spqrp: Sample Provenance Quality Resolver in Proteomics

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.

Version:	0.1.0
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
Published:	2026-06-17
DOI:	10.32614/CRAN.package.spqrp
Author:	Franziska Hradilak [aut, cre]
Maintainer:	Franziska Hradilak <Franziska.Hradilak at student.hpi.uni-potsdam.de>
BugReports:	https://github.com/fhradilak/spqrp_r/issues
License:	GPL-3
URL:	https://github.com/fhradilak/spqrp_r
NeedsCompilation:	no
Citation:	spqrp citation info
Materials:	README, NEWS
CRAN checks:	spqrp results

Documentation:

Reference manual:	spqrp.html , spqrp.pdf
Vignettes:	spqrp on mock data (source, R code)

Downloads:

Package source:	spqrp_0.1.0.tar.gz
Windows binaries:	r-devel: spqrp_0.1.0.zip, r-release: spqrp_0.1.0.zip, r-oldrel: spqrp_0.1.0.zip
macOS binaries:	r-release (arm64): spqrp_0.1.0.tgz, r-oldrel (arm64): spqrp_0.1.0.tgz, r-release (x86_64): spqrp_0.1.0.tgz, r-oldrel (x86_64): spqrp_0.1.0.tgz

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