{ "_id": "6aba916299f7aa8c6aa41790", "Package": "pdactrace", "Type": "Package", "Title": "Stage-Aware PDAC Atlas and Prospectively Frozen Tissue-to-Serum\nBiomarker Audit Framework", "Version": "0.99.25", "Authors@R": "c(\nperson(given = \"Jibeom\", family = \"Ko\",\nemail = \"rhwlqja1779@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0009-0002-8630-1973\")))", "Description": "pdactrace implements a transparent, deterministic\nclaim-audit framework for stage-aware pancreatic ductal\nadenocarcinoma (PDAC) tissue-to-blood biomarker evidence. It\nintegrates per-stage trajectory matching across bulk RNA-seq,\ntissue proteomics, single-cell origin, serum proteomics, and\npancreatitis context, with explicit anchor-enrichment\nevaluation against a curated external reference set. The\nframework comprises a 12-template competitive trajectory\ncatalog, a 3-axis + 2-gate reference score, an Evidence Math\nlayer, TRACE-D tissue-to-serum directional evidence\nconcordance, claim-tier classification, and weight-robustness\nand Pareto support audits. A prespecification layer supports\nfreezing candidate scores, directions and a decision rule under\na content hash before outcome labels are opened, with a\ndistinct inconclusive terminal state when a frozen gate fails.\nScope is deliberately PDAC-specific: the bundled atlas, the\nanchor reference set and every validated claim are PDAC, and no\nresult is claimed for any other disease. Separately, no\nsupervised classifier is trained or shipped, because validated\nnon-circular early-detection ground truth is unavailable in\nPDAC.", "License": "MIT + file LICENSE", "URL": "https://github.com/jibeomko/pdactrace", "BugReports": "https://github.com/jibeomko/pdactrace/issues", "biocViews": "Software, BiomedicalInformatics, Classification,\nTranscriptomics, Proteomics, GeneExpression,\nDifferentialExpression, SingleCell, Visualization, Annotation", "Encoding": "UTF-8", "LazyData": "false", "VignetteBuilder": "knitr", "RoxygenNote": "7.3.3", "Roxygen": "list(markdown = TRUE)", "Config/testthat/edition": "3", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://biocstaging.r-universe.dev", "Date/Publication": "2026-09-28 13:10:57 UTC", "RemoteUrl": "https://github.com/BiocStaging/pdactrace", "RemoteRef": "HEAD", "RemoteSha": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "NeedsCompilation": "no", "Packaged": { "Date": "2026-09-28 15:49:31 UTC", "User": "root" }, "Author": "Jibeom Ko [aut, cre] (ORCID: )", "Maintainer": "Jibeom Ko ", "_user": "biocstaging", "_type": "src", "_file": "pdactrace_0.99.25.tar.gz", "_fileid": "https://r2.ropensci.org/2e4a4a7c364da9ec015458b5c771f07858a1c0c68bc0f3b3694e8edfc00ed152", "_filesize": 6732176, "_sha256": "2e4a4a7c364da9ec015458b5c771f07858a1c0c68bc0f3b3694e8edfc00ed152", "_expires": "2027-01-06T16:10:07.000Z", "_created": "2026-09-28T15:49:31.000Z", "_published": "2026-09-28T16:10:10.595Z", "_bioccheck": { "error": 0, "warning": 0, "note": 9 }, "_host": "GitHub-Actions", "_buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536", "_status": "success", "_upstream": "https://github.com/BiocStaging/pdactrace", "_commit": { "id": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "author": "jibeomko ", "committer": "jibeomko ", "message": "Recompute the atlas audit features from the current template labels\n\nThe seven audit feature columns were frozen at v0.3.0, before the\n12-template catalog, so 286 genes whose best RNA template became\nMonotonic or Late kept Early-onset and RNA-layer credit, and genes whose\nprotein label changed kept their old layer and direction credit. They are\nnow recomputed from the current labels with .audit_compute_features(),\nthe code that already scores user evidence tables, so the atlas and user\ndata follow one rule. data-raw/attach_audit_columns.R, which copied the\nv0.3.0 CSV (and would have overwritten audit_score with the legacy\nvalue), now performs this recomputation; the MC and 3-axis columns were\nregenerated downstream.\n\n310 genes change score and 71 change class (11 leave high_confidence).\nThe anchor enrichment (7 hits, 39.3x), its leave-one-out and bootstrap\nsummaries, the top gene and the case-study genes are unchanged.\n\nR CMD check OK, BiocCheck 0 ERRORS 0 WARNINGS, 678 tests passing.