Datasets:

junidude14
/

PBISC-data

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paper-releases/20260928/diffusion/data/cohorts/giroux2022/identity_sex_sc_all.csv ADDED Viewed

	@@ -0,0 +1,42 @@

+sc_gsm,sc_XIST_cpm,sc_RPS4Y1_cpm,sc_DDX3Y_cpm,sc_UTY_cpm,sc_KDM5D_cpm,sc_Ysum_cpm,sc_Ysum3_cpm,sc_sex_call,sc_sex_score,sc_sex_call_3gene,sc_sex_score_3gene,sample_id,subject,sc_sex,paired
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+GSM6249273,95.3928507170811,0.12811288036137672,0.0,0.0,0.0,0.12811288036137672,0.0,female,6.4169428104372646,female,6.5908542432357775,3F3322_dNA,3F3322,FEMALE,False
+GSM6249274,145.9749304905936,0.2070833421971279,0.018825758381557083,0.0,0.0,0.225909100578685,0.018825758381557083,female,6.905574276168752,female,7.172518945362904,94D44E_dNA,94D44E,FEMALE,False
+GSM6249275,0.018991016052972935,992.2426067357297,67.26617885963013,54.086413718866915,24.40345562807022,1137.998654942297,145.75604820656727,male,-10.126408995991628,male,-7.170134819609134,52BA23_dNA,52BA23,MALE,False
+GSM6249276,139.81808693033042,0.09937319611253051,0.049686598056265255,0.0,0.0,0.14905979416879578,0.049686598056265255,female,6.937234963874654,female,7.067730187193432,655A91_dNA,655A91,FEMALE,False

paper-releases/20260928/diffusion/data/cohorts/giroux2022/pairs.csv ADDED Viewed

	@@ -0,0 +1,27 @@

+sample_id,bulk_gsm,sc_gsm,donor_id,row,bulk_title,sc_title,id_match,bulk_count_column,sc_author_library,group,timepoint,sex_geo,age_geo,serostatus_geo,author_cohort,n_cells_library,n_cells_retained,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,sc_Ysum3_cpm,sc_sex_call_3gene,sex_concordant,bulk_possible_mixture,expr_rho_own,expr_rho_best,expr_own_rank_among_sc,expr_best_is_own,expr_best_sc_gsm,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_gsm,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_gsm,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_gsm,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
+450905_d0,GSM6248814,GSM6249236,450905,0,"450905, 0, Mild, Negative","450905, 0, Mild, Negative [scRNA-Seq]",exact_subject_day,450905-0,26-0,mild,0,MALE,60,Negative,Mild,6037,5914,12529452.0,11414754.0,19912341.0,1.9952987568809875,695.0822749470607,-7.86041412100214,male,0.09581737514912178,623.1482992823135,-9.153737663601948,male,156.90095180668692,male,True,False,0.15908122056830967,0.15908122056830967,1,True,GSM6249236,1,True,3,False,1,1,9.349178378334585,8.900499389839453,0,0,1,1,1,1,450905,450905,GSM6249236,0.6217964944941629,0.6217964944941629,1,1,2,1,1,1,1,450905,450905,GSM6249236,0.5688582269727395,0.5688582269727395,1,1,2,1,1,1,1,450905,450905,GSM6249236,0.47167400960919403,0.47167400960919403,1,1,2,pass,True,
