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diagFDR: Assessing False Discovery Rate Claims in Proteomics

Provides scope, calibration and stability diagnostics to assess false discovery rate (FDR) claims in peptide and protein identification workflows based on target-decoy competition and related confidence measures. Includes the recomputed decoy ratio of the reported list, accepted decoy counts and local decoy support, the FDP-CV benchmark, threshold elasticity, posterior error probability (PEP) concordance with the decoys, equal-chance checks and p-value calibration, explicit target/decoy label-propagation rules for grouped units, picked-protein competition, external validation by entrapment (raw and size-corrected estimates, scope-discordant-set error rate), a ground-truth simulator of target-decoy competition, and an HTML report. Methods are described in Chion et al. (2026) <doi:10.64898/2026.04.16.718468>.

Version: 0.2.1
Depends: R (≥ 4.2.0)
Imports: dplyr, tibble, ggplot2, purrr, rlang, readr, xml2, cp4p, tidyr, scales, data.table, stats, utils
Suggests: arrow, knitr, officer, rvg, testthat (≥ 3.0.0), withr, rmarkdown, jsonlite
Published: 2026-10-28
DOI: 10.32614/CRAN.package.diagFDR
Author: Quentin Giai Gianetto ORCID iD [aut, cre], Marie Chion ORCID iD [ctb], Alexandre Godmer ORCID iD [ctb], Thibaut Douché ORCID iD [ctb], Mariette Matondo ORCID iD [ctb]
Maintainer: Quentin Giai Gianetto <quentin.giaigianetto at pasteur.fr>
BugReports: https://github.com/Jacky11/diagFDR/issues
License: GPL-3
URL: https://github.com/Jacky11/diagFDR, https://www.biorxiv.org/content/10.64898/2026.04.16.718468
NeedsCompilation: no
Citation: diagFDR citation info
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 quick start (source, R code)
diagFDR: generic elution groups diagnostics from Spectronaut (tsv report) (source, R code)

Downloads:

Package source: diagFDR_0.2.1.tar.gz
Windows binaries: r-devel: diagFDR_0.2.1.zip, r-release: diagFDR_0.2.1.zip, r-oldrel: diagFDR_0.2.1.zip
macOS binaries: r-release (arm64): diagFDR_0.2.1.tgz, r-oldrel (arm64): diagFDR_0.2.1.tgz, r-release (x86_64): diagFDR_0.2.1.tgz, r-oldrel (x86_64): diagFDR_0.2.1.tgz
Old sources: diagFDR archive

Linking:

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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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