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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 "cardelino" in publications use:'
type: software
license: GPL-3.0-only
title: 'cardelino: Clone Identification from Single Cell Data'
version: 1.7.0
doi: 10.1038/s41592-020-0766-3
abstract: Methods to infer clonal tree configuration for a population of cells using
  single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods
  are also provided to assign cells to inferred clones and explore differences in
  gene expression between clones. These methods can flexibly integrate information
  from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant
  alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts
  for stochastic dropout events as well as systematic allelic imbalance is used.
authors:
- family-names: Pullin
  given-names: Jeffrey
  email: jpullin@svi.edu.au
- family-names: Huang
  given-names: Yuanhua
  email: yuanhua@hku.hk
- family-names: McCarthy
  given-names: Davis
  email: dmccarthy@svi.edu.au
preferred-citation:
  type: article
  title: 'Cardelino: computational integration of somatic clonal substructure and
    single-cell transcriptomes'
  authors:
  - family-names: McCarthy
    given-names: Davis J.
  - family-names: Rostom
    given-names: Raghd
  - family-names: Huang
    given-names: Yuanhua
    email: yuanhua@hku.hk
  - family-names: Kunz
    given-names: Daniel J.
  - family-names: Danecek
    given-names: Petr
  - family-names: Bonder
    given-names: Marc Jan
  - family-names: Hagai
    given-names: Tzachi
  - family-names: Lyu
    given-names: Ruquian
  - name: Hipsci Consortium
  - family-names: Wang
    given-names: Wenyi
  - family-names: Gaffney
    given-names: Daniel J.
  - family-names: Simons
    given-names: Benjamin D.
  - family-names: Stegle
    given-names: Oliver
  - family-names: Teichmann
    given-names: Sarah A.
  journal: Nature Methods
  year: '2020'
  url: https://www.nature.com/articles/s41592-020-0766-3
  doi: 10.1038/s41592-020-0766-3
repository: https://bioc.r-universe.dev
repository-code: https://github.com/single-cell-genetics/cardelino
url: https://github.com/single-cell-genetics/cardelino
contact:
- family-names: McCarthy
  given-names: Davis
  email: dmccarthy@svi.edu.au