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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 "benchdamic" in publications use:'
type: software
license: Artistic-2.0
title: 'benchdamic: Benchmark of differential abundance methods on microbiome data'
version: 1.11.1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.benchdamic
abstract: 'Starting from a microbiome dataset (16S or WMS with absolute count values)
  it is possible to perform several analysis to assess the performances of many differential
  abundance detection methods. A basic and standardized version of the main differential
  abundance analysis methods is supplied but the user can also add his method to the
  benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each
  method''s distributional assumptions on the observed count data, ii) the ability
  to control the false discovery rate, iii) the within and between method concordances,
  iv) the truthfulness of the findings if any apriori knowledge is given. Several
  graphical functions are available for result visualization.'
authors:
- family-names: Calgaro
  given-names: Matteo
  email: mcalgaro93@gmail.com
  orcid: https://orcid.org/0000-0002-3056-518X
- family-names: Romualdi
  given-names: Chiara
  orcid: https://orcid.org/0000-0003-4792-9047
- family-names: Risso
  given-names: Davide
  email: mcalgaro93@gmail.com
  orcid: https://orcid.org/0000-0001-8508-5012
- family-names: Vitulo
  given-names: Nicola
  orcid: https://orcid.org/0000-0002-9571-0747
preferred-citation:
  type: article
  title: 'benchdamic: benchmarking of differential abundance methods for microbiome
    data'
  authors:
  - family-names: Calgaro
    given-names: Matteo
    email: mcalgaro93@gmail.com
    orcid: https://orcid.org/0000-0002-3056-518X
  - family-names: Romualdi
    given-names: Chiara
    orcid: https://orcid.org/0000-0003-4792-9047
  - family-names: Risso
    given-names: Davide
    email: mcalgaro93@gmail.com
    orcid: https://orcid.org/0000-0001-8508-5012
  - family-names: Vitulo
    given-names: Nicola
    orcid: https://orcid.org/0000-0002-9571-0747
  volume: '39'
  issue: '1'
  year: '2022'
  month: '12'
  journal: Bioinformatics
  url: https://doi.org/10.1093/bioinformatics/btac778
repository: https://bioc.r-universe.dev
repository-code: https://github.com/mcalgaro93/benchdamic
commit: 76860342448872dfb78a3c2043eefff7f716add6
url: https://github.com/mcalgaro93/benchdamic
contact:
- family-names: Calgaro
  given-names: Matteo
  email: mcalgaro93@gmail.com
  orcid: https://orcid.org/0000-0002-3056-518X
references:
- type: article
  title: Assessment of statistical methods from single cell, bulk RNA-seq, and metagenomics
    applied to microbiome data
  authors:
  - family-names: Calgaro
    given-names: Matteo
  - family-names: Romualdi
    given-names: Chiara
  - family-names: Waldron
    given-names: Levi
  - family-names: Risso
    given-names: Davide
  - family-names: Vitulo
    given-names: Nicola
  volume: '21'
  issue: '1'
  year: '2020'
  month: '8'
  journal: Genome Biology
  url: https://doi.org/10.1186/s13059-020-02104-1
  start: '191'