+450905_d14,GSM6248816,GSM6249238,450905,1,"450905, 14, Mild, Positive","450905, 14, Mild, Positive [scRNA-Seq]",exact_subject_day,450905-14,26-14,mild,14,MALE,60,Positive,Mild,7593,7407,13059936.0,11019428.0,27135797.0,0.7657005363579117,621.7488355226243,-8.462265926574371,male,0.0,868.2448404662184,-9.763618788419153,male,156.38339587319012,male,True,False,0.08205620780009519,0.10560964808652361,6,False,GSM6249236,2,False,4,False,1,1,5.378811791730247,4.877981665365109,0,0,1,1,1,1,450905,450905,GSM6249238,0.6949431558635568,0.6949431558635568,1,1,2,1,1,1,1,450905,450905,GSM6249238,0.6892199844280182,0.6892199844280182,1,1,2,1,1,1,1,450905,450905,GSM6249238,0.49049392013367854,0.49049392013367854,1,1,2,pass,True,
+0B943B_d0,GSM6248820,GSM6249242,0B943B,2,"0B943B, 0, Mild, Negative","0B943B, 0, Mild, Negative [scRNA-Seq]",exact_subject_day,0B943B-0,28-0,mild,0,MALE,34,Negative,Mild,11702,11344,16402853.0,13476230.0,41784760.0,0.18289501222744603,663.9088943856291,-9.134690833242756,male,0.0,894.6199428966288,-9.806742843018535,male,140.53980198180884,male,True,False,-0.02733470652670024,0.02837990682953512,16,False,GSM6249236,5,False,15,False,1,1,7.459798931832122,6.379649392788042,0,0,1,1,1,1,0B943B,0B943B,GSM6249242,0.5161866251895697,0.5161866251895697,1,1,2,1,1,1,1,0B943B,0B943B,GSM6249242,0.6242178429121948,0.6242178429121948,1,1,2,1,1,1,1,0B943B,0B943B,GSM6249242,0.4304830564190406,0.4304830564190406,1,1,2,pass,True,
+0B943B_d14,GSM6248822,GSM6249244,0B943B,3,"0B943B, 14, Mild, Positive","0B943B, 14, Mild, Positive [scRNA-Seq]",exact_subject_day,0B943B-14,28-14,mild,14,MALE,34,Positive,Mild,15916,15650,9812848.0,8392525.0,51732341.0,0.30572164166814775,603.596427866813,-8.854981274039613,male,0.0185961979366663,1024.594717716503,-9.975662783926767,male,140.02937046309722,male,True,False,0.13308042708446943,0.18508433035421684,15,False,GSM6249269,19,False,1,True,1,2,4.817215937599118,3.9633220114931302,0,0,2,2,1,1,0B943B,0B943B,GSM6249243,0.26311100252168385,0.26885176008292694,1,2,2,1,1,1,1,0B943B,0B943B,GSM6249244,0.377044690871284,0.377044690871284,1,1,2,2,1,1,1,0B943B,0B943B,GSM6249243,0.26189356239340866,0.26717906575038575,1,1,2,pass,True,"within subject, another day beats the own day in some day tests (residualised 1/2, centred 1/2); not a day failure"
+7085CA_d0,GSM6248823,GSM6249245,7085CA,4,"7085CA, 0, Mild, Negative","7085CA, 0, Mild, Negative [scRNA-Seq]",exact_subject_day,7085CA-0,29-0,mild,0,MALE,29,Negative,Mild,12988,12585,1062520.0,914386.0,46156960.0,0.0,563.7540940405828,-9.141479013880268,male,0.0,639.8613947363799,-9.323868554810476,male,141.4663814472404,male,True,False,0.22914104729903415,0.22914104729903415,1,True,GSM6249245,1,True,1,True,1,1,8.957926452096858,8.429474093410157,0,0,1,1,1,1,7085CA,7085CA,GSM6249245,0.46222412770147686,0.46222412770147686,1,1,3,1,1,1,1,7085CA,7085CA,GSM6249245,0.5684834088255171,0.5684834088255171,1,1,3,1,2,1,2,7085CA,56E219,GSM6249245,0.19924313739841293,0.19924313739841293,1,1,3,pass,True,"low-depth bulk (1,062,520 assigned reads)"
