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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 "phenoscapR" in publications use:'
type: software
license: MIT
title: 'phenoscapR: Read, Analyse, and Visualise Single-Cell Spatial Biology Data'
version: 0.2.0.9001
abstract: Tools for importing, processing, analysing, and visualising single-cell
  spatial biology data from multiplexed imaging platforms. Supports cell-table quality
  control, marker normalisation, phenotype summaries, spatial neighbourhood statistics
  such as Ripley's K function (Ripley (1977) <https://doi.org/10.1111/j.2517-6161.1977.tb01615.x>)
  and Moran's I (Moran (1950) <https://doi.org/10.2307/2332142>), and explicit sample
  and coordinate-frame registries. Patient-level inference enumerates label allocations
  for declared contrasts (exact permutation tests; Pitman (1937) <https://doi.org/10.2307/2984124>)
  and retains unavailable hypotheses when adjusting for multiple testing. Grouped
  summaries expose missingness, eligibility, and denominator provenance. Optional
  canonical cell-table import uses 'cellspecR' <https://github.com/CTTIR/cellspecR>;
  optional Self-Organising Nebulous Growths (SONG) embeddings (Senanayake et al. (2021)
  <https://doi.org/10.1109/TNNLS.2020.3023941>) use 'songR' <https://github.com/CTTIR/songR>.
  Both optional packages are available from <https://cttir.r-universe.dev>.
authors:
- family-names: Heller
  given-names: R.
  email: raban.heller@uni-ulm.de
  orcid: https://orcid.org/0000-0001-8006-9742
  affiliation: Ulm University
- family-names: Chteinberg
  given-names: E.
  orcid: https://orcid.org/0000-0002-9231-9291
  affiliation: Ulm University
- family-names: Witte
  given-names: H.
  orcid: https://orcid.org/0000-0001-5767-7125
  affiliation: Ulm University
preferred-citation:
  type: manual
  title: 'phenoscapR: Read, Analyse, and Visualise Single-Cell Spatial Biology Data'
  authors:
  - family-names: Heller
    given-names: R.
    email: raban.heller@uni-ulm.de
    orcid: https://orcid.org/0000-0001-8006-9742
    affiliation: Ulm University
  - family-names: Chteinberg
    given-names: E.
    orcid: https://orcid.org/0000-0002-9231-9291
    affiliation: Ulm University
  - family-names: Witte
    given-names: H.
    orcid: https://orcid.org/0000-0001-5767-7125
    affiliation: Ulm University
  year: '2026'
  notes: R package version 0.2.0.9001
  url: https://cttir.github.io/phenoscapR/
repository: https://cttir.r-universe.dev
repository-code: https://github.com/CTTIR/phenoscapR
commit: 72fb1bc9bccf210393071c7a1e2e4a4bb0f552a0
url: https://cttir.github.io/phenoscapR/
date-released: '2026-11-03'
contact:
- family-names: Heller
  given-names: R.
  email: raban.heller@uni-ulm.de
  orcid: https://orcid.org/0000-0001-8006-9742
  affiliation: Ulm University