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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 "Coralysis" in publications use:'
type: software
license: GPL-3.0-only
title: 'Coralysis: Coralysis sensitive identification of imbalanced cell types and
  states in single-cell data via multi-level integration'
version: 1.3.0
doi: 10.1101/2025.02.07.637023
identifiers:
- type: doi
  value: 10.32614/CRAN.package.Coralysis
abstract: Coralysis is an R package featuring a multi-level integration algorithm
  for sensitive integration, reference-mapping, and cell-state identification in single-cell
  data. The multi-level integration algorithm is inspired by the process of assembling
  a puzzle - where one begins by grouping pieces based on low-to high-level features,
  such as color and shading, before looking into shape and patterns. This approach
  progressively blends the batch effects and separates cell types across multiple
  rounds of divisive clustering.
authors:
- family-names: Sousa
  given-names: António
  email: aggode@utu.fi
  orcid: https://orcid.org/0000-0003-4779-6459
- family-names: Smolander
  given-names: Johannes
  orcid: https://orcid.org/0000-0003-3872-9668
- family-names: Junttila
  given-names: Sini
  orcid: https://orcid.org/0000-0003-3754-5584
- family-names: Elo
  given-names: Laura L
  orcid: https://orcid.org/0000-0001-5648-4532
preferred-citation:
  type: article
  title: Coralysis enables sensitive identification of imbalanced cell types and states
    in single-cell data via multi-level integration
  authors:
  - family-names: Sousa
    given-names: Antonio G.G.
  - family-names: Smolander
    given-names: Johannes
    orcid: https://orcid.org/0000-0003-3872-9668
  - family-names: Junttila
    given-names: Sini
    orcid: https://orcid.org/0000-0003-3754-5584
  - family-names: Elo
    given-names: Laura L.
  year: '2025'
  doi: 10.1101/2025.02.07.637023
  publisher:
    name: Cold Spring Harbor Laboratory
  journal: bioRxiv
  notes: R package version 1.3.0
repository: https://bioc.r-universe.dev
repository-code: https://github.com/elolab/Coralysis
commit: de2d3abc3491254c65937ad682f39031ff498695
url: https://elolab.github.io/Coralysis/
date-released: '2026-04-28'
contact:
- family-names: Sousa
  given-names: António
  email: aggode@utu.fi
  orcid: https://orcid.org/0000-0003-4779-6459