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# CITATION.cff file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "fuzzyCell" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'fuzzyCell: Bootstrap Classification Confidence for Spatial Cell-Type Analysis'
version: 0.99.1
abstract: 'Cell type labels in spatial single-cell data are uncertain, particularly
  between closely related subtypes. fuzzyCell estimates a per-cell classification
  confidence by bootstrapping (multinomial resampling of each cell''s counts followed
  by re-classification) and uses the resulting confidences as soft cell type weights.
  The weights are propagated through downstream analyses: cell type proportions, co-localisation
  (spicyR''s L-function, and Statial''s Kontextual test for relative co-localisation)
  and niche identification (lisaClust), each compared to the same analysis using hard
  labels. Cell types are organised with a user-supplied hierarchy of lineages, groups
  and subtypes. Helpers for testing against sample-level outcomes and for plotting
  are included.'
authors:
- family-names: Rao
  given-names: Shreya
  email: shreya.rajeshrao@sydney.edu.au
  orcid: https://orcid.org/0009-0007-8140-6844
- family-names: Patrick
  given-names: Ellis
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/shreyarajeshrao/fuzzyCell
commit: d171b9a457af9869138d4f998c8d3cec0fd8e6ea
url: https://github.com/shreyarajeshrao/fuzzyCell
date-released: '2026-10-29'
contact:
- family-names: Rao
  given-names: Shreya
  email: shreya.rajeshrao@sydney.edu.au
  orcid: https://orcid.org/0009-0007-8140-6844