diagFDR: Verifiable FDR Diagnostics for Proteomics

Provides methods to compute verifiable false discovery rate (FDR) diagnostic checks for workflows based on target-decoy competition and related confidence measures. Implements calibration, stability and tail diagnostics, including tail support, threshold elasticity, posterior error probability (PEP) reliability, and equal-chance checks. If you used this package in your research, please cite the associated preprint <doi:10.64898/2026.04.16.718468>. Detailed examples of using this package can also be found on the GitHub repository (<https://github.com/Jacky11/diagFDR>).

Version:	0.1.1
Depends:	R (≥ 4.2.0)
Imports:	dplyr, tibble, ggplot2, purrr, rlang, readr, xml2, cp4p, tidyr, scales, data.table
Suggests:	arrow, knitr, officer, rvg, testthat (≥ 3.0.0), withr, rmarkdown, jsonlite
Published:	2026-04-27
DOI:	10.32614/CRAN.package.diagFDR
Author:	Quentin Giai Gianetto [aut, cre]
Maintainer:	Quentin Giai Gianetto <quentin.giaigianetto at pasteur.fr>
License:	GPL-3
URL:	https://www.biorxiv.org/content/10.64898/2026.04.16.718468
NeedsCompilation:	no
CRAN checks:	diagFDR results

Documentation:

Reference manual:	diagFDR.html , diagFDR.pdf
Vignettes:	diagFDR: DIA-NN diagnostics from report.parquet (source, R code) diagFDR: MaxQuant diagnostics from msms.txt (source, R code) diagFDR: mokapot diagnostics (competed winners) (source, R code) diagFDR: generic PSM diagnostics from mzIdentML (.mzid) (source, R code) diagFDR: generic elution groups diagnostics from Spectronaut (tsv report) (source, R code)

Downloads:

Package source:	diagFDR_0.1.1.tar.gz
Windows binaries:	r-devel: diagFDR_0.1.1.zip, r-release: diagFDR_0.1.1.zip, r-oldrel: diagFDR_0.1.1.zip
macOS binaries:	r-release (arm64): diagFDR_0.1.1.tgz, r-oldrel (arm64): diagFDR_0.1.1.tgz, r-release (x86_64): diagFDR_0.1.1.tgz, r-oldrel (x86_64): diagFDR_0.1.1.tgz
Old sources:	diagFDR archive

Linking:

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