{"id":"W3138924738","doi":"10.1101/gr.269894.120","title":"Ultrafast functional profiling of RNA-seq data for nonmodel organisms","year":2021,"lang":"en","type":"article","venue":"Genome Research","topic":"Genomics and Phylogenetic Studies","field":"Biochemistry, Genetics and Molecular Biology","cited_by":26,"is_retracted":false,"has_abstract":true,"ca_institutions":"Environment and Climate Change Canada; McGill University","funders":"Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs; Genome Canada","keywords":"Biology; Bottleneck; Sequence assembly; Computational biology; RNA-Seq; Pipeline (software); Reference genome; Computer science; Workflow; DNA sequencing; Gene; Data mining; Transcriptome; Genetics; Database; 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":[0.004669402,0.001605942,0.001660523,0.002018667,0.001249949,0.002122674,0.001613966,0.0007873328,0.004239457],"category_scores_gemma":[0.005253346,0.0006685398,0.001758001,0.001524458,0.0005980181,0.001456822,0.001201095,0.001722001,0.002893551],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009926017,"about_ca_system_score_gemma":0.001600956,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.001878078,"about_ca_topic_score_gemma":0.004374784,"domain_scores_codex":[0.9983071,0.0003574582,0.0001293578,0.0005252574,0.000553739,0.0001270264],"domain_scores_gemma":[0.9971411,0.001443311,0.0003058943,0.0004906924,0.0004756349,0.0001434424],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.0006620119,0.0001669538,0.009693312,0.001822982,0.0004264104,0.0002007006,0.0004406877,0.009868601,0.9074457,0.0027834,0.006411907,0.06007722],"study_design_scores_gemma":[0.00009040249,0.0005042131,0.04805933,0.0002480235,0.0002513274,0.0008328955,0.0004160982,0.164839,0.7252223,0.01488757,0.04435842,0.0002904097],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"methods","genre_scores_codex":[0.1707238,0.001622768,0.7441029,0.0006088323,0.000189897,0.0003991704,0.0496342,0.02941914,0.003299338],"genre_scores_gemma":[0.2259877,0.001249911,0.6969134,0.0005431387,0.00007367423,0.001171396,0.06653431,0.005078489,0.002448088],"genre_candidate":"methods","genre_consensus":"methods","teacher_disagreement_score":0.004669402,"threshold_uncertainty_score":0.02469444,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.172815722806266,"score_gpt":0.3674804413055738,"score_spread":0.1946647184993078,"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."}}