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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 "monocle" in publications use:'
type: software
license: Artistic-2.0
title: 'monocle: Clustering, differential expression, and trajectory analysis for
  single- cell RNA-Seq'
version: 2.33.0
abstract: Monocle performs differential expression and time-series analysis for single-cell
  expression experiments. It orders individual cells according to progress through
  a biological process, without knowing ahead of time which genes define progress
  through that process. Monocle also performs differential expression analysis, clustering,
  visualization, and other useful tasks on single cell expression data. It is designed
  to work with RNA-Seq and qPCR data, but could be used with other types as well.
authors:
- family-names: Trapnell
  given-names: Cole
  email: coletrap@uw.edu
preferred-citation:
  type: article
  title: The dynamics and regulators of cell fate decisions are revealed by pseudo-temporal
    ordering of single cells
  authors:
  - family-names: Trapnell
    given-names: Cole
    email: coletrap@uw.edu
  - family-names: Cacchiarelli
    given-names: Davide
  - family-names: Grimsby
    given-names: Jonna
  - family-names: Pokharel
    given-names: Prapti
  - family-names: Li
    given-names: Shuqiang
  - family-names: Morse
    given-names: Michael
  - family-names: Lennon
    given-names: Niall J.
  - family-names: Livak
    given-names: Kenneth J.
  - family-names: Mikkelsen
    given-names: Tarjei S.
  - family-names: Rinn
    given-names: John L.
  year: '2014'
  journal: Nature Biotechnology
repository: https://bioc.r-universe.dev
date-released: '2024-03-13'
contact:
- family-names: Trapnell
  given-names: Cole
  email: coletrap@uw.edu
references:
- type: article
  title: Single-cell mRNA quantification and differential analysis with Census
  authors:
  - family-names: Qiu
    given-names: Xiaojie
  - family-names: Hill
    given-names: Andrew
  - family-names: Packer
    given-names: Jonathan
  - family-names: Lin
    given-names: Dejun
  - family-names: Ma
    given-names: Yi-An
  - family-names: Trapnell
    given-names: Cole
  year: '2017'
  journal: Nature Methods
- type: article
  title: Reverse graph embedding resolves complex single-cell developmental trajectories.
  authors:
  - family-names: Qiu
    given-names: Xiaojie
  - family-names: Mao
    given-names: Qi
  - family-names: Tang
    given-names: Ying
  - family-names: Wang
    given-names: Li
  - family-names: Chawla
    given-names: Raghav
  - family-names: Pliner
    given-names: Hannah
  - family-names: Trapnell
    given-names: Cole
  year: '2017'
  journal: BioRxiv