,1,4.209085317768675,3.727547261858314,HC,HC,1,1,1,1,SHD1,SHD1,B3_SHD1_HC,0.7145578131444356,0.7145578131444356,1,1,1,1,1,1,1,SHD1,SHD1,B3_SHD1_HC,0.6298625853159355,0.6298625853159355,1,1,1,1,1,1,1,SHD1,SHD1,B3_SHD1_HC,0.6625206107384806,0.6625206107384806,1,1,1,pass,True,
+SHD3_HC,GSM4929303,B3_SHD3_HC,SHD3,62,Batch 3 bulk RNAseq SHD3,SHD3,exact_subject_timepoint,HC,HC,B3,Healthy Control,HC,HC,na,,,Male,58,9440,4087,5353,99,0,5254,5175,False,23499307.0,22174479.0,25329055.0,0.0,1147.821082553626,-10.165938414750867,male,0.5282804166789146,955.1309933554776,-9.289155195186543,male,0.0021256038647342996,0.9377777777777778,male,pseudobulk,male,True,False,0.26556840349182004,0.26556840349182004,1,True,B3_SHD3_HC,1,True,10,False,1,1,4.0935705159519244,3.9187386959204704,HC,HC,1,1,1,1,SHD3,SHD3,B3_SHD3_HC,0.7176641272630181,0.7176641272630181,1,1,1,1,1,1,1,SHD3,SHD3,B3_SHD3_HC,0.6293422645423229,0.6293422645423229,1,1,1,1,1,1,1,SHD3,SHD3,B3_SHD3_HC,0.7195335289156346,0.7195335289156346,1,1,1,pass,True,
+SHD5_HC,GSM4929304,B3_SHD5_HC,SHD5,63,Batch 3 bulk RNAseq SHD5,SHD5,exact_subject_timepoint,HC,HC,B3,Healthy Control,HC,HC,na,,,Male,73,11962,5358,6604,80,0,6524,6397,False,22132242.0,20842563.0,32704740.0,0.0,1006.992423090259,-9.977269079044369,male,0.7038994268498917,1008.8931826753926,-9.21114680794592,male,0.003126465530717524,0.9351258402376114,male,pseudobulk,male,True,False,0.3008461533463362,0.3008461533463362,1,True,B3_SHD5_HC,1,True,3,False,1,1,4.419121152550814,3.9151875443196844,HC,HC,1,1,1,1,SHD5,SHD5,B3_SHD5_HC,0.6527227471204592,0.6527227471204592,1,1,1,1,1,1,1,SHD5,SHD5,B3_SHD5_HC,0.6645194130747797,0.6645194130747797,1,1,1,1,1,1,1,SHD5,SHD5,B3_SHD5_HC,0.6902645590099279,0.6902645590099279,1,1,1,pass,True,
+SHD6_HC,GSM4929305,B3_SHD6_HC,SHD6,64,Batch 3 bulk RNAseq SHD6,SHD6,exact_subject_timepoint,HC,HC,B3,Healthy Control,HC,HC,na,,,Female,74,9127,3531,5596,70,2972,2554,2487,False,25173064.0,23614439.0,12830684.0,936.358005525271,0.15890000518014016,9.65970026216249,female,117.98905058617814,27.757728451155412,2.0488071942222197,female,0.40570969039002813,0.13148371531966224,female,pseudobulk,female,True,False,0.27651156885107403,0.2795665826652944,2,False,B2_SHD7_HC,2,False,5,False,1,1,5.506392129512847,5.12444702971142,HC,HC,1,1,1,1,SHD6,SHD6,B3_SHD6_HC,0.6013606968712173,0.6013606968712173,1,1,1,1,1,1,1,SHD6,SHD6,B3_SHD6_HC,0.5535634720482265,0.5535634720482265,1,1,1,1,1,1,1,SHD6,SHD6,B3_SHD6_HC,0.6352807755569551,0.6352807755569551,1,1,1,pass,True,