# --------------------------------------------
# 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 "CytoPipeline" in publications use:'
type: software
license: GPL-3.0-only
title: 'CytoPipeline: Automation and visualization of flow cytometry data analysis
  pipelines'
version: 1.5.1
doi: 10.1186/s12859-024-05691-z
identifiers:
- type: doi
  value: 10.32614/CRAN.package.CytoPipeline
abstract: This package provides support for automation and visualization of flow cytometry
  data analysis pipelines. In the current state, the package focuses on the preprocessing
  and quality control part. The framework is based on two main S4 classes, i.e. CytoPipeline
  and CytoProcessingStep. The pipeline steps are linked to corresponding R functions
  - that are either provided in the CytoPipeline package itself, or exported from
  a third party package, or coded by the user her/himself. The processing steps need
  to be specified centrally and explicitly using either a json input file or through
  step by step creation of a CytoPipeline object with dedicated methods. After having
  run the pipeline, obtained results at all steps can be retrieved and visualized
  thanks to file caching (the running facility uses a BiocFileCache implementation).
  The package provides also specific visualization tools like pipeline workflow summary
  display, and 1D/2D comparison plots of obtained flowFrames at various steps of the
  pipeline.
authors:
- family-names: Hauchamps
  given-names: Philippe
  email: philippe.hauchamps@uclouvain.be
  orcid: https://orcid.org/0000-0003-2865-1852
- family-names: Gatto
  given-names: Laurent
  email: laurent.gatto@uclouvain.be
  orcid: https://orcid.org/0000-0002-1520-2268
preferred-citation:
  type: article
  title: 'CytoPipeline and CytoPipelineGUI: a Bioconductor R package suite for building
    and visualizing automated pre-processing pipelines for flow cytometry data'
  authors:
  - family-names: Hauchamps
    given-names: Philippe
    email: philippe.hauchamps@uclouvain.be
    orcid: https://orcid.org/0000-0003-2865-1852
  - family-names: Bayat
    given-names: Babak
  - family-names: Delandre
    given-names: Simon
  - family-names: Hamrouni
    given-names: Mehdi
  - family-names: Toussaint
    given-names: Marie
  - family-names: Temmerman
    given-names: Stephane
  - family-names: Lin
    given-names: Dan
  - family-names: Gatto
    given-names: Laurent
    email: laurent.gatto@uclouvain.be
    orcid: https://orcid.org/0000-0002-1520-2268
  journal: BMC Bioinformatics
  year: '2024'
  volume: '25'
  issue: '1'
  doi: 10.1186/s12859-024-05691-z
  start: '80'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/UCLouvain-CBIO/CytoPipeline
commit: 365c1dd20ff5014849ec02ce9ab46654b23e147a
url: https://uclouvain-cbio.github.io/CytoPipeline
contact:
- family-names: Hauchamps
  given-names: Philippe
  email: philippe.hauchamps@uclouvain.be
  orcid: https://orcid.org/0000-0003-2865-1852