Package: spqrp
Title: Sample Provenance Quality Resolver in Proteomics
Version: 0.1.0
Authors@R: c(
    person("Franziska", "Hradilak",
           email = "Franziska.Hradilak@student.hpi.uni-potsdam.de",
           role = c("aut", "cre")))
Description: Detect sample-provenance inconsistencies and potential
        mix-ups in mass-spectrometry-based plasma-proteome cohorts.
        Provides a clustering-based approach (build a nearest-neighbour
        graph in a dimensionality-reduced space and iteratively split
        large components by edge weight), a threshold-based approach
        (classify sample pairs as belonging or not-belonging from a
        pairwise distance cutoff), parameter optimization over distance
        metrics and cutoffs, and a pairwise random-forest classifier
        for protein importance ranking. This is a native R port of the
        author's Python package 'spqrp'
        (<https://github.com/fhradilak/spqrp>), implementing methods
        from an associated manuscript currently in preparation.
License: GPL-3
URL: https://github.com/fhradilak/spqrp_r
BugReports: https://github.com/fhradilak/spqrp_r/issues
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.5.0)
Imports: cli, dplyr (>= 1.1.0), ggplot2 (>= 3.5.0), igraph (>= 2.0.0),
        lgr, pROC, randomForest, ranger (>= 0.16.0), rlang, solitude
        (>= 1.1.3), stats, tibble, tidyr (>= 1.3.0), utils, withr
Suggests: knitr, plotly (>= 4.10.0), recipes, rmarkdown, smacof,
        testthat (>= 3.0.0), themis, uwot (>= 0.2.0), vdiffr
Config/testthat/edition: 3
VignetteBuilder: knitr
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libglpk-dev libicu-dev libxml2-dev
Repository: https://fhradilak.r-universe.dev
Date/Publication: 2026-06-22 09:27:55 UTC
RemoteUrl: https://github.com/fhradilak/spqrp_r
RemoteRef: HEAD
RemoteSha: 724422e65321410329db3cf3f7620562ae683cd8
NeedsCompilation: no
Packaged: 2026-10-20 08:16:09 UTC; root
Author: Franziska Hradilak [aut, cre]
Maintainer: Franziska Hradilak <Franziska.Hradilak@student.hpi.uni-potsdam.de>