{"id":"W4414474889","doi":"10.1093/bioinformatics/btag366","title":"LCR-modules: a collection of workflows for cancer genome analysis","year":2025,"lang":"en","type":"preprint","venue":"Bioinformatics","topic":"Genetics, Bioinformatics, and Biomedical Research","field":"Biochemistry, Genetics and Molecular Biology","cited_by":1,"is_retracted":false,"has_abstract":true,"ca_institutions":"BC Cancer Agency; Spinal Cord Injury BC; Canada's Michael Smith Genome Sciences Centre; Simon Fraser University","funders":"Michael Smith Health Research BC","keywords":"Workflow; Genomics; Exome sequencing; Suite; Genome; Scalability; Flexibility (engineering); Exome; Pipeline (software)","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":[0.00774251,0.003738911,0.001517321,0.004708661,0.001308867,0.00309656,0.003806224,0.00122793,0.01590431],"category_scores_gemma":[0.01216104,0.002158277,0.003686646,0.004287385,0.0009684283,0.002095574,0.005555491,0.003343558,0.02193085],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00181671,"about_ca_system_score_gemma":0.005612588,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.005463279,"about_ca_topic_score_gemma":0.006655255,"domain_scores_codex":[0.9960317,0.0008840844,0.0005180493,0.001069152,0.001165509,0.0003315283],"domain_scores_gemma":[0.9935637,0.001833636,0.0004407589,0.002222606,0.001289047,0.0006504577],"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":[0.001641833,0.0002796031,0.007284627,0.003348786,0.0008612912,0.0005863324,0.0009122977,0.0218344,0.03420993,0.01700308,0.6143039,0.2977339],"study_design_scores_gemma":[0.001065916,0.0003432666,0.01294648,0.0005960459,0.0003806658,0.001375399,0.000205964,0.09310053,0.08070057,0.05766224,0.7509373,0.0006856186],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.004306781,0.001087857,0.3972587,0.0006263258,0.0001901169,0.001220651,0.0687011,0.5207639,0.005844539],"genre_scores_gemma":[0.02854741,0.001371969,0.5590123,0.001069475,0.0001594953,0.00319103,0.3246986,0.07618853,0.005761195],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.01590431,"threshold_uncertainty_score":0.05320519,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02317833863942167,"score_gpt":0.3131928350839846,"score_spread":0.290014496444563,"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."}}