Package: pdactrace
Type: Package
Title: Stage-Aware PDAC Atlas and Prospectively Frozen Tissue-to-Serum
        Biomarker Audit Framework
Version: 0.99.25
Authors@R: c(
    person(given = "Jibeom", family = "Ko",
           email = "rhwlqja1779@gmail.com",
           role = c("aut", "cre"),
           comment = c(ORCID = "0009-0002-8630-1973")))
Description: pdactrace implements a transparent, deterministic
        claim-audit framework for stage-aware pancreatic ductal
        adenocarcinoma (PDAC) tissue-to-blood biomarker evidence. It
        integrates per-stage trajectory matching across bulk RNA-seq,
        tissue proteomics, single-cell origin, serum proteomics, and
        pancreatitis context, with explicit anchor-enrichment
        evaluation against a curated external reference set. The
        framework comprises a 12-template competitive trajectory
        catalog, a 3-axis + 2-gate reference score, an Evidence Math
        layer, TRACE-D tissue-to-serum directional evidence
        concordance, claim-tier classification, and weight-robustness
        and Pareto support audits. A prespecification layer supports
        freezing candidate scores, directions and a decision rule under
        a content hash before outcome labels are opened, with a
        distinct inconclusive terminal state when a frozen gate fails.
        Scope is deliberately PDAC-specific: the bundled atlas, the
        anchor reference set and every validated claim are PDAC, and no
        result is claimed for any other disease. Separately, no
        supervised classifier is trained or shipped, because validated
        non-circular early-detection ground truth is unavailable in
        PDAC.
License: MIT + file LICENSE
URL: https://github.com/jibeomko/pdactrace
BugReports: https://github.com/jibeomko/pdactrace/issues
biocViews: Software, BiomedicalInformatics, Classification,
        Transcriptomics, Proteomics, GeneExpression,
        DifferentialExpression, SingleCell, Visualization, Annotation
Encoding: UTF-8
LazyData: false
Depends: R (>= 4.5.0)
Imports: data.table, ggplot2, patchwork, glue, methods, stats, utils,
        withr, SummarizedExperiment
Suggests: DESeq2, digest, limma, mixOmics, S4Vectors, BiocFileCache,
        glmnet, testthat (>= 3.0.0), knitr, rmarkdown, pkgdown
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: 2026-09-28 15:49:31 UTC; root
Author: Jibeom Ko [aut, cre] (ORCID: <https://orcid.org/0009-0002-8630-1973>)
Maintainer: Jibeom Ko <rhwlqja1779@gmail.com>