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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 "pipeComp" in publications use:'
type: software
license: GPL-1.0-only
title: 'pipeComp: pipeComp pipeline benchmarking framework'
version: 1.15.0
doi: 10.1186/s13059-020-02136-7
identifiers:
- type: doi
  value: 10.32614/CRAN.package.pipeComp
abstract: A simple framework to facilitate the comparison of pipelines involving various
  steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally,
  a set of functions consecutively executed on the output of the previous one, and
  optionally accompanied by step-wise evaluation and aggregation functions. Given
  such an object, a set of alternative parameters/methods, and benchmark datasets,
  the `runPipeline` function then proceeds through all combinations arguments, avoiding
  recomputing the same step twice and compiling evaluations on the fly to avoid storing
  potentially large intermediate data.
authors:
- family-names: Germain
  given-names: Pierre-Luc
  email: pierre-luc.germain@hest.ethz.ch
  orcid: https://orcid.org/0000-0003-3418-4218
- family-names: Sonrel
  given-names: Anthony
  email: anthony.sonrel@uzh.ch
  orcid: https://orcid.org/0000-0002-2414-715X
- family-names: Robinson
  given-names: Mark D.
  email: mark.robinson@imls.uzh.ch
  orcid: https://orcid.org/0000-0002-3048-5518
preferred-citation:
  type: article
  title: pipeComp, a General Framework for the Evaluation of Computational Pipelines,
    Reveals Performant Single-Cell RNA-Seq Preprocessing Tools
  authors:
  - family-names: Germain
    given-names: Pierre-Luc
    email: pierre-luc.germain@hest.ethz.ch
    orcid: https://orcid.org/0000-0003-3418-4218
  - family-names: Sonrel
    given-names: Anthony
    email: anthony.sonrel@uzh.ch
    orcid: https://orcid.org/0000-0002-2414-715X
  - family-names: Robinson
    given-names: Mark D.
    email: mark.robinson@imls.uzh.ch
    orcid: https://orcid.org/0000-0002-3048-5518
  year: '2020'
  notes: package version 1.15.0
  doi: 10.1186/s13059-020-02136-7
  volume: '21'
  journal: Genome Biology
repository: https://bioc.r-universe.dev
repository-code: https://github.com/plger/pipeComp
commit: 1356fefbef02b4eeccb5f29190e64f4f6e0b4eaf
url: https://doi.org/10.1186/s13059-020-02136-7
contact:
- family-names: Germain
  given-names: Pierre-Luc
  email: pierre-luc.germain@hest.ethz.ch
  orcid: https://orcid.org/0000-0003-3418-4218