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# CITATION.cff 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 "cellreportR" in publications use:'
type: software
license: MIT
title: 'cellreportR: Cell Culture Microscopy Assay Analysis and Reporting'
version: 0.2.1.9000
abstract: Analysis and reporting pipeline for cell culture assays read out by microscopy,
  starting from segmented single-cell exports such as those written by 'segmantR',
  'CellProfiler' or 'QuPath'. Recovers the experimental design from the directory
  tree and the file naming convention, resolves acquisitions into the analysis unit
  of replication, and standardizes every cell against the control condition of its
  own batch. Applies threshold and biological quality control gates, then estimates
  effect sizes with confidence intervals at both unit and cell level so that the cost
  of treating cells as replicates is visible rather than assumed. Sample sizes for
  a follow-up study are solved from the confidence bound nearer the null instead of
  the observed point estimate, after Cohen (1988, ISBN:9780805802832). Figures, machine-readable
  tables and a generated file of every quoted number are emitted from the same objects,
  and an interactive 'shiny' application provides guided analysis and report export.
authors:
- family-names: Heller
  given-names: Raban
  email: raban.heller@charite.de
  orcid: https://orcid.org/0000-0001-8006-9742
- family-names: Schwindling
  given-names: Leila
- family-names: Büchner
  given-names: Alexander
- family-names: Lindenberger
  given-names: Lucia
- family-names: Müller
  given-names: Steffen
- family-names: Hannemann
  given-names: Michael
- family-names: Achatz
  given-names: Gerhard
- family-names: Rothmiller
  given-names: Simone
preferred-citation:
  type: manual
  title: 'cellreportR: Cell Culture Microscopy Assay Analysis and Reporting'
  authors:
  - family-names: Heller
    given-names: Raban
    orcid: https://orcid.org/0000-0001-8006-9742
    email: raban.heller@charite.de
  - family-names: Schwindling
    given-names: Leila
  - family-names: Büchner
    given-names: Alexander
  - family-names: Lindenberger
    given-names: Lucia
  - family-names: Müller
    given-names: Steffen
  - family-names: Hannemann
    given-names: Michael
  - family-names: Achatz
    given-names: Gerhard
  - family-names: Rothmiller
    given-names: Simone
  year: '2026'
  notes: R package version 0.2.1.9000
  url: https://github.com/CTTIR/cellreportR
repository: https://cttir.r-universe.dev
repository-code: https://github.com/CTTIR/cellreportR
commit: 987ac519f6364e243d8ccb0972d07a0f44adaa5d
url: https://cttir.github.io/cellreportR/
date-released: '2026-11-03'
contact:
- family-names: Heller
  given-names: Raban
  email: raban.heller@charite.de
  orcid: https://orcid.org/0000-0001-8006-9742