# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "diagFDR" in publications use:'
type: software
license: GPL-3.0-only
title: 'diagFDR: Assessing False Discovery Rate Claims in Proteomics'
version: 0.2.1
doi: 10.64898/2026.04.16.718468
identifiers:
- type: doi
  value: 10.32614/CRAN.package.diagFDR
abstract: 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) <https://doi.org/10.64898/2026.04.16.718468>.
authors:
- family-names: Giai Gianetto
  given-names: Quentin
  email: quentin.giaigianetto@pasteur.fr
  orcid: https://orcid.org/0000-0001-6815-2498
preferred-citation:
  type: article
  title: 'diagFDR: Assessing False Discovery Rate Claims in Proteomics with Scope,
    Calibration and Stability Diagnostics'
  authors:
  - family-names: Chion
    given-names: Marie
  - family-names: Godmer
    given-names: Alexandre
  - family-names: Douché
    given-names: Thibaut
  - family-names: Matondo
    given-names: Mariette
  - family-names: Giai Gianetto
    given-names: Quentin
    email: quentin.giaigianetto@pasteur.fr
    orcid: https://orcid.org/0000-0001-6815-2498
  journal: bioRxiv
  year: '2026'
  doi: 10.64898/2026.04.16.718468
  notes: R package version 0.2.1
repository: https://jacky11.r-universe.dev
repository-code: https://github.com/Jacky11/diagFDR
commit: aba106639928e6ca62f74f362d6cfd1d0bca0f59
url: https://www.biorxiv.org/content/10.64898/2026.04.16.718468
date-released: '2026-10-25'
contact:
- family-names: Giai Gianetto
  given-names: Quentin
  email: quentin.giaigianetto@pasteur.fr
  orcid: https://orcid.org/0000-0001-6815-2498