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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 "cloneRate" in publications use:'
type: software
license: MIT
title: 'cloneRate: Estimate Growth Rates from Phylogenetic Trees'
version: 0.2.3
doi: 10.1093/bioinformatics/btad561
identifiers:
- type: doi
  value: 10.32614/CRAN.package.cloneRate
abstract: Quickly estimate the net growth rate of a population or clone whose growth
  can be approximated by a birth-death branching process. Input should be phylogenetic
  tree(s) of clone(s) with edge lengths corresponding to either time or mutations.
  Based on coalescent results in Johnson et al. (2023) <https://doi.org/10.1093/bioinformatics/btad561>.
  Simulation techniques as well as growth rate methods build on prior work from Lambert
  A. (2018) <https://doi.org/10.1016/j.tpb.2018.04.005> and Stadler T. (2009) <https://doi.org/10.1016/j.jtbi.2009.07.018>.
authors:
- family-names: Johnson
  given-names: Brian
  email: brian.d.johnson97@gmail.com
  orcid: https://orcid.org/0000-0002-9477-4677
- family-names: Shuai
  given-names: Yubo
- family-names: Schweinsberg
  given-names: Jason
  orcid: https://orcid.org/0000-0002-4152-0059
- family-names: Curtius
  given-names: Kit
  orcid: https://orcid.org/0000-0002-2678-0960
preferred-citation:
  type: article
  title: 'cloneRate: fast estimation of single-cell clonal dynamics using coalescent
    theory'
  authors:
  - family-names: Johnson
    given-names: Brian
    email: brian.d.johnson97@gmail.com
    orcid: https://orcid.org/0000-0002-9477-4677
  - family-names: Shuai
    given-names: Yubo
  - family-names: Schweinsberg
    given-names: Jason
    orcid: https://orcid.org/0000-0002-4152-0059
  - family-names: Curtius
    given-names: Kit
    orcid: https://orcid.org/0000-0002-2678-0960
  journal: Bioinformatics
  year: '2023'
  url: https://doi.org/10.1093/bioinformatics/btad561
  doi: 10.1093/bioinformatics/btad561
repository: https://cran.r-universe.dev
repository-code: https://github.com/bdj34/cloneRate
commit: d5c4ff9c514370d26c179ad6d0ac58a895f15bd5
url: https://bdj34.github.io/cloneRate/
date-released: '2023-09-22'
contact:
- family-names: Johnson
  given-names: Brian
  email: brian.d.johnson97@gmail.com
  orcid: https://orcid.org/0000-0002-9477-4677