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, threshold elasticity, posterior error probability (PEP) concordance with the decoys, equal-chance checks and p-value calibration, with an HTML report. 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: | 0.1.2 |
| 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: | 2026-10-19 |
| 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 |
| Materials: | NEWS |
| CRAN checks: | diagFDR results |
| Package source: | diagFDR_0.1.2.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 |
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