+7085CA_d7,GSM6248824,GSM6249246,7085CA,5,"7085CA, 7, Mild, Negative","7085CA, 7, Mild, Negative [scRNA-Seq]",exact_subject_day,7085CA-7,29-7,mild,7,MALE,29,Negative,Mild,9782,9515,14121758.0,11545014.0,35513839.0,0.5665017060907006,754.3678343730292,-8.913489200001145,male,0.0,992.8679558750208,-9.956910379531614,male,159.6525650451114,male,True,False,-0.010959410275586104,0.053727078635866066,12,False,GSM6249243,1,True,14,False,1,1,4.07489054260006,3.4641879281696255,0,0,1,1,1,1,7085CA,7085CA,GSM6249246,0.6620815323402268,0.6620815323402268,1,1,3,1,1,1,1,7085CA,7085CA,GSM6249246,0.7691411716755798,0.7691411716755798,1,1,3,1,1,1,1,7085CA,7085CA,GSM6249246,0.4903095708134218,0.4903095708134218,1,1,3,pass,True,
+7085CA_d14,GSM6248825,GSM6249247,7085CA,6,"7085CA, 14, Mild, Positive","7085CA, 14, Mild, Positive [scRNA-Seq]",exact_subject_day,7085CA-14,29-14,mild,14,MALE,29,Positive,Mild,12349,11887,19290452.0,16547440.0,46953178.0,0.31103470255647714,846.1699083048961,-9.335801661495353,male,0.0,958.1392896192127,-9.905596533538114,male,151.9870530394582,male,True,False,-0.06753495149842315,0.013607626744199667,22,False,GSM6249243,4,False,37,False,1,1,4.048242148244487,3.5677220758937156,0,0,1,1,1,1,7085CA,7085CA,GSM6249247,0.5928925450589622,0.5928925450589622,1,1,3,1,1,1,1,7085CA,7085CA,GSM6249247,0.7235484764876138,0.7235484764876138,1,1,3,1,1,1,1,7085CA,7085CA,GSM6249247,0.5402989083448329,0.5402989083448329,1,1,3,pass,True,
+2AD75E_d0,GSM6248826,GSM6249248,2AD75E,7,"2AD75E, 0, Mild, Negative","2AD75E, 0, Mild, Negative [scRNA-Seq]",exact_subject_day,2AD75E-0,31-0,mild,0,MALE,27,Negative,Mild,7780,7693,12016475.0,10896967.0,30355002.0,3.3287632188308134,862.3161118381222,-7.639790215133883,male,0.0,1098.4295136120782,-10.102539398066417,male,120.83551636683512,male,True,False,-0.09226182789690884,0.045389188186943444,36,False,GSM6249243,4,False,20,False,1,1,6.988301071957416,6.181421139431003,0,0,1,1,1,1,2AD75E,2AD75E,GSM6249248,0.4411565848463888,0.4411565848463888,1,1,3,1,1,1,1,2AD75E,2AD75E,GSM6249248,0.6965830123800317,0.6965830123800317,1,1,3,1,2,1,2,2AD75E,82CCF5,GSM6249248,0.25149515474386247,0.25149515474386247,1,1,3,pass,True,
+2AD75E_d7,GSM6248827,GSM6249249,2AD75E,8,"2AD75E, 7, Mild, Negative","2AD75E, 7, Mild, Negative [scRNA-Seq]",exact_subject_day,2AD75E-7,31-7,mild,7,MALE,27,Negative,Mild,10566,10499,11247214.0,10118367.0,38368166.0,4.534456266236243,1034.8340486808554,-7.548135585439152,male,0.025219629557436105,1223.8834027928165,-10.222495702795651,male,115.48068374349992,male,True,False,-0.09439304908216761,0.046814456679841625,35,False,GSM6249243,7,False,24,False,1,1,4.71117903465959,3.7952856047773724,0,0,1,1,1,1,2AD75E,2AD75E,GSM6249249,0.4834773378112605,0.4834773378112605,1,1,3,1,1,1,1,2AD75E,2AD75E,GSM6249249,0.5799426428471963,0.5799426428471963,1,1,3,1,2,1,2,2AD75E,450905,GSM6249249,0.209431722458563,0.209431722458563,1,1,3,pass,True,
