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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 "biocohort" in publications use:'
type: software
license: MIT
title: 'biocohort: Cohort Objects for Subjects and Samples in Omics Studies'
version: 0.1.1.9000
doi: 10.5281/zenodo.22685057
identifiers:
- type: doi
  value: 10.32614/CRAN.package.biocohort
abstract: Keeps the subjects, samples, and analysis outputs of a study in one validated
  object. It starts from a sample manifest with one row per sample, which is read,
  checked, and split into a subject table and a sample map. Species and assay are
  plain values in those tables rather than fixed types, so the same object serves
  any organism and any omics assay. From that object the package writes the sample
  sheet a pipeline expects, pairs tumor and normal samples on demand, and records
  where each analysis writes its output so the files can be loaded back in by subject
  or by pair. Manual corrections are kept in an audit trail. Results can also be translated
  across genome builds or species, with liftover for coordinates and ortholog mapping
  for genes.
authors:
- family-names: Bharti
  given-names: Samuel
  email: samuelbharti.io@gmail.com
  orcid: https://orcid.org/0000-0003-4190-7058
preferred-citation:
  type: manual
  title: 'biocohort: Cohort Objects for Subjects and Samples in Omics Studies'
  authors:
  - family-names: Bharti
    given-names: Samuel
    email: samuelbharti.io@gmail.com
    orcid: https://orcid.org/0000-0003-4190-7058
  year: '2026'
  notes: R package version 0.1.1.9000
  url: https://www.samuelbharti.com/biocohort/
  doi: 10.5281/zenodo.22685057
repository: https://samuelbharti.r-universe.dev
repository-code: https://github.com/samuelbharti/biocohort
commit: a7c03ed100fb348800e08038c6eaf52e89ba8cc9
url: https://www.samuelbharti.com/biocohort/
date-released: '2026-09-29'
contact:
- family-names: Bharti
  given-names: Samuel
  email: samuelbharti.io@gmail.com
  orcid: https://orcid.org/0000-0003-4190-7058