\n", "time": 1790601057 }, "_maintainer": { "name": "Jibeom Ko", "email": "rhwlqja1779@gmail.com", "login": "jibeomko", "orcid": "0009-0002-8630-1973", "description": "", "uuid": 155090232 }, "_distro": "resolute", "_jobs": [ { "job": 109010741899, "time": 284, "config": "bioc-checks", "r": "4.6.1", "check": "NOTE", "artifact": "10980159849" }, { "job": 109010741802, "time": 424, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10981895017" }, { "job": 109010741932, "time": 459, "config": "linux-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10981515528" }, { "job": 109010742232, "time": 385, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "OK", "artifact": "10981351266" }, { "job": 109010742106, "time": 423, "config": "macos-release-arm64", "r": "4.6.1", "check": "OK", "artifact": "10981912127" }, { "job": 109007300812, "time": 477, "config": "source", "r": "4.6.1", "check": "OK", "artifact": "10981151848" }, { "job": 109010741830, "time": 165, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "10981022990" }, { "job": 109010742211, "time": 446, "config": "windows-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10980819767" }, { "job": 109010742092, "time": 344, "config": "windows-oldrel-x86_64", "r": "4.5.3", "check": "OK", "artifact": "10980199898" }, { "job": 109010742033, "time": 405, "config": "windows-release-x86_64", "r": "4.6.1", "check": "OK", "artifact": "10981785050" } ], "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.5.0", "role": "Depends" }, { "package": "data.table", "role": "Imports" }, { "package": "ggplot2", "role": "Imports" }, { "package": "patchwork", "role": "Imports" }, { "package": "glue", "role": "Imports" }, { "package": "methods", "role": "Imports" }, { "package": "stats", "role": "Imports" }, { "package": "utils", "role": "Imports" }, { "package": "withr", "role": "Imports" }, { "package": "SummarizedExperiment", "role": "Imports" }, { "package": "DESeq2", "role": "Suggests" }, { "package": "digest", "role": "Suggests" }, { "package": "limma", "role": "Suggests" }, { "package": "mixOmics", "role": "Suggests" }, { "package": "S4Vectors", "role": "Suggests" }, { "package": "BiocFileCache", "role": "Suggests" }, { "package": "glmnet", "role": "Suggests" }, { "package": "testthat", "version": ">= 3.0.0", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "pkgdown", "role": "Suggests" } ], "_owner": "biocstaging", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2026-19", "n": 38 }, { "week": "2026-22", "n": 12 }, { "week": "2026-39", "n": 3 }, { "week": "2026-40", "n": 4 } ], "_tags": [], "_topics": [ "software", "biomedicalinformatics", "classification", "transcriptomics", "proteomics", "geneexpression", "differentialexpression", "singlecell", "visualization", "annotation" ], "_stars": 0, "_contributors": [ { "user": "jibeomko", "count": 57, "uuid": 155090232 } ], "_userbio": { "uuid": 278472782, "type": "organization", "name": "BiocStaging", "followers": 2 }, "_downloads": { "count": 0, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/pdactrace" }, "_devurl": "https://github.com/jibeomko/pdactrace", "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/manual.pdf", "extra/NEWS.html", "extra/NEWS.txt", "extra/pdactrace.html", "extra/readme.html", "extra/readme.md", "LICENSE" ], "_cranurl": false, "_exports": [ "align_patient", "align_patient_profile", "anchor_enrichment", "as_summarized_experiment", "assemble_user_evidence", "atlas_provenance", "build_evidence_graph", "case_study", "classify_claim_tier", "classify_prot_trajectory", "classify_protein_trajectory", "classify_trajectory", "compare_candidates", "compare_genes", "compute_audit_score", "compute_pareto_class", "compute_pareto_layers", "compute_trace_d", "download_phase_csvs", "early_pattern_names", "early_patterns", "evaluate_anchor_enrichment", "evaluate_pareto_stability", "evidence_math", "explain_gene", "explain_score", "explain_user_evidence_model", "extract_graph_features", "fit_stage_de", "fit_stage_de_protein", "fit_user_evidence_model", "format_provenance", "list_atlas_metadata", "list_candidates", "list_data_sources", "make_evidence_features", "mid_pattern_names_excluded", "mid_patterns", "model_card", "NCS_W_15COL", "NCS_W_DOUBLE", "NCS_W_SINGLE", "NCS_W_TRIPLE", "pdactrace_axes_theme", "pdactrace_pal_class", "pdactrace_pal_dir", "pdactrace_pal_group", "pdactrace_pal_pattern", "pdactrace_panel_theme", "pdactrace_save", "plot_candidate_landscape", "plot_celltype_full", "plot_filter_diagnostics", "plot_filter_trace", "plot_gene_evidence", "plot_gene_hexagon", "plot_gene_template", "plot_meta_forest", "plot_panel_heatmap", "plot_per_cohort", "plot_serum_direction", "plot_stage_effect", "plot_template_atlas", "predict_user_evidence_model", "project_user_cohort", "project_user_serum_cohort", "propagate_uncertainty", "query_gene", "query_gene_detailed", "query_panel", "report_gene", "run_weight_robustness", "sb_average_precision", "sb_binary_auc", "sb_default_one_shot_rule", "sb_loco_stability", "sb_method_scores", "sb_multiblock_plsda_scores", "sb_observability", "sb_one_shot", "sb_pareto_fronts", "sb_simulate", "sb_topk_recall", "sb_validate_effects", "schema_spec", "score_anchor_similarity", "score_trajectory", "stagebridge", "summarize_gene_evidence", "summarize_translation_gap", "trace_filters", "viz_gene" ], "_datasets": [ { "name": "atlas_metadata", "title": "Atlas metadata", "object": "atlas_metadata", "file": "atlas_metadata.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "default_templates", "title": "Default trajectory templates (12-template catalog, v0.4.0)", "object": "default_templates", "file": "default_templates.rda", "class": [ "list" ], "fields": [], "table": true, "tojson": true }, { "name": "meta_analysis", "title": "Random-effects meta-analysis table", "object": "meta_analysis", "file": "meta_analysis.rda", "class": [ "data.table", "data.frame" ], "fields": [ "gene_symbol", "meta_Mid_vs_Early_beta", "meta_Mid_vs_Early_se", "meta_Mid_vs_Early_pval", "meta_Mid_vs_Early_tau2", "meta_Mid_vs_Early_I2", "meta_Mid_vs_Early_k", "meta_Late_vs_Early_beta", "meta_Late_vs_Early_se", "meta_Late_vs_Early_pval", "meta_Late_vs_Early_tau2", "meta_Late_vs_Early_I2", "meta_Late_vs_Early_k", "meta_Normal_vs_Early_beta", "meta_Normal_vs_Early_se", "meta_Normal_vs_Early_pval", "meta_Normal_vs_Early_tau2", "meta_Normal_vs_Early_I2", "meta_Normal_vs_Early_k", "meta_Mid_vs_Early_padj", "meta_Late_vs_Early_padj", "meta_Normal_vs_Early_padj", "meta_cohort_divergent" ], "rows": 17054, "table": true, "tojson": true }, { "name": "pdactrace_data_sources", "title": "Public-data accession table backing list_data_sources()", "object": "pdactrace_data_sources", "file": "pdactrace_data_sources.rda", "class": [ "data.table", "data.frame" ], "fields": [ "accession", "layer", "source_type", "used_for", "citation", "url" ], "rows": 26, "table": true, "tojson": true }, { "name": "pdactrace_external_anchors", "title": "External PDAC biomarker anchor provenance table", "object": "pdactrace_external_anchors", "file": "pdactrace_external_anchors.rda", "class": [ "data.frame" ], "fields": [ "gene", "source", "source_type", "evidence_tier", "assay_context", "early_detection", "gene_level_mapping", "include_primary_eval", "include_secondary_eval", "pmid_or_url", "note" ], "rows": 30, "table": true, "tojson": true }, { "name": "pdactrace_protein_betas", "title": "Per-stage tissue-protein effect-size table for trajectory plotting", "object": "pdactrace_protein_betas", "file": "pdactrace_protein_betas.rda", "class": [ "data.table", "data.frame" ], "fields": [ "gene_symbol", "prot_beta_N", "prot_beta_E", "prot_beta_M", "prot_beta_L", "prot_pattern_12", "prot_pattern_rho", "prot_lrt_padj" ], "rows": 5917, "table": true, "tojson": true }, { "name": "pdactrace_reference", "title": "pdactrace reference DB schema (v0.4.0, 12-template catalog with Early × 4 surface)", "object": "pdactrace_reference", "file": "pdactrace_reference.rda", "class": [ "data.table", "data.frame" ], "fields": [ "gene_symbol", "ensembl_id", "entrez_id", "rna_lrt_padj", "rna_beta_N", "rna_beta_E", "rna_beta_M", "rna_beta_L", "rna_padj_E", "rna_padj_M", "rna_padj_L", "rna_wald_padj_E", "rna_wald_padj_M", "rna_wald_padj_L", "rna_lfcSE_E", "rna_lfcSE_M", "rna_lfcSE_L", "rna_pattern", "rna_pattern_rho", "rna_pattern_rho_runner_up", "rna_stouffer_z", "rna_stouffer_p", "rna_stouffer_padj", "rna_cohort_agreement", "rna_per_cohort_trend", "rna_per_cohort_monotonic", "excluded_mid_pattern", "excluded_late_pattern", "excluded_monotonic_pattern", "prot_pattern", "prot_tier", "rnaprot_concordant", "cell_origin_top", "cell_origin_distrib", "cell_origin_padj", "cell_specificity_tau", "serum_detected", "serum_n_cohorts_detected", "serum_log2fc_PDAC_vs_HC", "serum_log2fc_Pan_vs_HC", "translation_class", "phase77_strict", "resectable_marker", "resectable_pattern_phase29", "panel_member", "flt_signal_peptide", "flt_serum_measurable", "flt_serum_significant", "flt_pancreatitis_pdac", "flt_pancreatitis_hc", "flt_direction_match", "flt_final", "ann_pool_logfc", "ann_pool_padj", "ann_pan_vs_hc_logfc", "ann_pan_vs_hc_pval", "ann_pan_excluded_phase60", "ann_pdac_mean", "ann_pan_mean", "ann_hc_mean", "ann_pdac_vs_pan_pval", "provenance", "last_updated", "evidence_scope", "serum_direction_label", "direction_model_trainable", "direction_model_card_ref", "meta_NvE_beta", "meta_NvE_se", "meta_NvE_pval", "meta_NvE_padj", "meta_NvE_I2", "meta_NvE_k", "meta_MvE_beta", "meta_MvE_pval", "meta_MvE_padj", "meta_MvE_I2", "meta_MvE_k", "meta_LvE_beta", "meta_LvE_pval", "meta_LvE_padj", "meta_LvE_I2", "meta_LvE_k", "meta_cohort_divergent", "max_abs_beta_meta", "max_I2_meta", "audit_score_layer", "audit_score_direction", "audit_score_early", "audit_score_serum", "audit_score_rescue", "audit_leakage_mult", "audit_heterogeneity_mult", "audit_score_raw", "audit_is_housekeeping", "audit_is_plasma_high_abundance", "audit_rescue_eligible", "audit_evidence_strength", "audit_biological_coherence", "audit_translational_relevance", "audit_leakage_gate", "audit_heterogeneity_gate", "audit_positive_score", "audit_score", "audit_class", "audit_score_median", "audit_score_lo95", "audit_score_hi95", "audit_uncertainty_width", "audit_rank_median", "audit_rank_lo95", "audit_rank_hi95", "audit_confidence_class" ], "rows": 10113, "table": false, "tojson": true }, { "name": "toy_coldata", "title": "Synthetic stage / cohort metadata for runnable examples", "object": "toy_coldata", "file": "toy_coldata.rda", "class": [ "data.frame" ], "fields": [ "sample", "stage", "cohort" ], "rows": 24, "table": true, "tojson": true }, { "name": "toy_counts", "title": "Synthetic RNA count matrix for runnable examples", "object": "toy_counts", "file": "toy_counts.rda", "class": [ "matrix", "array" ], "fields": [ "S01", "S02", "S03", "S04", "S05", "S06", "S07", "S08", "S09", "S10", "S11", "S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S20", "S21", "S22", "S23", "S24" ], "rows": 50, "table": true, "tojson": true }, { "name": "toy_protein", "title": "Synthetic tissue-protein log2 intensity matrix for runnable examples", "object": "toy_protein", "file": "toy_protein.rda", "class": [ "matrix", "array" ], "fields": [ "S01", "S02", "S03", "S04", "S05", "S06", "S07", "S08", "S09", "S10", "S11", "S12", "S13", "S14", "S15", "S16", "S17", "S18", "S19", "S20", "S21", "S22", "S23", "S24" ], "rows": 50, "table": true, "tojson": true } ], "_help": [ { "page": "pdactrace-package", "title": "pdactrace . PDAC-TRACE: queryable stage-aware tissue-to-serum biomarker atlas", "topics": [ "pdactrace-package", "pdactrace" ] }, { "page": "align_patient_profile", "title": "Align a single patient's omics profile against atlas stage trajectories", "topics": [ "align_patient", "align_patient_profile" ] }, { "page": "as_summarized_experiment", "title": "Convert pdactrace_reference into a SummarizedExperiment", "topics": [ "as_summarized_experiment" ] }, { "page": "assemble_user_evidence", "title": "Assemble user multi-omics inputs into a per-gene evidence table", "topics": [ "assemble_user_evidence" ] }, { "page": "atlas_metadata", "title": "Atlas metadata", "topics": [ "atlas_metadata" ] }, { "page": "atlas_provenance", "title": "Atlas provenance (version, build date, source repo, DOIs)", "topics": [ "atlas_provenance" ] }, { "page": "build_evidence_graph", "title": "Build a transparent evidence graph for one gene", "topics": [ "build_evidence_graph" ] }, { "page": "case_study", "title": "Summarize audit-score case-study genes", "topics": [ "case_study" ] }, { "page": "classify_claim_tier", "title": "Classify tissue-to-blood biomarker claim tiers", "topics": [ "classify_claim_tier" ] }, { "page": "classify_protein_trajectory", "title": "Classify each protein's trajectory against the 12-template catalog", "topics": [ "classify_protein_trajectory", "classify_prot_trajectory" ] }, { "page": "classify_trajectory", "title": "Classify each gene's trajectory against the 12-template catalog", "topics": [ "classify_trajectory" ] }, { "page": "compare_candidates", "title": "Compare multiple candidate genes side-by-side", "topics": [ "compare_candidates" ] }, { "page": "compare_genes", "title": "Side-by-side Evidence Math comparison across multiple genes", "topics": [ "compare_genes" ] }, { "page": "compute_audit_score", "title": "Compute the frozen pdactrace audit score (3-axis + 2-gate)", "topics": [ "compute_audit_score" ] }, { "page": "compute_pareto_class", "title": "Classify Pareto evidence support", "topics": [ "compute_pareto_class" ] }, { "page": "compute_pareto_layers", "title": "Compute weight-free Pareto layers on the three evidence axes", "topics": [ "compute_pareto_layers" ] }, { "page": "compute_trace_d", "title": "Algorithm 1 — TRACE-D: Tissue-to-serum Directional Evidence Concordance", "topics": [ "compute_trace_d" ] }, { "page": "default_templates", "title": "Default trajectory templates (12-template catalog, v0.4.0)", "topics": [ "default_templates" ] }, { "page": "download_phase_csvs", "title": "Download the two large upstream phase CSVs into a local cache", "topics": [ "download_phase_csvs" ] }, { "page": "early_pattern_names", "title": "Early-onset pattern names (the 4 atlas-surfaced patterns)", "topics": [ "early_patterns", "early_pattern_names" ] }, { "page": "evaluate_anchor_enrichment", "title": "Evaluate external-anchor enrichment in top-ranked genes", "topics": [ "anchor_enrichment", "evaluate_anchor_enrichment" ] }, { "page": "evaluate_pareto_stability", "title": "Evaluate Monte-Carlo Pareto stability under perturbed evidence", "topics": [ "evaluate_pareto_stability" ] }, { "page": "evidence_math", "title": "Per-axis mathematical evidence for one gene", "topics": [ "evidence_math" ] }, { "page": "explain_gene", "title": "Print a per-axis evidence summary for one gene", "topics": [ "explain_gene" ] }, { "page": "explain_score", "title": "Decompose a gene's audit score into its three axes and two gates", "topics": [ "explain_score" ] }, { "page": "explain_user_evidence_model", "title": "Explain a 'pdactrace_user_model' via its top contributing features", "topics": [ "explain_user_evidence_model" ] }, { "page": "extract_graph_features", "title": "Extract graph-aware audit features", "topics": [ "extract_graph_features" ] }, { "page": "fit_stage_de", "title": "Fit a stage-aware DESeq2 LRT model on user RNA-seq data", "topics": [ "fit_stage_de", "fit_stage_de,ANY-method", "fit_stage_de,SummarizedExperiment-method" ] }, { "page": "fit_stage_de_protein", "title": "Fit a stage-aware limma model on user tissue-protein intensity data", "topics": [ "fit_stage_de_protein", "fit_stage_de_protein,ANY-method", "fit_stage_de_protein,SummarizedExperiment-method" ] }, { "page": "fit_user_evidence_model", "title": "Fit a user-supplied supervised model on the evidence feature matrix", "topics": [ "fit_user_evidence_model" ] }, { "page": "format_provenance", "title": "Human-readable evidence labels for the bundled phase tags", "topics": [ "format_provenance" ] }, { "page": "list_atlas_metadata", "title": "Inspect atlas metadata", "topics": [ "list_atlas_metadata" ] }, { "page": "list_candidates", "title": "List candidate genes by biology-level filter parameters", "topics": [ "list_candidates" ] }, { "page": "list_data_sources", "title": "List the public datasets that contributed to the pdactrace atlas", "topics": [ "list_data_sources" ] }, { "page": "make_evidence_features", "title": "Build a flat numeric feature matrix for downstream modelling", "topics": [ "make_evidence_features" ] }, { "page": "meta_analysis", "title": "Random-effects meta-analysis table", "topics": [ "meta_analysis" ] }, { "page": "mid_pattern_names_excluded", "title": "Mid-onset pattern names (excluded from atlas surface)", "topics": [ "mid_patterns", "mid_pattern_names_excluded" ] }, { "page": "model_card", "title": "Model card metadata for the optional ML layer", "topics": [ "model_card" ] }, { "page": "pdactrace_data_sources", "title": "Public-data accession table backing list_data_sources()", "topics": [ "pdactrace_data_sources" ] }, { "page": "pdactrace_external_anchors", "title": "External PDAC biomarker anchor provenance table", "topics": [ "pdactrace_external_anchors" ] }, { "page": "pdactrace_protein_betas", "title": "Per-stage tissue-protein effect-size table for trajectory plotting", "topics": [ "pdactrace_protein_betas" ] }, { "page": "pdactrace_save", "title": "Save a ggplot to PDF using cairo_pdf", "topics": [ "pdactrace_save" ] }, { "page": "pdactrace-palettes", "title": "Palettes for pdactrace figures", "topics": [ "pdactrace-palettes", "pdactrace_pal_class", "pdactrace_pal_dir", "pdactrace_pal_group", "pdactrace_pal_pattern" ] }, { "page": "pdactrace-theme", "title": "pdactrace NCS-grade ggplot2 theme", "topics": [ "NCS_W_15COL", "NCS_W_DOUBLE", "NCS_W_SINGLE", "NCS_W_TRIPLE", "pdactrace-theme", "pdactrace_axes_theme", "pdactrace_panel_theme" ] }, { "page": "plot_candidate_landscape", "title": "Visualise the candidate landscape across tissue and serum", "topics": [ "plot_candidate_landscape" ] }, { "page": "plot_celltype_full", "title": "Full 11-celltype expression bar", "topics": [ "plot_celltype_full" ] }, { "page": "plot_filter_diagnostics", "title": "Filter diagnostic step bar with underlying metric annotation", "topics": [ "plot_filter_diagnostics" ] }, { "page": "plot_filter_trace", "title": "Visualise tissue-to-serum filter passage with serum direction context", "topics": [ "plot_filter_trace" ] }, { "page": "plot_gene_evidence", "title": "Multi-panel ggplot composite of gene evidence", "topics": [ "plot_gene_evidence" ] }, { "page": "plot_gene_hexagon", "title": "Hexagonal evidence radar for one or more genes", "topics": [ "plot_gene_hexagon" ] }, { "page": "plot_gene_template", "title": "Per-gene template-overlay plot", "topics": [ "plot_gene_template" ] }, { "page": "plot_meta_forest", "title": "Random-effects meta-analysis forest plot per gene", "topics": [ "plot_meta_forest" ] }, { "page": "plot_panel_heatmap", "title": "Compare a gene panel across evidence layers as a heatmap", "topics": [ "plot_panel_heatmap" ] }, { "page": "plot_per_cohort", "title": "Per-cohort sign vote bar with Stouffer summary", "topics": [ "plot_per_cohort" ] }, { "page": "plot_serum_direction", "title": "Per-gene serum direction context, coloured by translation class", "topics": [ "plot_serum_direction" ] }, { "page": "plot_stage_effect", "title": "Forest plot of per-stage effect size", "topics": [ "plot_stage_effect" ] }, { "page": "plot_template_atlas", "title": "Per-template trajectory atlas plots", "topics": [ "plot_template_atlas" ] }, { "page": "predict_user_evidence_model", "title": "Predict from a 'pdactrace_user_model'", "topics": [ "predict_user_evidence_model" ] }, { "page": "project_user_cohort", "title": "End-to-end user-cohort projection through the audit framework", "topics": [ "project_user_cohort" ] }, { "page": "project_user_serum_cohort", "title": "Project a user-supplied serum proteomics cohort (binary contrast)", "topics": [ "project_user_serum_cohort" ] }, { "page": "propagate_uncertainty", "title": "Propagate audit-score uncertainty", "topics": [ "propagate_uncertainty" ] }, { "page": "query_gene", "title": "Query the pdactrace reference atlas for a single gene", "topics": [ "query_gene" ] }, { "page": "query_gene_detailed", "title": "Detailed gene-level evidence - 5 granularity tables", "topics": [ "query_gene_detailed" ] }, { "page": "query_panel", "title": "Query the pdactrace reference atlas for multiple genes", "topics": [ "query_panel" ] }, { "page": "report_gene", "title": "Render a pdactrace evidence report for one gene or a panel", "topics": [ "report_gene" ] }, { "page": "run_weight_robustness", "title": "Evaluate ranking robustness across plausible audit weights", "topics": [ "run_weight_robustness" ] }, { "page": "sb_average_precision", "title": "Average precision", "topics": [ "sb_average_precision" ] }, { "page": "sb_binary_auc", "title": "Binary area under the ROC curve", "topics": [ "sb_binary_auc" ] }, { "page": "sb_default_one_shot_rule", "title": "Default frozen thresholds for 'sb_one_shot()'", "topics": [ "sb_default_one_shot_rule" ] }, { "page": "sb_loco_stability", "title": "Leave-one-cohort-out rank stability", "topics": [ "sb_loco_stability" ] }, { "page": "sb_method_scores", "title": "Score candidates with StageBridge and benchmark comparators", "topics": [ "sb_method_scores" ] }, { "page": "sb_multiblock_plsda_scores", "title": "Score shared features with matched-sample multiblock PLS-DA", "topics": [ "sb_multiblock_plsda_scores" ] }, { "page": "sb_observability", "title": "Calculate depth-adjusted blood observability", "topics": [ "sb_observability" ] }, { "page": "sb_one_shot", "title": "Run one prospectively locked destination-cohort audit to a terminal decision", "topics": [ "sb_one_shot" ] }, { "page": "sb_pareto_fronts", "title": "Assign exact non-dominated Pareto fronts", "topics": [ "sb_pareto_fronts" ] }, { "page": "sb_simulate", "title": "Simulate a multi-cohort, multi-omic biomarker benchmark", "topics": [ "sb_simulate" ] }, { "page": "sb_topk_recall", "title": "Recall among the top-ranked candidates", "topics": [ "sb_topk_recall" ] }, { "page": "sb_validate_effects", "title": "Validate a StageBridge effect table", "topics": [ "sb_validate_effects" ] }, { "page": "schema_spec", "title": "Schema column specification", "topics": [ "schema_spec" ] }, { "page": "score_anchor_similarity", "title": "Descriptive feature-space similarity to bundled external anchors", "topics": [ "score_anchor_similarity" ] }, { "page": "score_trajectory", "title": "Score one