+2AD75E_d14,GSM6248828,GSM6249250,2AD75E,9,"2AD75E, 14, Mild, Positive","2AD75E, 14, Mild, Positive [scRNA-Seq]",exact_subject_day,2AD75E-14,31-14,mild,14,MALE,27,Positive,Mild,13759,13692,12765026.0,11548826.0,48216890.0,2.0368152794988434,968.035631106431,-8.317846747492862,male,0.0,1212.5011694834884,-10.244959783515547,male,110.97897922955082,male,True,False,-0.10531039518726602,0.05055857791259602,41,False,GSM6249243,1,True,20,False,1,1,4.913247516272855,3.9093652438239115,0,0,1,1,1,1,2AD75E,2AD75E,GSM6249250,0.4195337205682596,0.4195337205682596,1,1,3,1,1,1,1,2AD75E,2AD75E,GSM6249250,0.4842306534259869,0.4842306534259869,1,1,3,1,1,1,1,2AD75E,2AD75E,GSM6249250,0.3317906508304005,0.3317906508304005,1,1,3,pass,True,
+B85D75_d0,GSM6248829,GSM6249251,B85D75,10,"B85D75, 0, Severe, Negative","B85D75, 0, Severe, Negative [scRNA-Seq]",exact_subject_day,B85D75-0,34-0,severe,0,FEMALE,32,Negative,Moderate,12034,11441,14568786.0,12769047.0,30093488.0,4734.780234948883,1.8532772737549994,10.69676646763529,female,194.57932542858146,0.191295420706454,7.359078840667686,female,0.031882570117742336,female,True,False,-0.0516222821981265,0.0036714194570383434,8,False,GSM6249243,1,True,40,False,1,1,5.597826446116799,5.130458402285133,0,0,1,1,1,1,B85D75,B85D75,GSM6249251,0.5625005309961268,0.5625005309961268,1,1,2,1,1,1,1,B85D75,B85D75,GSM6249251,0.7058898585984786,0.7058898585984786,1,1,2,1,1,1,1,B85D75,B85D75,GSM6249251,0.5072856933711418,0.5072856933711418,1,1,2,pass,True,
+B85D75_d7,GSM6248830,GSM6249252,B85D75,11,"B85D75, 7, Severe, Positive","B85D75, 7, Severe, Positive [scRNA-Seq]",exact_subject_day,B85D75-7,34-7,severe,7,FEMALE,32,Positive,Moderate,12686,12328,14230124.0,12496138.0,35246423.0,4097.645248909988,1.7568364126693485,10.537917747972562,female,114.90493391628291,0.16383783353082165,6.637908120540016,female,0.0,female,True,False,-0.029523498757584157,0.0478886155594585,18,False,GSM6249243,1,True,17,False,1,1,4.47301955526521,3.845994869663477,0,0,1,1,1,1,B85D75,B85D75,GSM6249252,0.6243863866142141,0.6243863866142141,1,1,2,1,1,1,1,B85D75,B85D75,GSM6249252,0.6231006114420126,0.6231006114420126,1,1,2,1,1,1,1,B85D75,B85D75,GSM6249252,0.5614555208328301,0.5614555208328301,1,1,2,pass,True,
+180E1A_d0,GSM6248831,GSM6249253,180E1A,12,"180E1A, 0, Severe, Negative","180E1A, 0, Severe, Negative [scRNA-Seq]",exact_subject_day,180E1A-0,39-0,severe,0,FEMALE,29,Negative,Moderate,7418,7157,652157.0,545708.0,25035909.0,3966.8362066189584,0.0,11.954136756763932,female,186.2923142693945,0.1140332468492519,7.393355599465688,female,0.03801108228308397,female,True,False,0.01820714545735822,0.05081176029525473,6,False,GSM6249243,1,True,14,False,1,2,5.980845242246288,5.2739857206095175,0,0,1,1,1,1,180E1A,180E1A,GSM6249253,0.3451052632916858,0.3451052632916858,1,1,3,1,1,1,1,180E1A,180E1A,GSM6249253,0.4238191178243678,0.4238191178243678,1,1,3,7,11,7,5,94D44E,0BF51C,GSM6249274,0.1116617129061133,0.16558723848042697,1,2,3,pass,True,"within subject, another day beats the own day in some day tests (residualised 1/1, centred 1/2); not a day failure; low-depth bulk (652,157 assigned reads)"
