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# CITATION 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 "PRONE" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'PRONE: The PROteomics Normalization Evaluator'
version: 1.6.0
doi: 10.1093/bib/bbaf201
identifiers:
- type: doi
  value: 10.32614/CRAN.package.PRONE
abstract: High-throughput omics data are often affected by systematic biases introduced
  throughout all the steps of a clinical study, from sample collection to quantification.
  Normalization methods aim to adjust for these biases to make the actual biological
  signal more prominent. However, selecting an appropriate normalization method is
  challenging due to the wide range of available approaches. Therefore, a comparative
  evaluation of unnormalized and normalized data is essential in identifying an appropriate
  normalization strategy for a specific data set. This R package provides different
  functions for preprocessing, normalizing, and evaluating different normalization
  approaches. Furthermore, normalization methods can be evaluated on downstream steps,
  such as differential expression analysis and statistical enrichment analysis. Spike-in
  data sets with known ground truth and real-world data sets of biological experiments
  acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can
  be analyzed.
authors:
- family-names: Arend
  given-names: Lis
  email: lis.arend@tum.de
  orcid: https://orcid.org/0000-0001-7990-8385
preferred-citation:
  type: article
  title: Systematic evaluation of normalization approaches in tandem mass tag and
    label-free protein quantification data using PRONE
  authors:
  - family-names: Arend
    given-names: Lis
    email: lis.arend@tum.de
    orcid: https://orcid.org/0000-0001-7990-8385
  - family-names: Adamowicz
    given-names: Klaudia
  - family-names: Schmidt
    given-names: Johannes R.
  - family-names: Burankova
    given-names: Yuliya
  - family-names: Zolotareva
    given-names: Olga
  - family-names: Tsoy
    given-names: Olga
  - family-names: Pauling
    given-names: Josch K.
  - family-names: Kalkhof
    given-names: Stefan
  - family-names: Baumbach
    given-names: Jan
  - family-names: List
    given-names: Markus
  - family-names: Laske
    given-names: Tanja
  year: '2025'
  journal: Briefings in Bioinformatics
  doi: 10.1093/bib/bbaf201
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/daisybio/PRONE
commit: 5a69c1f6d2be6e431a45802d163958f45b7d35ee
url: https://github.com/daisybio/PRONE
date-released: '2026-04-28'
contact:
- family-names: Arend
  given-names: Lis
  email: lis.arend@tum.de
  orcid: https://orcid.org/0000-0001-7990-8385