{"id":"W3101058692","doi":"10.1186/s12859-020-03734-9","title":"MADA: a web service for analysing DNA methylation array data","year":2020,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":6,"is_retracted":false,"has_abstract":true,"ca_institutions":"University of Saskatchewan","funders":"National Key Research and Development Program of China; Higher Education Discipline Innovation Project; National Natural Science Foundation of China","keywords":"DNA methylation; Methylation; Workflow; Bioconductor; Computer science; Computational biology; Visualization; Bioinformatics; Data mining; Biology; Database; Genetics; Gene; Gene expression","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":[0.0003225988,0.0001419779,0.0001527337,0.00003590502,0.0000923722,0.00006241526,0.0003513962,0.0001338038,0.000008323632],"category_scores_gemma":[0.0002991609,0.0001363593,0.00006562102,0.0002069936,0.00001771733,0.00002117344,0.0001522253,0.00005346787,0.00001366797],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008463517,"about_ca_system_score_gemma":0.0001350765,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000003712634,"about_ca_topic_score_gemma":0.00006839858,"domain_scores_codex":[0.999021,0.00002806736,0.0003900781,0.0002252525,0.0001475826,0.000188036],"domain_scores_gemma":[0.998976,0.00003223396,0.000195854,0.0005474247,0.0001408059,0.0001076782],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0001747018,0.00004727062,0.001565128,0.0007140278,0.0001651578,2.055657e-7,0.0006865832,0.0102051,0.9716709,0.0001599333,0.003028271,0.0115827],"study_design_scores_gemma":[0.0006030459,0.0001290389,0.0001559116,0.000009530349,0.00008327185,5.940457e-7,0.0002511999,0.8156647,0.1170007,0.0001049847,0.06576613,0.0002309096],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.04280082,0.000453825,0.9547622,0.0005802632,0.00009331722,0.0003431611,0.0002365418,0.00002518776,0.0007046884],"genre_scores_gemma":[0.3714364,0.0002247774,0.6179187,0.002170114,0.0007552354,0.000022983,0.007341006,0.00004727854,0.00008349736],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.8546702,"threshold_uncertainty_score":0.5560572,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.08744543724510032,"score_gpt":0.3051757837573827,"score_spread":0.2177303465122824,"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."}}