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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 "circaTime" in publications use:'
type: software
license: Artistic-2.0
title: 'circaTime: Unified Inference of Circadian Phase from Bulk and Pseudobulk Transcriptomes'
version: 0.99.3
identifiers:
- type: doi
  value: 10.32614/CRAN.package.circaTime
abstract: 'Provides a single SummarizedExperiment-based interface to published circadian
  phase (time-of-sample-collection) inference methods for bulk and donor-level pseudobulk
  transcriptomes, along with a shared cross-validation benchmarking harness, cross-dataset
  transfer testing, and a calibrated uncertainty layer: bootstrap and Bayesian confidence
  intervals validated for real coverage, a fixed or dynamically-selected clock-gene
  quality flag, and consensus phase estimation across every bundled engine. Does not
  implement a new phase-inference algorithm; unifies existing published methods that
  are otherwise scattered across incompatible standalone implementations.'
authors:
- family-names: Uysal
  given-names: Alperen
  email: dralperenuysal@gmail.com
  orcid: https://orcid.org/0000-0003-3777-6411
preferred-citation:
  type: manual
  title: 'circaTime: Unified Inference of Circadian Phase from Bulk and Pseudobulk
    Transcriptomes'
  authors:
  - family-names: Uysal
    given-names: Alperen
    email: dralperenuysal@gmail.com
    orcid: https://orcid.org/0000-0003-3777-6411
  year: '2026'
  notes: R package version 0.99.2
  url: https://github.com/dralperenuysal/circaTime
repository: https://biocstaging.r-universe.dev
repository-code: https://github.com/dralperenuysal/circaTime
commit: 4790ef8d4a85371303706cd6f2a623750e716f59
url: https://github.com/dralperenuysal/circaTime
date-released: '2026-10-08'
contact:
- family-names: Uysal
  given-names: Alperen
  email: dralperenuysal@gmail.com
  orcid: https://orcid.org/0000-0003-3777-6411
references:
- type: unpublished
  title: 'circaTime: a unified interface for inferring circadian phase from bulk and
    pseudobulk transcriptomes'
  authors:
  - family-names: Uysal
    given-names: Alperen
    email: dralperenuysal@gmail.com
    orcid: https://orcid.org/0000-0003-3777-6411
  year: '2026'
  notes: Manuscript in preparation