{"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":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.004801534,0.004853339,0.003008199,0.002397497,0.0009616503,0.00358551,0.004348769,0.001468628,0.04815375],"category_scores_gemma":[0.01162236,0.002324468,0.002853937,0.001439735,0.00118981,0.002618862,0.003901779,0.004984639,0.0573526],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0008987628,"about_ca_system_score_gemma":0.002655137,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001812775,"about_ca_topic_score_gemma":0.001930234,"domain_scores_codex":[0.9980672,0.0005196367,0.0001910507,0.0005485454,0.0004584541,0.0002151501],"domain_scores_gemma":[0.9973639,0.001414824,0.00030982,0.0004724123,0.0002802986,0.000158733],"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":[0.003866281,0.0003049127,0.009861992,0.007586143,0.003072858,0.001534145,0.001152563,0.01209539,0.05473466,0.01931424,0.709568,0.1769087],"study_design_scores_gemma":[0.00117682,0.0003969609,0.006623559,0.0008442155,0.0008887195,0.002008041,0.000279296,0.1087936,0.1033419,0.050081,0.7249003,0.0006656526],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.005274127,0.001300808,0.426511,0.0003655276,0.0003174233,0.0004076406,0.04474149,0.5174105,0.00367141],"genre_scores_gemma":[0.03951361,0.001586342,0.5858213,0.001036128,0.000144313,0.003020081,0.09905207,0.2609476,0.008878603],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.04815375,"threshold_uncertainty_score":0.1610904,"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."}}