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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 "strainspy" in publications use:'
type: software
license: MIT
title: 'strainspy: Strain Level Microbiome Wide Association Studies'
version: 0.99.3
doi: 10.64898/2026.08.30.748153
identifiers:
- type: doi
  value: 10.32614/CRAN.package.strainspy
abstract: Fits statistical models to detect microbial strains associated with a phenotype.
  For small sample sizes, models can be fitted using empirical Bayes maximum a posteriori
  (MAP) priors to improve detection power. Supports various experimental design scenarios,
  including repeated measures.
authors:
- family-names: Tonkin-Hill
  given-names: Gerry
  email: g.tonkinhill@gmail.com
- family-names: Mallawaarachchi
  given-names: Sudaraka
  email: smallawaarachchi@gmail.com
  orcid: https://orcid.org/0000-0001-8899-3323
preferred-citation:
  type: article
  title: Accurate detection of metagenomic strain-level associations using average
    nucleotide identity with StrainSpy
  authors:
  - family-names: Mallawaarachchi
    given-names: Sudaraka
    email: smallawaarachchi@gmail.com
    orcid: https://orcid.org/0000-0001-8899-3323
  - family-names: Tandon
    given-names: Kshitij
  - family-names: Rajan
    given-names: Nikhil
  - family-names: Marcelino
    given-names: Vannessa Rossetto
  - family-names: Sandhu
    given-names: Shahneen
  - family-names: Bedoui
    given-names: Sammy
  - family-names: Ingle
    given-names: Danielle J.
  - family-names: Gunjur
    given-names: Ashray
  - family-names: Tonkin-Hill
    given-names: Gerry
    email: g.tonkinhill@gmail.com
  journal: bioRxiv
  year: '2026'
  doi: 10.64898/2026.08.30.748153
  url: https://www.biorxiv.org/content/10.64898/2026.08.30.748153v1
repository: https://sudaraka88.r-universe.dev
repository-code: https://github.com/gtonkinhill/strainspy
commit: a961691294dad5448b7fd0087a47f5f0c55bd21d
url: https://sudaraka88.r-universe.dev/strainspy
date-released: '2026-10-14'
contact:
- family-names: Mallawaarachchi
  given-names: Sudaraka
  email: smallawaarachchi@gmail.com
  orcid: https://orcid.org/0000-0001-8899-3323