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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 "tradeSeq" in publications use:'
type: software
license: MIT
title: 'tradeSeq: trajectory-based differential expression analysis for sequencing
  data'
version: 1.13.13
doi: 10.1038/s41467-020-14766-3
identifiers:
- type: doi
  value: 10.32614/CRAN.package.tradeSeq
abstract: tradeSeq provides a flexible method for fitting regression models that can
  be used to find genes that are differentially expressed along one or multiple lineages
  in a trajectory. Based on the fitted models, it uses a variety of tests suited to
  answer different questions of interest, e.g. the discovery of genes for which expression
  is associated with pseudotime, or which are differentially expressed (in a specific
  region) along the trajectory. It fits a negative binomial generalized additive model
  (GAM) for each gene, and performs inference on the parameters of the GAM.
authors:
- family-names: Liu
  given-names: Zaoqu
  email: liuzaoqu@163.com
  orcid: https://orcid.org/0000-0002-0452-742X
- family-names: Berge
  given-names: Koen
  name-particle: Van den
  email: koen.vandenberge@ugent.be
- family-names: Bezieux
  given-names: Hector
  name-particle: Roux de
  email: hector.rouxdebezieux@berkeley.edu
  orcid: https://orcid.org/0000-0002-1489-8339
- family-names: Street
  given-names: Kelly
- family-names: Clement
  given-names: Lieven
preferred-citation:
  type: article
  title: Trajectory-based differential expression analysis for single-cell sequencing
    data
  authors:
  - family-names: Berge
    given-names: Koen
    name-particle: Van den
    email: koen.vandenberge@ugent.be
  - family-names: Bézieux
    given-names: Hector
    name-particle: Roux de
  - family-names: Street
    given-names: Kelly
  - family-names: Saelens
    given-names: Wouter
  - family-names: Cannoodt
    given-names: Robrecht
  - family-names: Saeys
    given-names: Yvan
  - family-names: Dudoit
    given-names: Sandrine
  - family-names: Clement
    given-names: Lieven
  journal: Nature Communications
  year: '2020'
  volume: '11'
  issue: '1'
  url: https://www.nature.com/articles/s41467-020-14766-3
  doi: 10.1038/s41467-020-14766-3
  start: '1201'
repository: https://zaoqu-liu.r-universe.dev
repository-code: https://github.com/Zaoqu-Liu/tradeSeq
commit: b8b64d76d180ba67fa4e4ff694a184ebb0b29f61
url: https://zaoqu-liu.github.io/tradeSeq
date-released: '2019-03-17'
contact:
- family-names: Liu
  given-names: Zaoqu
  email: liuzaoqu@163.com
  orcid: https://orcid.org/0000-0002-0452-742X