{"id":"W4224268760","doi":"10.1016/j.xpro.2022.101379","title":"Analyzing single cell transcriptome data from severe COVID-19 patients","year":2022,"lang":"en","type":"article","venue":"STAR Protocols","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Genome Canada; McGill University Health Centre","funders":"","keywords":"Transcriptome; In silico; Cell type; Computational biology; Gene; Coronavirus disease 2019 (COVID-19); Cell; Biology; Downregulation and upregulation; Gene expression; Disease; Genetics; Medicine; Pathology","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0002440334,0.000213562,0.0002008786,0.0000480182,0.0003451182,0.00005739296,0.0009225474,0.00009228168,0.0006266278],"category_scores_gemma":[0.00005528298,0.0002295888,0.00009481723,0.0001454231,0.00005250648,0.00001214159,0.0003853391,0.0002023525,0.00001146938],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00008084316,"about_ca_system_score_gemma":0.0002239745,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0002357159,"about_ca_topic_score_gemma":0.0000902083,"domain_scores_codex":[0.9981748,0.0001937323,0.0003086753,0.0007131262,0.0002821023,0.0003275585],"domain_scores_gemma":[0.9986241,0.00001821119,0.0001135349,0.0009981443,0.0000459379,0.0002000239],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001009905,0.001441184,0.03972044,0.0001407984,0.00009813337,0.00001383287,0.0004634224,0.0003457929,0.9280642,0.000005752527,0.02684434,0.00185223],"study_design_scores_gemma":[0.005493097,0.001468089,0.001582625,0.00001660829,0.0000496969,0.000003292659,0.0002476819,0.00028555,0.05430429,0.0002427843,0.9356146,0.0006916432],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9514683,0.0001875696,0.003929823,0.0002137379,0.0002936354,0.03600101,0.006269028,0.00007868055,0.001558185],"genre_scores_gemma":[0.9701398,0.000006163734,0.001697376,0.001476696,0.0002381222,0.01695448,0.008625194,0.00007283538,0.0007893604],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.9087703,"threshold_uncertainty_score":0.936236,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06122659611412789,"score_gpt":0.3019704749183524,"score_spread":0.2407438788042245,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}