{"id":"W4412347897","doi":"10.1093/bioinformatics/btaf401","title":"shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data","year":2025,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Single-cell and spatial transcriptomics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"Western University","funders":"Physicians' Services Incorporated Foundation; Academic Medical Organization of Southwestern Ontario","keywords":"Bioconductor; MIT License; Computer science; Personalization; Normalization (sociology); Visualization; Profiling (computer programming); Open source; Transcriptome; Software; World Wide Web; Information retrieval; Data mining; Operating system; Biology; Gene; Gene expression","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":[0.002292017,0.001882138,0.001500754,0.002305551,0.0009227779,0.001768023,0.002647818,0.0009862586,0.1174783],"category_scores_gemma":[0.004779428,0.001381179,0.001595696,0.001991694,0.0005511932,0.001839404,0.003664452,0.002028801,0.04354361],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009751813,"about_ca_system_score_gemma":0.002007627,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.004805972,"about_ca_topic_score_gemma":0.008788505,"domain_scores_codex":[0.999144,0.0001067888,0.00008856702,0.0002605574,0.000284899,0.00011515],"domain_scores_gemma":[0.9984263,0.0006177535,0.0001376282,0.0003045575,0.0003872334,0.0001266114],"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":[0.0008145974,0.000048267,0.002420759,0.001916022,0.0002843681,0.0005021341,0.0006646151,0.001127282,0.02701943,0.00277385,0.8974637,0.06496498],"study_design_scores_gemma":[0.0009308202,0.0002151683,0.01579995,0.0007523547,0.0002279116,0.001379835,0.0005317318,0.04791443,0.08445726,0.0203458,0.8269935,0.000451135],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.006099695,0.0005303681,0.1834481,0.0004235306,0.0003707623,0.0003777509,0.1577869,0.6449934,0.005969433],"genre_scores_gemma":[0.05642139,0.001113281,0.3977973,0.00144261,0.0001746386,0.004057987,0.2689285,0.2509363,0.01912804],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.1174783,"threshold_uncertainty_score":0.3930041,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.01549082276673245,"score_gpt":0.2864497330268734,"score_spread":0.270958910260141,"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."}}