+180E1A_d7,GSM6248832,GSM6249254,180E1A,13,"180E1A, 7, Severe, Positive","180E1A, 7, Severe, Positive [scRNA-Seq]",exact_subject_day,180E1A-7,39-7,severe,7,FEMALE,29,Positive,Moderate,10845,10591,14325667.0,11535441.0,34116911.0,3671.940720107483,0.9772668874684857,10.859212280103034,female,178.43458180762164,0.16699539710586958,7.264515281723884,female,0.13916283092155798,female,True,False,0.02871672849117923,0.06165185037245661,7,False,GSM6249243,1,True,9,False,1,1,5.111617417993341,4.360388640970583,0,0,1,1,1,1,180E1A,180E1A,GSM6249254,0.5397001982291783,0.5397001982291783,1,1,3,1,1,1,1,180E1A,180E1A,GSM6249254,0.590813144596412,0.590813144596412,1,1,3,1,1,1,1,180E1A,180E1A,GSM6249254,0.2803841390892291,0.2803841390892291,1,1,3,pass,True,
+180E1A_d14,GSM6248833,GSM6249255,180E1A,14,"180E1A, 14, Severe, Positive","180E1A, 14, Severe, Positive [scRNA-Seq]",exact_subject_day,180E1A-14,39-14,severe,14,FEMALE,29,Positive,Moderate,12891,12511,16329107.0,13105524.0,35560519.0,3453.46503026773,1.0410857127704534,10.72490982434346,female,198.07801053746184,0.3203849745854619,7.236231438056302,female,0.05339749576424365,female,True,False,0.035388180528137254,0.04846558916575721,3,False,GSM6249243,1,True,13,False,1,1,5.189212617833347,4.4070681025402925,0,0,1,1,1,1,180E1A,180E1A,GSM6249255,0.6616178966411204,0.6616178966411204,1,1,3,1,1,1,1,180E1A,180E1A,GSM6249255,0.632635670669305,0.632635670669305,1,1,3,1,1,1,1,180E1A,180E1A,GSM6249255,0.37248669420584657,0.37248669420584657,1,1,3,pass,True,
+82CCF5_d0,GSM6248834,GSM6249256,82CCF5,15,"82CCF5, 0, Severe, Negative","82CCF5, 0, Severe, Negative [scRNA-Seq]",exact_subject_day,82CCF5-0,41-0,severe,0,FEMALE,32,Negative,Moderate,10381,10125,11169648.0,8757626.0,29847355.0,2099.7975943377983,0.26858500822944464,10.693501255918061,female,218.84846338359947,0.06339758498945523,7.691684543608564,female,0.031698792494727616,female,True,False,0.13722930660516175,0.1617695083948158,4,False,GSM6249269,33,False,2,False,2,3,4.708911664736707,4.394847754870909,0,0,1,4,1,1,82CCF5,82CCF5,GSM6249256,0.2835775297327315,0.2835775297327315,1,3,3,1,3,1,1,82CCF5,82CCF5,GSM6249256,0.43256072559319225,0.43256072559319225,1,3,3,1,4,1,2,82CCF5,40067F,GSM6249256,0.2648284135055324,0.2648284135055324,1,3,3,pass,True,"within subject, another day beats the own day in some day tests (residualised 1/3, centred 2/3); not a day failure"
+82CCF5_d7,GSM6248835,GSM6249257,82CCF5,16,"82CCF5, 7, Severe, Positive","82CCF5, 7, Severe, Positive [scRNA-Seq]",exact_subject_day,82CCF5-7,41-7,severe,7,FEMALE,32,Positive,Moderate,11000,10860,14155585.0,11226191.0,41267686.0,2924.4287678679475,5.015688154180841,8.925702593207006,female,114.25136687820046,4.230675867808718,4.461642678353947,female,0.7629087630474738,female,True,False,-0.04783983681767933,0.03285335122106258,19,False,GSM6249258,2,False,29,False,1,1,4.502175133291828,3.7055372961108994,0,0,1,1,1,1,82CCF5,82CCF5,GSM6249257,0.6500692138488139,0.6500692138488139,1,1,3,1,1,1,1,82CCF5,82CCF5,GSM6249257,0.6530457930554503,0.6530457930554503,1,1,3,1,1,1,1,82CCF5,82CCF5,GSM6249257,0.45377486276609424,0.45377486276609424,1,1,3,pass,True,
