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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 "stPipe" in publications use:'
type: software
license: GPL-3.0-only
title: 'stPipe: Upstream pre-processing for Sequencing-Based Spatial Transcriptomics'
version: 1.3.0
doi: 10.1093/nargab/lqaf167
identifiers:
- type: doi
  value: 10.32614/CRAN.package.stPipe
abstract: This package serves as an upstream pipeline for pre-processing sequencing-based
  spatial transcriptomics data. Functions includes FASTQ trimming, BAM file reformatting,
  index building, spatial barcode detection, demultiplexing, gene count matrix generation
  with UMI deduplication, QC, and revelant visualization. Config is an essential input
  for most of the functions which aims to improve reproducibility.
authors:
- family-names: Xu
  given-names: Yang
  email: xu.ya@wehi.edu.au
  orcid: https://orcid.org/0009-0008-3274-6516
- family-names: Sargeant
  given-names: Callum
  email: sargeant.ca@wehi.edu.au
- family-names: Su
  given-names: Shian
  email: su.s@wehi.edu.au
- family-names: Tian
  given-names: Luyi
  email: tian.l@wehi.edu.au
preferred-citation:
  type: article
  title: 'stPipe: a flexible and streamlined R/Bioconductor pipeline for preprocessing
    sequencing-based spatial transcriptomics data'
  authors:
  - family-names: Xu
    given-names: Yang
    email: xu.ya@wehi.edu.au
    orcid: https://orcid.org/0009-0008-3274-6516
  - family-names: Sargeant
    given-names: Callum J
  - family-names: You
    given-names: Yue
  - family-names: You
    given-names: Yupei
  - family-names: Su
    given-names: Shian
    email: su.s@wehi.edu.au
  - family-names: Wang
    given-names: Changqing
  - family-names: Tian
    given-names: Luyi
    email: tian.l@wehi.edu.au
  - family-names: Chen
    given-names: Yunshun
  - family-names: Ritchie
    given-names: Matthew E
  journal: NAR Genomics and Bioinformatics
  year: '2025'
  volume: '7'
  issue: '4'
  month: '12'
  doi: 10.1093/nargab/lqaf167
  start: lqaf167
repository: https://bioc.r-universe.dev
repository-code: https://github.com/mritchielab/stPipe/issues/new
commit: 287ceed10e841dece4bd6886acc006fb43096d94
url: https://github.com/mritchielab/stPipe
date-released: '2026-04-28'
contact:
- family-names: Xu
  given-names: Yang
  email: xu.ya@wehi.edu.au
  orcid: https://orcid.org/0009-0008-3274-6516