{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002021361,0.001321943,0.001452527,0.0008141199,0.0009679921,0.001814335,0.003962978,0.001989423,0.01300899],"category_scores_gemma":[0.004667434,0.0009462152,0.002218318,0.0009170386,0.000725744,0.0009052848,0.001662503,0.003092365,0.003939832],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001475408,"about_ca_system_score_gemma":0.003446992,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.01283881,"about_ca_topic_score_gemma":0.01314958,"domain_scores_codex":[0.999463,0.0001414797,0.00003205908,0.0001252758,0.0001815399,0.0000566275],"domain_scores_gemma":[0.9985058,0.0008549583,0.00008990104,0.0001425732,0.0002714566,0.0001352933],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0002623668,0.0001367913,0.003725401,0.0007326974,0.0004390244,0.0002516003,0.000311614,0.8976111,0.01594875,0.03790759,0.02484145,0.01783152],"study_design_scores_gemma":[0.00004186672,0.00002317396,0.0002470784,0.00001955691,0.00002398527,0.00002913824,0.00002059995,0.9776349,0.002314097,0.009280176,0.01033353,0.00003185529],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.01983412,0.0004028485,0.9294776,0.0004118023,0.0002246427,0.0002878589,0.01185067,0.03091352,0.006596938],"genre_scores_gemma":[0.1831926,0.001163488,0.756123,0.0009441216,0.0001570885,0.004317916,0.0257838,0.02158402,0.006733879],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.01300899,"threshold_uncertainty_score":0.04351938,"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."}}