+82CCF5_d14,GSM6248836,GSM6249258,82CCF5,17,"82CCF5, 14, Severe, Positive","82CCF5, 14, Severe, Positive [scRNA-Seq]",exact_subject_day,82CCF5-14,41-14,severe,14,FEMALE,32,Positive,Moderate,11327,11056,12008410.0,9213537.0,32158837.0,2865.908142709984,2.4982491437251064,9.678646924242123,female,198.78591969489415,0.146857210176488,7.4446253203934525,female,0.0,female,True,False,0.053907445928401104,0.053907445928401104,1,True,GSM6249258,2,False,14,False,2,1,4.519871270195661,3.776314079652304,0,0,1,1,1,1,82CCF5,82CCF5,GSM6249258,0.594531350965186,0.594531350965186,1,1,3,1,1,1,1,82CCF5,82CCF5,GSM6249258,0.618983725410239,0.618983725410239,1,1,3,1,1,1,1,82CCF5,82CCF5,GSM6249258,0.5240468355404357,0.5240468355404357,1,1,3,pass,True,"within subject, another day beats the own day in some day tests (residualised 1/1, centred 2/1); not a day failure"
+BAAF62_d0,GSM6248840,GSM6249259,BAAF62,18,"BAAF62, 0, Mild, Negative","BAAF62, 0, Mild, Negative [scRNA-Seq]",exact_subject_day,BAAF62-0,46-0,mild,0,MALE,28,Negative,Mild,15026,14741,12598095.0,10511151.0,49414388.0,0.9525249650840067,746.8589497062849,-8.581281390500562,male,0.0,997.8641546970997,-9.964144674928491,male,147.9001899236132,male,True,False,-0.013369431746549696,0.06157274431725398,22,False,GSM6249243,1,True,9,False,1,1,5.018642315853149,4.280760958360486,0,0,1,1,1,1,BAAF62,BAAF62,GSM6249259,0.6118948760483133,0.6118948760483133,1,1,3,1,1,1,1,BAAF62,BAAF62,GSM6249259,0.6633092300795905,0.6633092300795905,1,1,3,1,1,1,1,BAAF62,BAAF62,GSM6249259,0.5540876787296131,0.5540876787296131,1,1,3,pass,True,
+BAAF62_d7,GSM6248841,GSM6249260,BAAF62,19,"BAAF62, 7, Mild, Positive","BAAF62, 7, Mild, Positive [scRNA-Seq]",exact_subject_day,BAAF62-7,46-7,mild,7,MALE,28,Positive,Mild,7653,7297,17826544.0,15843127.0,33831342.0,4.095016958979823,973.8286905190373,-7.579917953444957,male,0.0,1117.0385742241622,-10.126754249123932,male,146.42604214443895,male,True,False,-0.09189148319643123,0.00784938523434505,27,False,GSM6249243,8,False,42,False,1,1,4.528943630896581,3.900593428239128,0,0,1,1,1,1,BAAF62,BAAF62,GSM6249260,0.5158976037048986,0.5158976037048986,1,1,3,1,2,1,1,BAAF62,BAAF62,GSM6249260,0.46442340574462265,0.46442340574462265,1,2,3,1,1,1,1,BAAF62,BAAF62,GSM6249260,0.40290154734883904,0.40290154734883904,1,1,3,pass,True,