or more genes against all 12 templates", "topics": [ "score_trajectory" ] }, { "page": "stagebridge", "title": "Rank stage-resolved multi-omic biomarker candidates", "topics": [ "stagebridge" ] }, { "page": "summarize_gene_evidence", "title": "Human-readable text summary of gene evidence", "topics": [ "summarize_gene_evidence" ] }, { "page": "summarize_translation_gap", "title": "Summarize the tissue-to-blood translation gap", "topics": [ "summarize_translation_gap" ] }, { "page": "toy_coldata", "title": "Synthetic stage / cohort metadata for runnable examples", "topics": [ "toy_coldata" ] }, { "page": "toy_counts", "title": "Synthetic RNA count matrix for runnable examples", "topics": [ "toy_counts" ] }, { "page": "toy_protein", "title": "Synthetic tissue-protein log2 intensity matrix for runnable examples", "topics": [ "toy_protein" ] }, { "page": "trace_filters", "title": "Trace which selection filters a gene passed or failed", "topics": [ "trace_filters" ] }, { "page": "viz_gene", "title": "Single-call visual evidence + scoring canvas for one gene", "topics": [ "viz_gene" ] } ], "_readme": "https://github.com/BiocStaging/pdactrace/raw/HEAD/README.md", "_rundeps": [ "abind", "Biobase", "BiocGenerics", "cli", "cpp11", "data.table", "DelayedArray", "farver", "generics", "GenomicRanges", "ggplot2", "glue", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "Matrix", "MatrixGenerics", "matrixStats", "patchwork", "R6", "RColorBrewer", "rlang", "S4Arrays", "S4Vectors", "S7", "scales", "Seqinfo", "SparseArray", "SummarizedExperiment", "vctrs", "viridisLite", "withr", "XVector" ], "_vignettes": [ { "source": "lookup_basics.Rmd", "filename": "lookup_basics.html", "title": "Lookup basics: querying the pdactrace atlas ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "1. Single-gene query — query_gene()", "2. Multi-gene comparison — query_panel()", "3. Multi-parameter candidate listing — list_candidates()", "4. Filter audit trail — trace_filters()", "5. Plain-text summary — summarize_gene_evidence()", "Atlas metadata", "Next", "Session" ], "created": "2026-05-07 09:56:21", "modified": "2026-05-27 11:13:21", "commits": 2 }, { "source": "audit_case_studies.Rmd", "filename": "audit_case_studies.html", "title": "Audit-class case studies — LGALS3BP / LTBP1 / ALB / GAPDH ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "Side-by-side audit summary", "Detailed audit features per gene", "Case 1 — LGALS3BP (high_confidence anchor)", "Case 2 — LTBP1 (supported_uncertain, Class B inverse exemplar)", "Case 3 — ALB (penalized, plasma high-abundance gate)", "Case 4 — GAPDH (excluded, housekeeping gate)", "Take-away", "Session information" ], "created": "2026-05-07 09:56:21", "modified": "2026-09-27 11:14:08", "commits": 3 }, { "source": "audit_framework.Rmd", "filename": "audit_framework.html", "title": "Audit framework: 3 axes + 2 gates + 4 classes (v0.3.0) ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "1. Why a hand-engineered rule (and not a supervised model)", "2. The 6-function API at a glance", "3. LTBP1 — the supported_uncertain exemplar", "4. GAPDH — the housekeeping negative control", "5. Anchor enrichment evaluation (post-freeze)", "6. Reading the case_study() output", "7. What the audit framework does not claim", "Session info" ], "created": "2026-05-07 09:56:21", "modified": "2026-09-28 11:34:07", "commits": 3 }, { "source": "user_cohort_extension.Rmd", "filename": "user_cohort_extension.html", "title": "Apply pdactrace to your own multi-omics cohort ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "Step 1 — Load the bundled toy cohort", "Step 2 — Fit the stage-aware RNA model", "Step 3 — Fit the protein limma model", "Step 4 — Assemble the user evidence table", "Step 5 — Run the audit framework on user evidence", "Step 6 — Bioconductor-native input via SummarizedExperiment (v0.99.2)", "Step 7 — Single-patient trajectory alignment (v0.4.1)", "Scope boundary", "Appendix A — Stage harmonization (TNM / AJCC -> Normal / Early / Mid / Late)", "Appendix B -- Serum projection (binary group contrast, no stage)" ], "created": "2026-05-07 09:56:21", "modified": "2026-09-27 11:14:08", "commits": 5 }, { "source": "reproducibility.Rmd", "filename": "reproducibility.html", "title": "Reproducibility from raw data ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "Layer 1 — Offline, bundled", "Layer 2 — User cohort", "Layer 3 — Re-derive the bundled atlas", "Layer 4 — From FASTQ", "Provenance summary", "Session