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# 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 "NADIA" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'NADIA: Missing Value-Aware Differential Abundance Analysis of DIA Proteomics
  Data'
version: 0.99.1
doi: 10.5281/zenodo.22504221
identifiers:
- type: doi
  value: 10.32614/CRAN.package.NADIA
abstract: Provides an end-to-end workflow for differential abundance analysis of protein
  quantification data, with particular attention to missing values in data-independent
  acquisition (DIA) proteomics. Quantification reports exported from Spectronaut,
  DIA-NN and Proteome Discoverer for TMT and label-free experiments (DDA/DIA) are
  converted into a common data structure, normalised, optionally batch-corrected,
  imputed and analysed using limma or limpa. The package includes individual and two-stage
  imputation strategies that treat values assumed to be missing at random and missing
  not at random separately. Data-driven functions evaluate and rank normalisation
  and imputation workflows using simulated missingness or spike-in datasets with known
  ground truth, allowing method selection to be justified for each dataset. Results
  can be explored through interactive Highcharts visualisations, static ggplot2 and
  ComplexHeatmap figures, and sortable tables.
authors:
- family-names: Ciordia
  given-names: Sergio
  email: sciordia@gmail.com
  orcid: https://orcid.org/0000-0002-5726-853X
preferred-citation:
  type: manual
  title: 'NADIA: Missing Value-Aware Differential Abundance Analysis of DIA Proteomics
    Data'
  authors:
  - family-names: Ciordia
    given-names: Sergio
    orcid: https://orcid.org/0000-0002-5726-853X
    email: sciordia@gmail.com
  year: '2026'
  notes: R package version 0.99.1
  url: https://github.com/sciordia/NADIA
  doi: 10.5281/zenodo.22504221
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/sciordia/NADIA
commit: c4a896085c0e2b7966e6ddf55af3f07aa3a4c114
url: https://sciordia.github.io/NADIA/
date-released: '2026-09-06'
contact:
- family-names: Ciordia
  given-names: Sergio
  email: sciordia@gmail.com
  orcid: https://orcid.org/0000-0002-5726-853X