{"id":"W4408787684","doi":"10.1186/s12859-025-06103-6","title":"ChIPbinner: an R package for analyzing broad histone marks binned in uniform windows from ChIP-Seq or CUT&amp;RUN/TAG data","year":2025,"lang":"en","type":"article","venue":"BMC Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University; McGill Genome Centre","funders":"National Cancer Institute; Fonds de Recherche du Québec - Santé; Canadian Institutes of Health Research; National Institutes of Health","keywords":"Computational biology; Chromatin; Chromatin immunoprecipitation; Histone; Biology; Computer science; Genome; DNA microarray; DNA sequencing; Epigenetics; Software; Principal component analysis; Genetics; DNA; Gene; Artificial intelligence; 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":[0.005965017,0.005227145,0.003777929,0.003146679,0.0008354445,0.003042931,0.005550951,0.001718166,0.05119758],"category_scores_gemma":[0.02382997,0.002583966,0.004168783,0.00239495,0.001367928,0.001979281,0.003871003,0.004406037,0.03883308],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0009506127,"about_ca_system_score_gemma":0.00408933,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003929596,"about_ca_topic_score_gemma":0.004701589,"domain_scores_codex":[0.9966596,0.001184852,0.000290657,0.0008635529,0.0007349095,0.0002663983],"domain_scores_gemma":[0.9904811,0.006357104,0.001045532,0.001051923,0.0007295008,0.0003348821],"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":[0.002249747,0.0001821189,0.01304145,0.01223382,0.00565855,0.001322146,0.0009812056,0.02488213,0.02601754,0.02169724,0.7736278,0.1181064],"study_design_scores_gemma":[0.00159828,0.0005058644,0.01720231,0.001461193,0.002260488,0.001901,0.0002427134,0.1425909,0.05107163,0.06210665,0.7181922,0.0008668479],"study_design_candidate":"not_applicable","study_design_consensus":"not_applicable","genre_codex":"software","genre_gemma":"software","genre_scores_codex":[0.004413607,0.001590634,0.4284284,0.0005324956,0.0004184872,0.0004809508,0.1089012,0.4520932,0.003141158],"genre_scores_gemma":[0.04246618,0.001868394,0.5561395,0.00187317,0.0002288679,0.005873701,0.1149139,0.2704426,0.00619361],"genre_candidate":"software","genre_consensus":"software","teacher_disagreement_score":0.05119758,"threshold_uncertainty_score":0.171273,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02586712216503084,"score_gpt":0.2977455756890775,"score_spread":0.2718784535240467,"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."}}