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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 "MAPFX" in publications use:'
type: software
license: GPL-2.0-only
title: 'MAPFX: MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing
  Data from the Massively-Parallel Cytometry Experiments'
version: 1.1.0
doi: 10.1101/2024.02.28.582452
abstract: MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC
  experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further
  imputes the ‘missing’ infinity markers in the wells without those measurements.
  The pipeline starts by performing background correction on raw intensities to remove
  the noise from electronic baseline restoration and fluorescence compensation by
  adapting a normal-exponential convolution model. Unwanted technical variation, from
  sources such as well effects, is then removed using a log-normal model with plate,
  column, and row factors, after which infinity markers are imputed using the informative
  backbone markers as predictors. The completed dataset can then be used for clustering
  and other statistical analyses. Additionally, MAPFX can be used to normalise data
  from FFC assays as well.
authors:
- family-names: Liao
  given-names: Hsiao-Chi
  email: chelsea.acad@gmail.com
  orcid: https://orcid.org/0000-0002-9586-1246
preferred-citation:
  type: article
  title: 'MAssively-Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing
    Data from the Massively-Parallel Cytometry Experiments'
  authors:
  - family-names: Liao
    given-names: Hsiao-Chi
    email: chelsea.acad@gmail.com
    orcid: https://orcid.org/0000-0002-9586-1246
  - family-names: Speed
    given-names: Terence P.
  - family-names: McCarthy
    given-names: Davis J.
  - family-names: Salim
    given-names: Agus
  year: '2024'
  doi: 10.1101/2024.02.28.582452
  publisher:
    name: Cold Spring Harbor Laboratory
  url: https://www.biorxiv.org/content/early/2024/03/03/2024.02.28.582452
  journal: bioRxiv
repository: https://bioc.r-universe.dev
repository-code: https://github.com/HsiaoChiLiao/MAPFX
url: https://github.com/HsiaoChiLiao/MAPFX
contact:
- family-names: Liao
  given-names: Hsiao-Chi
  email: chelsea.acad@gmail.com
  orcid: https://orcid.org/0000-0002-9586-1246
references:
- type: article
  title: High-throughput single-cell quantification of hundreds of proteins using
    conventional flow cytometry and machine learning
  authors:
  - family-names: Becht
    given-names: Etienne
  - family-names: Tolstrup
    given-names: Daniel
  - family-names: Dutertre
    given-names: Charles-Antoine
  - family-names: Morawski
    given-names: Peter A.
  - family-names: Campbell
    given-names: Daniel J.
  - family-names: Ginhoux
    given-names: Florent
  - family-names: Newell
    given-names: Evan W.
  - family-names: Gottardo
    given-names: Raphael
  - family-names: Headley
    given-names: Mark B.
  year: '2021'
  doi: 10.1126/sciadv.abg0505
  publisher:
    name: American Association for the Advancement of Science's (AAAS)
  url: https://www.science.org/doi/abs/10.1126/sciadv.abg0505
  journal: Science Advances