{"id":"W2020001055","doi":"10.12688/f1000research.4680.2","title":"shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R","year":2014,"lang":"en","type":"preprint","venue":"F1000Research","topic":"Epigenetics and DNA Methylation","field":"Biochemistry, Genetics and Molecular Biology","cited_by":128,"is_retracted":false,"has_abstract":true,"ca_institutions":"","funders":"National Institute of Dental and Craniofacial Research; Natural Sciences and Engineering Research Council of Canada; Johns Hopkins University","keywords":"Bioconductor; DNA methylation; Epigenome; Computational biology; Biology; Methylation; Computer science; Genetics; DNA; Gene","routes":{"ca_aff":false,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":true},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.01519589,0.003138013,0.002971072,0.002740833,0.001039794,0.003817728,0.004451791,0.001506182,0.09841491],"category_scores_gemma":[0.03774416,0.002606855,0.002944321,0.002251481,0.001321249,0.002081844,0.003536995,0.004160717,0.06411903],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001296463,"about_ca_system_score_gemma":0.00301284,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003308765,"about_ca_topic_score_gemma":0.006106958,"domain_scores_codex":[0.99188,0.002758674,0.0007467901,0.002028686,0.00206971,0.0005161257],"domain_scores_gemma":[0.9887215,0.005683857,0.0009513737,0.002757909,0.001585453,0.000299945],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"not_applicable","study_design_scores_codex":[0.001734124,0.00008620513,0.008168567,0.004858098,0.001760851,0.0006004481,0.001144265,0.007985836,0.05115881,0.01359709,0.7230431,0.1858625],"study_design_scores_gemma":[0.001093544,0.0002954534,0.01729062,0.0008011879,0.0007740876,0.0009739076,0.0001803697,0.06997929,0.125937,0.04862176,0.7332225,0.0008302902],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.00307932,0.0008547717,0.5679095,0.0003875678,0.000369376,0.0004285883,0.06494188,0.3586721,0.003356997],"genre_scores_gemma":[0.02591733,0.0005721711,0.6618772,0.0009754399,0.0001617781,0.005049684,0.0561368,0.2409799,0.008329713],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.09841491,"threshold_uncertainty_score":0.3292306,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03868394049446166,"score_gpt":0.381758396364011,"score_spread":0.3430744558695493,"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."}}