{"id":"W3135165543","doi":"10.1186/s13059-021-02270-w","title":"simATAC: a single-cell ATAC-seq simulation framework","year":2021,"lang":"en","type":"article","venue":"Genome biology","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":53,"is_retracted":false,"has_abstract":true,"ca_institutions":"Vector Institute; University of Toronto; University Health Network","funders":"Natural Sciences and Engineering Research Council of Canada; Canadian Institute for Advanced Research","keywords":"Computational biology; Biology; In silico; Chromatin; Benchmarking; Transposase; Genetics; Gene; Genome; Transposable element","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":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.00009876726,0.0001960242,0.0002096381,0.0000371042,0.00009714742,0.00002906241,0.0001968114,0.0004329389,0.0001607538],"category_scores_gemma":[0.0001224054,0.0002001609,0.0001279789,0.0001271054,0.00009030924,0.000003394429,0.0001125013,0.0001455158,0.00007535908],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00002278127,"about_ca_system_score_gemma":0.0000870944,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000007200747,"about_ca_topic_score_gemma":0.00001621089,"domain_scores_codex":[0.9986845,0.0001055357,0.000259782,0.0005252573,0.00006302218,0.0003619094],"domain_scores_gemma":[0.9991772,0.00004938634,0.00007663086,0.0004757633,0.0001261379,0.00009487315],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00006363077,0.0001597238,0.004057922,0.00001999381,0.00003686296,0.000008970709,0.00005510604,0.001090006,0.9926991,0.0002093243,0.00007134546,0.001527963],"study_design_scores_gemma":[0.001208949,0.0008628926,0.002804485,0.00001668809,0.00005861553,0.00003211703,0.00008997632,0.000607942,0.5345196,0.002615842,0.4564129,0.0007699534],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9110031,0.00388301,0.08070073,0.0001866099,0.0006773046,0.000146924,0.00009485049,0.00004191845,0.003265561],"genre_scores_gemma":[0.9912117,0.0001774647,0.004996361,0.0009687445,0.0006335043,0.000008783881,0.001030755,0.00003415754,0.0009385596],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.4581795,"threshold_uncertainty_score":0.8162326,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.0235879297693315,"score_gpt":0.2599572462291556,"score_spread":0.2363693164598241,"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."}}