+BAAF62_d14,GSM6248842,GSM6249261,BAAF62,20,"BAAF62, 14, Mild, Positive","BAAF62, 14, Mild, Positive [scRNA-Seq]",exact_subject_day,BAAF62-14,46-14,mild,14,MALE,28,Positive,Mild,12226,11923,13248643.0,11681720.0,49546525.0,2.792738848801345,1008.9335187007455,-8.056804574437741,male,0.0,1082.315106699813,-10.081237229132793,male,118.29765052116296,male,True,False,-0.10927704866485165,0.049303804336933994,38,False,GSM6249243,33,False,29,False,3,1,4.445845882874645,3.8133049365454377,0,0,1,1,1,1,BAAF62,BAAF62,GSM6249261,0.5672655890794956,0.5672655890794956,1,1,3,1,1,1,1,BAAF62,BAAF62,GSM6249261,0.5882269068339814,0.5882269068339814,1,1,3,1,1,1,1,BAAF62,BAAF62,GSM6249261,0.4316550271659003,0.4316550271659003,1,1,3,pass,True,"within subject, another day beats the own day in some day tests (residualised 1/1, centred 3/1); not a day failure"
+40067F_d0,GSM6248855,GSM6249265,40067F,21,"40067F, 0, Severe, Negative","40067F, 0, Severe, Negative [scRNA-Seq]",exact_subject_day,40067F-0,59-0,severe,0,MALE,52,Negative,Moderate,8198,8097,13704771.0,12253032.0,36261324.0,1.4593458000867,625.8404463671811,-7.9936798597617145,male,0.0,975.859635103056,-9.932007466104604,male,132.44416249167512,male,True,False,-0.02047134810873917,0.05852749302688727,33,False,GSM6249269,3,False,10,False,2,2,4.801587181280263,5.809566012944008,14,0,3,5,1,1,40067F,40067F,GSM6249266,0.2787243400362438,0.6304462474008999,2,2,2,8,8,1,2,40067F,0E1F8E,GSM6249266,0.1276384651754907,0.5859810728455882,2,2,2,17,18,2,1,0BF51C,40067F,GSM6249269,0.04946219704968274,0.47221028972691587,2,2,2,"fail: day: within subject 40067F, own day 0 ranks 2/2 (residualised k=5, bulk->sc/sc->bulk) and 2/2 (centred) among 2 paired days; ISG peak day bulk=14 sc=0",False,"subject ISG peak day differs between assays (bulk day 14, sc day 0)"
+40067F_d14,GSM6248856,GSM6249266,40067F,22,"40067F, 14, Severe, Negative","40067F, 14, Severe, Negative [scRNA-Seq]",exact_subject_day,40067F-14,59-14,severe,14,MALE,52,Negative,Moderate,14438,14268,8509732.0,7671730.0,53554307.0,1.4101501668912724,721.7618604205162,-8.228253530236339,male,0.036030127095192425,968.778057335534,-9.870444844480886,male,110.79264081771672,male,True,False,-0.012580332452240564,0.09148018471604706,36,False,GSM6249269,2,False,6,False,2,2,6.753591942127169,4.121609079392945,14,0,2,2,1,1,40067F,40067F,GSM6249265,0.42485664488178776,0.45332369927243643,2,2,2,2,3,1,1,40067F,40067F,GSM6249265,0.29642934174250996,0.37397772158157144,2,2,2,3,9,1,1,40067F,40067F,GSM6249265,0.14917821615809584,0.36248620927901587,2,2,2,"fail: day: within subject 40067F, own day 14 ranks 2/2 (residualised k=5, bulk->sc/sc->bulk) and 2/2 (centred) among 2 paired days; ISG peak day bulk=14 sc=0",False,"subject ISG peak day differs between assays (bulk day 14, sc day 0)"
+0BF51C_d0,GSM6248866,GSM6249269,0BF51C,23,"0BF51C, 0, Severe, Negative","0BF51C, 0, Severe, Negative [scRNA-Seq]",exact_subject_day,0BF51C-0,145-0,severe,0,FEMALE,45,Negative,Moderate,6683,6510,15448400.0,13540186.0,23043252.0,2647.782294606561,1.4240956992309883,10.093666901945511,female,138.17850494844762,0.12459738949364077,6.951384001897747,female,0.08306492632909385,female,True,False,0.3008360689744506,0.3008360689744506,1,True,GSM6249269,1,True,1,True,1,1,8.579900799925364,8.114537351390977,0,0,1,1,1,1,0BF51C,0BF51C,GSM6249269,0.3503676532664595,0.3503676532664595,1,1,3,1,1,1,1,0BF51C,0BF51C,GSM6249269,0.7557743212994172,0.7557743212994172,1,1,3,1,2,1,2,0BF51C,40067F,GSM6249269,0.4683423868142303,0.4683423868142303,1,1,3,pass,True,
