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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.

Version: 0.1.0
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: 2026-04-13
DOI: 10.32614/CRAN.package.diagFDR (may not be active yet)
Author: Quentin Giai Gianetto [aut, cre]
Maintainer: Quentin Giai Gianetto <quentin.giaigianetto at pasteur.fr>
License: GPL-3
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_0.1.0.tar.gz
Windows binaries: r-devel: not available, r-release: not available, r-oldrel: not available
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): diagFDR_0.1.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=diagFDR to link to this page.

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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