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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 "DRomics" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'DRomics: Dose Response for Omics'
version: 2.6-0
doi: 10.24072/pcjournal.325
identifiers:
- type: doi
  value: 10.32614/CRAN.package.DRomics
- type: url
  value: https://lbbe-software.github.io/DRomics/
abstract: Several functions are provided for dose-response (or concentration-response)
  characterization from omics data. 'DRomics' is especially dedicated to omics data
  obtained using a typical dose-response design, favoring a great number of tested
  doses (or concentrations) rather than a great number of replicates (no need of replicates).
  'DRomics' provides functions 1) to check, normalize and or transform data, 2) to
  select monotonic or biphasic significantly responding items (e.g. probes, metabolites),
  3) to choose the best-fit model among a predefined family of monotonic and biphasic
  models to describe each selected item, 4) to derive a benchmark dose or concentration
  and a typology of response from each fitted curve. In the available version data
  are supposed to be single-channel microarray data in log2, RNAseq data in raw counts,
  or already pretreated continuous omics data (such as metabolomic data) in log scale.
  In order to link responses across biological levels based on a common method, 'DRomics'
  also handles apical data as long as they are continuous and follow a normal distribution
  for each dose or concentration, with a common standard error. For further details
  see Delignette-Muller et al (2023) <DOI:10.24072/pcjournal.325> and Larras et al
  (2018) <DOI:10.1021/acs.est.8b04752>.
authors:
- family-names: Delignette-Muller
  given-names: Marie-Laure
  email: marielaure.delignettemuller@vetagro-sup.fr
  orcid: https://orcid.org/0000-0001-5453-3994
- family-names: Billoir
  given-names: Elise
  email: elise.billoir@univ-lorraine.fr
  orcid: https://orcid.org/0000-0001-9012-3298
- family-names: Siberchicot
  given-names: Aurelie
  email: aurelie.siberchicot@univ-lyon1.fr
  orcid: https://orcid.org/0000-0002-7638-8318
preferred-citation:
  type: article
  title: 'DRomics: a turnkey tool to support the use of the dose-response framework
    for omics data in ecological risk assessment'
  authors:
  - name: Marie Laure Delignette-Muller
  - name: Aurélie Siberchicot
  - name: Floriane Larras
  - name: Elise Billoir
  journal: Peer Community Journal,
  year: '2023'
  doi: 10.24072/pcjournal.325
  url: https://peercommunityjournal.org/articles/10.24072/pcjournal.325/
repository: https://lbbe-software.r-universe.dev
repository-code: https://github.com/lbbe-software/DRomics
commit: 3a4f32b45a637bb99486044b3b70540e0ad0c4fb
url: https://lbbe.univ-lyon1.fr/fr/dromics
contact:
- family-names: Siberchicot
  given-names: Aurelie
  email: aurelie.siberchicot@univ-lyon1.fr
  orcid: https://orcid.org/0000-0002-7638-8318
references:
- type: article
  title: 'DRomics: a turnkey tool to support the use of the dose-response framework
    for omics data in ecological risk assessment'
  authors:
  - name: Floriane Larras
  - name: Elise Billoir
  - name: Vincent Baillard
  - name: Aurélie Siberchicot
  - name: Stefan Scholz
  - name: Wubet Tefaye
  - name: Mika Tarkka
  - name: Mechthild Schmitt-Jansen
  - name: Marie Laure Delignette-Muller
  journal: Environmental Science & Technology
  year: '2018'
  doi: 10.1021/acs.est.8b04752
  url: https://doi.org/10.1021/acs.est.8b04752