{"id":"W3209241819","doi":"10.1016/j.xpro.2021.100875","title":"RHybridFinder: An R package to process immunopeptidomic data for putative hybrid peptide discovery","year":2021,"lang":"en","type":"article","venue":"STAR Protocols","topic":"vaccines and immunoinformatics approaches","field":"Biochemistry, Genetics and Molecular Biology","cited_by":4,"is_retracted":false,"has_abstract":true,"ca_institutions":"Université de Montréal; University of Ottawa; Centre Hospitalier Universitaire Sainte-Justine","funders":"Fonds de Recherche du Québec - Santé; National Health and Medical Research Council; Natural Sciences and Engineering Research Council of Canada; Institut de Valorisation des Données; Fondation Charles-Bruneau; Canada Foundation for Innovation; Canadian Institutes of Health Research; Chung Hua University; Victorian Cancer Agency","keywords":"Computational biology; R package; Computer science; Protocol (science); Inference; Peptide; Major histocompatibility complex; Software package; Identification (biology); Database search engine; Software; Combinatorial chemistry; Bioinformatics; Chemistry; Biology; Genetics; Biochemistry; Programming language; Gene; Search engine; Information retrieval; Artificial intelligence; Medicine","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":[0.0003619904,0.0002482895,0.0002622782,0.00003384995,0.0001595184,0.0002536527,0.0007437088,0.00006544364,0.0000152828],"category_scores_gemma":[0.0002450116,0.0002269586,0.00008514497,0.0001022059,0.00003280355,0.00008215741,0.0005458304,0.000100172,0.00001526894],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00001929374,"about_ca_system_score_gemma":0.0003965141,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.000008472624,"about_ca_topic_score_gemma":0.0000183161,"domain_scores_codex":[0.9984039,0.00005560472,0.0003893382,0.0006012001,0.0001564886,0.0003934428],"domain_scores_gemma":[0.9979645,0.00001531163,0.0001355753,0.001547637,0.0002270717,0.000109915],"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":[0.003219556,0.001249885,0.000694023,0.00159283,0.0007253631,0.00003141821,0.001525001,0.0006482815,0.9181861,0.000543852,0.0439806,0.02760305],"study_design_scores_gemma":[0.002933637,0.001537503,0.0006419397,0.0001282101,0.00003802693,0.00005831393,0.002169548,0.0009002308,0.8141295,0.0005769068,0.1761399,0.0007463303],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.7912338,0.0002084504,0.07595416,0.0006190569,0.0001489594,0.1247973,0.005702084,0.00006731798,0.001268795],"genre_scores_gemma":[0.6864552,0.00003806086,0.06421831,0.002013121,0.0009151738,0.210883,0.03011105,0.0002538494,0.005112248],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1321593,"threshold_uncertainty_score":0.9255104,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04438475523477024,"score_gpt":0.3471581455298931,"score_spread":0.3027733902951228,"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."}}