information" ], "created": "2026-05-08 02:12:26", "modified": "2026-09-27 12:13:37", "commits": 4 }, { "source": "methodology_validation.Rmd", "filename": "methodology_validation.html", "title": "Methodology validation: cutoff sensitivity + tool comparison ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "Section A -- Cutoff sensitivity", "A1. Trajectory classification cutoff (rho_cutoff)", "A2. Three-axis weight sensitivity", "Section B -- Tool comparison", "Section C -- Negative control depletion", "C1. Top-N depletion (negative controls absent from the most-prioritised candidates)", "C2. Bottom-N enrichment (negative controls concentrated at the lowest-priority end)", "Section D -- Held-out PDAC cohort projection (v0.99.12)", "Section E -- Three-way baseline: where does enrichment come from?", "Limitations of these analyses" ], "created": "2026-05-10 09:05:44", "modified": "2026-09-28 12:54:38", "commits": 5 }, { "source": "prespecification_audit.Rmd", "filename": "prespecification_audit.html", "title": "Prespecified scoring and the frozen one-shot audit ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "Step 1 -- A simulated multi-cohort, multi-omic benchmark", "Step 2 -- Depth-adjusted blood observability", "Step 3 -- Rank candidates", "Step 4 -- Does the ranking survive dropping a cohort?", "Step 5 -- Comparators, scored honestly", "Step 6 -- The frozen one-shot audit", "Why a calibration check matters", "Scope" ], "created": "2026-09-27 11:14:08", "modified": "2026-09-28 11:34:07", "commits": 2 }, { "source": "cross_cancer_demonstration.Rmd", "filename": "cross_cancer_demonstration.html", "title": "Portability of the R API to a non-PDAC cohort ", "author": "Jibeom Ko", "engine": "knitr::rmarkdown", "headings": [ "Goal", "Step 1 -- Build a synthetic non-PDAC cohort", "Step 2 -- Project through the framework (one call)", "Step 3 -- What changes between PDAC and non-PDAC?", "Step 4 -- Translation discipline transfers, but the join target changes", "Limitations" ], "created": "2026-05-10 09:05:44", "modified": "2026-09-27 11:14:08", "commits": 2 } ], "_score": 4.204119982655925, "_indexed": true, "_nocasepkg": "pdactrace", "_universes": [ "biocstaging", "jibeomko" ], "_previous": "0.99.21", "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.99.25", "date": "2026-09-28T15:53:39.000Z", "distro": "resolute", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/988e6ef2b29142ddca43b508a61fa4f18c8dd18a35f89a285364d038c78d5fd5", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" }, { "r": "4.6.1", "os": "linux", "version": "0.99.25", "date": "2026-09-28T15:53:40.000Z", "distro": "resolute", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/951f6735141269a37406ebd083e8956d4c457efbbd5e970ffb056d2df703e3ba", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" }, { "r": "4.5.3", "os": "mac", "version": "0.99.25", "date": "2026-09-28T15:57:57.000Z", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/be28260ed48a5975c896831dd50fd56ca30d4f283a573a056e4fefabd866fa9c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" }, { "r": "4.6.1", "os": "mac", "version": "0.99.25", "date": "2026-09-28T16:04:19.000Z", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/0930d6264ea902ee305326134922e7166ac0089b276966f8fdc6ae3779b09aa3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" }, { "r": "4.6.0", "os": "wasm", "version": "0.99.25", "date": "2026-09-28T15:53:38.000Z", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/9412450d95c3101409530469a4eb0ff933ff519b49d6c8660d0771b0fd32c113", "status": "success", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" }, { "r": "4.7.0", "os": "win", "version": "0.99.25", "date": "2026-09-28T15:53:10.000Z", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/ac720abf1a5db0dfaf7470a16a9785e42fd8d00722257ce5e64f9189abecb082", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" }, { "r": "4.5.3", "os": "win", "version": "0.99.25", "date": "2026-09-28T15:52:20.000Z", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/3fdac41eb3388bc31db9745abd53075ce83cf88a3799c5a429a03774774508ad", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" }, { "r": "4.6.1", "os": "win", "version": "0.99.25", "date": "2026-09-28T15:52:25.000Z", "commit": "131aa2c00e8e02fb75eeb180d47927fbc16c0f82", "fileid": "https://r2.ropensci.org/a935f3cf80cf94c3d8b1418dca7ed47061df0921d5d8fbbb456665237e253ac7", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/biocstaging/actions/runs/36445637536" } ] }