{"id":"W2952228520","doi":"10.1093/bioinformatics/btz130","title":"LIONS: analysis suite for detecting and quantifying transposable element initiated transcription from RNA-seq","year":2019,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Chromosomal and Genetic Variations","field":"Agricultural and Biological Sciences","cited_by":33,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canada's Michael Smith Genome Sciences Centre; Terry Fox Research Institute; University of British Columbia","funders":"Natural Sciences and Engineering Research Council of Canada; University of British Columbia","keywords":"RNA-Seq; Transposable element; Suite; Container (type theory); Computer science; Source code; Computational biology; Transcription (linguistics); Transcriptome; Biology; Genetics; Genome; Gene; Gene expression; Programming language","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":[0.00439762,0.003770534,0.001963537,0.002511428,0.001196253,0.002886249,0.002420383,0.001225436,0.02637666],"category_scores_gemma":[0.00597147,0.001965396,0.002163789,0.001437131,0.0008302658,0.001518339,0.001932017,0.003445518,0.01732418],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001341019,"about_ca_system_score_gemma":0.002807429,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.002548429,"about_ca_topic_score_gemma":0.00505465,"domain_scores_codex":[0.998031,0.0003635882,0.0002171181,0.0006401767,0.0005600405,0.000188096],"domain_scores_gemma":[0.997531,0.001343954,0.0003307982,0.0002671324,0.0003810108,0.0001460942],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.003335126,0.0003321994,0.01425901,0.009087341,0.001614849,0.0009020987,0.001616224,0.01026287,0.2974446,0.01274106,0.533531,0.1148736],"study_design_scores_gemma":[0.001017579,0.0009177681,0.03175991,0.0009111885,0.0006989854,0.0012329,0.0004545337,0.1936991,0.3423914,0.02168964,0.4042369,0.000989979],"study_design_candidate":"bench_or_experimental","study_design_consensus":null,"genre_codex":"software","genre_gemma":"methods","genre_scores_codex":[0.01311841,0.0008251815,0.3821922,0.0002957401,0.0002777594,0.001022512,0.1643701,0.4321993,0.005698772],"genre_scores_gemma":[0.0423418,0.0006993104,0.6297289,0.001679543,0.0001322131,0.008106146,0.2133252,0.09494003,0.009046806],"genre_candidate":"methods","genre_consensus":null,"teacher_disagreement_score":0.02637666,"threshold_uncertainty_score":0.08823872,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.06000712540145275,"score_gpt":0.2551174693935599,"score_spread":0.1951103439921071,"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."}}