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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 "bambu" in publications use:'
type: software
license: GPL-3.0-only
title: 'bambu: Context-Aware Transcript Quantification from Long Read RNA-Seq data'
version: 3.14.0
doi: 10.1038/s41592-023-01908-w
identifiers:
- type: doi
  value: 10.32614/CRAN.package.bambu
abstract: bambu is a R package for multi-sample transcript discovery and quantification
  using long read RNA-Seq data. You can use bambu after read alignment to obtain expression
  estimates for known and novel transcripts and genes. The output from bambu can directly
  be used for visualisation and downstream analysis such as differential gene expression
  or transcript usage.
authors:
- family-names: Chen
  given-names: Ying
  email: chen_ying@gis.a-star.edu.sg
- family-names: Sim
  given-names: Andre
  email: andre_sim@gis.a-star.edu.sg
- family-names: Wan
  given-names: Yuk Kei
  email: Wan_Yuk_Kei@gis.a-star.edu.sg
- family-names: Goeke
  given-names: Jonathan
  email: gokej@gis.a-star.edu.sg
preferred-citation:
  type: article
  title: Context-aware transcript quantification from long-read RNA-seq data with
    Bambu
  authors:
  - family-names: Chen
    given-names: Ying
    email: chen_ying@gis.a-star.edu.sg
  - family-names: Sim
    given-names: Andre
    email: andre_sim@gis.a-star.edu.sg
  - family-names: Wan
    given-names: Yuk Kei
    email: Wan_Yuk_Kei@gis.a-star.edu.sg
  - family-names: Yeo
    given-names: Keith
  - family-names: Lee
    given-names: Joseph Jing Xian
  - family-names: Ling
    given-names: Min Hao
  - family-names: Love
    given-names: Michael I.
  - family-names: Göke
    given-names: Jonathan
  year: '2023'
  journal: Nature Methods
  doi: 10.1038/s41592-023-01908-w
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/GoekeLab/bambu
commit: ab2faa6dd26dec095021485613db89b608f71100
url: https://github.com/GoekeLab/bambu
date-released: '2026-04-28'
contact:
- family-names: Chen
  given-names: Ying
  email: chen_ying@gis.a-star.edu.sg