+0BF51C_d7,GSM6248867,GSM6249270,0BF51C,24,"0BF51C, 7, Severe, Positive","0BF51C, 7, Severe, Positive [scRNA-Seq]",exact_subject_day,0BF51C-7,145-7,severe,7,FEMALE,45,Positive,Moderate,10802,10105,12578022.0,10840683.0,35695750.0,3009.5352035479027,1.5900751326400924,10.182810324195037,female,179.1641857750729,0.16119135022498685,7.277562710586747,female,0.0,female,True,False,0.08079708976054678,0.10252031020275594,6,False,GSM6249243,8,False,3,False,2,1,5.260331844609236,4.632573881224139,0,0,1,1,1,1,0BF51C,0BF51C,GSM6249270,0.36634122030339916,0.36634122030339916,1,1,3,1,1,1,1,0BF51C,0BF51C,GSM6249270,0.5129007947077222,0.5129007947077222,1,1,3,1,1,1,1,0BF51C,0BF51C,GSM6249270,0.3745737118451222,0.3745737118451222,1,1,3,pass,True,"within subject, another day beats the own day in some day tests (residualised 1/1, centred 2/1); not a day failure"
+0BF51C_d14,GSM6248868,GSM6249271,0BF51C,25,"0BF51C, 14, Severe, Positive","0BF51C, 14, Severe, Positive [scRNA-Seq]",exact_subject_day,0BF51C-14,145-14,severe,14,FEMALE,45,Positive,Moderate,12144,11419,14700603.0,12825821.0,47149820.0,3613.049070163993,1.2244395689074796,10.665958473837524,female,136.90558058718076,0.10210738408948444,6.967272228866301,female,0.02042147681789689,female,True,False,0.018753943621370475,0.07368492171616436,10,False,GSM6249243,1,True,7,False,1,1,4.398159267362902,3.9058158035658876,0,0,1,1,1,1,0BF51C,0BF51C,GSM6249271,0.5736009711111696,0.5736009711111696,1,1,3,1,1,1,1,0BF51C,0BF51C,GSM6249271,0.563643674121221,0.563643674121221,1,1,3,1,1,1,1,0BF51C,0BF51C,GSM6249271,0.44061978994064965,0.44061978994064965,1,1,3,pass,True,

paper-releases/20260928/diffusion/data/cohorts/giroux2022/samples.csv ADDED Viewed

	@@ -0,0 +1,27 @@

+row,sample_id,donor_id,group,n_cells
+0,450905_d0,450905,mild,5914
+1,450905_d14,450905,mild,7407
+2,0B943B_d0,0B943B,mild,11344
+3,0B943B_d14,0B943B,mild,15650
+4,7085CA_d0,7085CA,mild,12585
+5,7085CA_d7,7085CA,mild,9515
+6,7085CA_d14,7085CA,mild,11887
+7,2AD75E_d0,2AD75E,mild,7693
+8,2AD75E_d7,2AD75E,mild,10499
+9,2AD75E_d14,2AD75E,mild,13692
+10,B85D75_d0,B85D75,severe,11441
+11,B85D75_d7,B85D75,severe,12328
+12,180E1A_d0,180E1A,severe,7157
+13,180E1A_d7,180E1A,severe,10591
+14,180E1A_d14,180E1A,severe,12511
+15,82CCF5_d0,82CCF5,severe,10125
+16,82CCF5_d7,82CCF5,severe,10860
+17,82CCF5_d14,82CCF5,severe,11056
+18,BAAF62_d0,BAAF62,mild,14741
+19,BAAF62_d7,BAAF62,mild,7297
+20,BAAF62_d14,BAAF62,mild,11923
+21,40067F_d0,40067F,severe,8097
+22,40067F_d14,40067F,severe,14268
+23,0BF51C_d0,0BF51C,severe,6510
+24,0BF51C_d7,0BF51C,severe,10105
+25,0BF51C_d14,0BF51C,severe,11419