{"id":"W4309012390","doi":"10.1101/2022.11.11.516066","title":"CelltypeR: A flow cytometry pipeline to annotate, characterize and isolate single cells from brain organoids","year":2022,"lang":"en","type":"preprint","venue":"bioRxiv (Cold Spring Harbor Laboratory)","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; Montreal Neurological Institute and Hospital","funders":"Canadian Institutes of Health Research; Québec Consortium for Drug Discovery; Fondation Brain Canada; McGill University","keywords":"Cell type; Organoid; Cell sorting; Flow cytometry; Cell; Biology; Computational biology; Induced pluripotent stem cell; Substantia nigra; Neuroscience; Computer science; Cell biology; Embryonic stem cell; Dopamine; Molecular biology; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002735951,0.002068552,0.001311319,0.002040099,0.001084486,0.00230134,0.002178952,0.001101597,0.01030609],"category_scores_gemma":[0.002731163,0.00117343,0.001672205,0.0009040642,0.0007776894,0.001151836,0.002130024,0.002490878,0.009640155],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001401727,"about_ca_system_score_gemma":0.002668153,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003334726,"about_ca_topic_score_gemma":0.00434165,"domain_scores_codex":[0.9988832,0.00008297664,0.00009658322,0.0004573529,0.0003518587,0.0001280142],"domain_scores_gemma":[0.9989663,0.0003178467,0.00009364857,0.0002798529,0.0002376125,0.0001048007],"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":[0.0008718736,0.0001940829,0.004907892,0.001053293,0.0003174443,0.0004525963,0.0005391517,0.01743425,0.7530544,0.01101889,0.07464173,0.1355144],"study_design_scores_gemma":[0.0003096624,0.0001810226,0.009544829,0.0001108652,0.0001019319,0.0005813861,0.0002005765,0.2010026,0.5999921,0.02244858,0.1652209,0.0003056155],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.009613219,0.0001422007,0.8738104,0.0002233916,0.0001325645,0.0003933952,0.02135695,0.09265741,0.001670561],"genre_scores_gemma":[0.05520702,0.0003870944,0.8532959,0.0005147411,0.00007758225,0.002963351,0.06063563,0.02167783,0.005240849],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01030609,"threshold_uncertainty_score":0.03447729,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01103001069287625,"score_gpt":0.2017711105007333,"score_spread":0.1907410998078571,"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."}}