# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "FLAMES" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'FLAMES: FLAMES: Full Length Analysis of Mutations and Splicing in long read
  RNA-seq data'
version: 2.6.0
doi: 10.1101/2025.10.19.683327
identifiers:
- type: doi
  value: 10.32614/CRAN.package.FLAMES
abstract: Semi-supervised isoform detection and annotation from both bulk and single-cell
  long read RNA-seq data. Flames provides automated pipelines for analysing isoforms,
  as well as intermediate functions for manual execution.
authors:
- family-names: Wang
  given-names: Changqing
  email: wang.ch@wehi.edu.au
- family-names: Tian
  given-names: Luyi
  email: tian.l@wehi.edu.au
- family-names: Voogd
  given-names: Oliver
  email: voogd.o@wehi.edu.au
- family-names: Schuster
  given-names: Jakob
  email: schuster.j@wehi.edu.au
- family-names: Su
  given-names: Shian
  email: su.s@wehi.edu.au
- family-names: Prawer
  given-names: Yair D.J.
  email: sefi.prawer@unimelb.edu.au
- family-names: You
  given-names: Yupei
  email: you.yu@wehi.edu.au
preferred-citation:
  type: article
  title: Igniting Full-Length Isoform Analysis in Single-Cell and Spatial \\RNA-seq\\
    Data with \\FLAMESv2\\
  authors:
  - family-names: Wang
    given-names: Changqing
    email: wang.ch@wehi.edu.au
  - family-names: Prawer
    given-names: Yair D J
  - family-names: Voogd
    given-names: Oliver
    email: voogd.o@wehi.edu.au
  - family-names: Schuster
    given-names: Jakob
    email: schuster.j@wehi.edu.au
  - family-names: Paoli-Iseppi
    given-names: Ricardo De
  - family-names: Li
    given-names: Anran
  - family-names: Hallab
    given-names: Jeannette
  - family-names: Tian
    given-names: Luyi
    email: tian.l@wehi.edu.au
  - family-names: Peng
    given-names: Hongke
  - family-names: David
    given-names: Margaux
  - family-names: Du
    given-names: Mei R M
  - family-names: Velasco
    given-names: Silvia
  - family-names: Garone
    given-names: Maria G
  - family-names: Dong
    given-names: Xueyi
  - family-names: Zeglinski
    given-names: Kathleen
  - family-names: Pavan
    given-names: Chiara
  - family-names: Law
    given-names: Kevin C L
  - family-names: Abu-Bonsrah
    given-names: Kwaku Dad
  - family-names: Hunt
    given-names: Cameron P J
  - family-names: Parish
    given-names: Clare L
  - family-names: Gouil
    given-names: Quentin
  - family-names: Thijssen
    given-names: Rachel
  - family-names: Davidson
    given-names: Nadia M
  - family-names: Ritchie
    given-names: Matthew E
  - family-names: Clark
    given-names: Michael B
  - family-names: You
    given-names: Yupei
    email: you.yu@wehi.edu.au
  journal: bioRxiv
  year: '2025'
  month: '10'
  publisher:
    name: bioRxiv
  doi: 10.1101/2025.10.19.683327
  url: https://doi.org/10.1101/2025.10.19.683327
  start: 2025.10.19.683327
repository: https://bioc-release.r-universe.dev
repository-code: https://github.com/mritchielab/FLAMES
commit: 407178bcaebe1626ff536cbfc81f5eb2268baa6e
url: https://mritchielab.github.io/FLAMES
date-released: '2025-07-22'
contact:
- family-names: Wang
  given-names: Changqing
  email: wang.ch@wehi.edu.au
references:
- type: article
  title: Comprehensive Characterization of Single-Cell Full-Length Isoforms in Human
    and Mouse with Long-Read Sequencing
  authors:
  - family-names: Tian
    given-names: Luyi
  - family-names: Jabbari
    given-names: Jafar S
  - family-names: Thijssen
    given-names: Rachel
  - name: et al.
  journal: Genome Biology
  year: '2021'
  volume: '22'
  issue: '1'
  doi: 10.1186/s13059-021-02525-6
  start: '310'